Gene Regulation Ontology en 0.2 protein identification protein subunit RHR Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]). RNA polymerase activity GO:0003899 DNA-directed RNA polymerase activity; GO:0003968 RNA-directed RNA polymerase activity An RNA synthesized on a DNA or RNA template by an RNA polymerase. [SO:0000673] SO:0000673 transcript transcript GO:0006354 RNA elongation The extension of an RNA molecule after transcription initiation by the addition of ribonucleotides catalyzed by an RNA polymerase. [GO:0006354] RNA elongation A set of genes/proteins under regulation by the same stimulus stimulon nucleic acid molecule A transcription factor containing forkhead/winged-helix domain forkhead/winged-helix transcription factor molecular binding binding to molecular entity substrate negative regulation of transcription by transcription repressor Any process involving transcription repressor activity that stops, prevents or reduces the rate of transcription (modified from [GO:0016481]). bHSH transcription factor A transcription factor containing bHSH domain p53-like transcription factor regulation of modification of molecular entity information biopolymer Any process that modulates the frequency, rate or extent of gene expression. regulation of gene expression mutant gene A gene that has changed (e.g. lost, gained, or exchanged some of the material it received from its parent), affecting the normal transmission and expression of a trait. formation of translation initiation complex Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site. [GO:0001732] GO:0001732 formation of translation initiation complex cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. [GO:0048869] GO:0048869 cellular developmental process A process of producing a protein from its gene via transcription and translation in eukaryotes. It is usually controlled at various points in the sequence leading to protein synthesis. eukaryotic gene expression GO:0006396 RNA processing Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GO:0006396] RNA processing basic domain enhancesome Regulatory proteins bound to DNA. bHLH transcription factor A transcription factor containing bHLH domain homeo box negative polarity RNA polymerase binding site of DNA An agent that opposes the action or reduces the physiological activity of another. antagonist solution gene mutation regulation of translation GO:0006417 regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0006417] virus NCBI Taxonomy ID: 10239 Viruses structural domain of transcription activator protein binding site of protein A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon. [SO:0000057] SO:0000057 operator operator A transcription factor containing basic domain. basic domain transcription factor CHEBI:32958 phosphate group phosphate group expression profiling phosphorelay system two-component sensory transduction system two-component system phospho-relay system two-component signal transduction system two-component regulatory system System of proteins and other molecular entities responding to environmental changes. Characterized usually by first a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and, second, a response regulator to which the phosphoryl group is transferred. The responder is typically a DNA-binding protein that regulates transcription. Several of these systems are quite complex, involving many proteins in a signaling cascade or contributing to several responses simultaneously. They are involved in a variety processes such as chemotaxis, osmoregulation, magnesium transport, pH tolerance, sporulation, or response of virulent species to host cell's environments. The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA bindin! SAND domain RNA coding ORF organism TEA domain transcription factor Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTS domain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism. [InterPro: IPR000818] transcription of regulon genes binding GO:0005488 binding The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488] acetylation eukaryotic cell histone fold histone fold transcription factor mRNA messenger RNA GO:0006401 RNA catabolic process The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [GO:0006401] RNA catabolism fusion of gene with reporter gene gas The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. [IMR:0001720, MeSH:D005740] IMR:0001720 gas cell fate determination Process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment. [GO:0001709] GO:0001709 cell fate determination physical contact GO:0006353 transcription termination The process by which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA. [GO:0006353] transcription termination STAT transcription factor The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT p! housekeeping gene experimental method A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GO:0016043] GO:0016043 cellular component organization and biogenesis cellular component organization and biogenesis phenotype posttranscriptional modification response to drug GO:0042493 response to drug A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GO:0042493] reporter gene construction binding site of protein The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell. [GO:0007165] GO:0007165 signal transduction signaling pathway inhibition The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. [GO:0032774] GO:0032774 RNA biosynthetic process RNA biosynthesis locus control region LCR A region that enhances the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. It is required for normal regulation of expression of some genes. SO:0000037 locus control region A transcription factor that binds to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein (other transcription factors of cofactors) or protein or macromolecular complex. (modified from [GO:0003700]) transcription factor A transcription factor containing WRKY domain. WRKY transcription factor architectural proteins Proteins that bend DNA. The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350] GO:0006350 transcription transcription A domain consisting of a conserved 124 amino acid N-terminal sequence, found in several developmentally regulated proteins in fruit fly, mouse and human paired box binding of protein to DNA IMR:0000947 chemical chemical organismal process activation AP2-EREBP-related domain A domain consisting of the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding sequence. IMR:0100022 second messenger second messenger occurrent protein GO:0016987 sigma factor activity sigma factor activity A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] beta scaffold domain with minor groove contacts binding of protein transcription of stimulon genes intra organismal process tryptophan cluster regulation of transcription of regulon A transcription factor containing the homeobox domain. It is usually involved in the control of gene expression during morphogenesis and development. [PANTHER:MF00038] homeobox transcription factor A DNA sequence in eukaryotic DNA to which RNA polymerase binds, to begin transcription. [SO] eukaryotic RNA polymerase promoter A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition. [GO:0032502] developmental process GO:0032502 developmental process A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. [SO:0000613] SO:0000613 bacterial RNApol promoter bacterial RNA polymerase promoter protein protein interaction molecular interaction gene region A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene. mutation continuant biological process physiological process GO:0008150 biological process Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. [GO:0008150] process 1 A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. [SO:0000169] SO:0000169 RNApol I promoter RNA polymerase I promoter 2 GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. [GO:0007154] cell communication A transcription factor that binds to other transcription factors / the core RNA polymerase II complex but does not bind DNA itself. transcription cofactor binding of DNA binding domain of protein to DNA single strand DNA CHEBI: 33838 nucleosides IMR:0001697 nucleoside Ribosyl or deoxyribosyl derivatives of the pyrimidine or purine bases adenine, guanine, xanthine, thymine, cytosine, and uracil. [CHEBI: 33838] nucleoside transposition Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites. [GO:0032196] GO:0032196 transposition activation of polymerase cold shock domain ��A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic single-strand nucleic-acid binding proteins. This domain, which is known as the 'cold-shock domain' (CSD)...[InterPro: IPR011129] coiled chromosomal DNA positive polarity protein binding site of DNA RNA protein interaction The aggregation and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. [GO:0022618] GO:0022618 protein-RNA complex assembly Any transcription regulator that prevents or downregulates transcription. transcription repressor pathway SAND domain transcription factor A transcription factor containing SAND domain IMR:0001695 amino acid amino acid CHEBI:33709 amino acids Carboxylic acids containing one or more amino groups. [CHEBI:33709] binding of transcription repressor to silencer translation elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. [GO:0006414] GO:0006414 translational elongation GO:0043687 post-translational protein modification The covalent alteration of one or more amino acids occurring in a protein after the protein has been completely translated and released from the ribosome. [GO:0043687] posttranslational modification Heat shock factor (HSF) is a transcriptional activator of heat shock genes: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus. The DNA-binding component of HSF lies to the N-terminus of the first NLS region, a! HSF domain activation of process metabolic pathway GO:0008152 metabolic process Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GO:0008152] three dimensional molecular structure 3D structure of a molecule Any of the unicellular prokaryotic organisms, which vary in terms of morphology, oxygen and nutritional requirements and motility and can exist either as independent (free-living) organisms or as parasites (dependent upon another organism for life). NCBI Taxonomy ID: 2 Bacteria bacterium GO:0016049 cell growth The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. [GO:0016049] cell growth regulatory DNA regulatory sequence SO:0005836 regulatory region A DNA sequence that controls the expression of a gene. [SO:0005836, http://www.genpromag.com/scripts/glossary.asp?LETTER=R] Typically binding sites for proteins required for transcription, such as gene regulatory proteins and polymerases. Any transcription regulator activity required for initiation or upregulation of transcription. [GO:0016563] transcription activator activity GO:0016563 transcription activator activity cell solvent DNA protein interaction The synthesis of RNA on a template of DNA. [GO:0006351] transcription DNA-dependent prokaryote protein mutation SO:0000551 polyA signal sequence poly-A signal sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. [SO:0000551, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).[GO:0005515] GO:0005515 protein binding binding to protein The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.[GO:0006810] transport GO:0006810 transport RNA polymerase III promoter type 1 copper-fist domain TBP domain polymerase DM-domain-containing transcription factor A transcription factor containing DM domain. A protein that has catalytic activity. enzyme Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box, that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit.! MADS conformation GO:0003700 transcription factor activity The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GO:0003700] transcription factor activity exon on DNA complex of protein and DNA chromatin GO:0051258 protein polymerization The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. [GO:0051258] protein polymerization GO:0005575 cellular component cell component The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. [GO:0005575] GO:0006415 translational termination translation termination The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). [GO:0006415] minor groove binding of TF to TF binding site of protein bZIP transcription factor A transcription factor that contains a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region for protein dimerization. protein coding DNA region positive regulation of translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0045727] GO:0045727 positive regulation of protein biosynthetic process major groove WRKY domain The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural stud! gene regulation pathway A chain of deoxyribonucleotides that is part of a longer chain of deoxyribunucleotides. DNA region feedback loop atom DNA molecule A chain of deoxyribonucleotides as it occures at a whole. enhancer SO:0000165 enhancer A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. [SO:0000165, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] intron on RNA CG island SO:0000307 CpG_island CpG island Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. [SO:0000307] SO:0000236 ORF he inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. [SO:0000236] ORF protein coding gene gene regulatory protein A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nucleotides can carry chemical energy (e.g. ATP), form coenzymes (e.g. CoA), be used as specific signaling molecules (e.g. cAMP) in the cell. Nucleotides are the subunits of the nucleic acids. [IMR:0001349, ISBN:0815340729] CHEBI:25608 nucleoside phosphates IMR:0001349 nucleotide nucleotide GO:0006457 protein folding The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GO:0006457] protein folding negative regulation of transcription Any process that stops, prevents or reduces the frequency, rate or extent of transcription. [GO:0016481] GO:0016481 negative regulation of transcription DNA binding domain of protein IMR:0001656 vitamin vitamin CHEBI:33229 vitamin Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. [GO:0050789] GO:0050789 regulation of biological process regulatory process DNA fragment RNA polymerase II promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. [SO:0000170] SO:0000170 RNApol II promoter activation of protein transcription factor complex 2 polymerase activity formation of transcription initiation complex beta barrel alpha helix domain deoxynucleotide non physical continuant A non physical continuant is an entity that has no spatial dimension and no mass . Transcriptionally active form of chromatin. euchromatin Processes that are carried out within the cell intra cellular process protein targeting The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif. [GO:0006605] GO:0006605 protein targeting The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent RNA polymerase II transcript. [GO:0009452] 5' capping GO:0009452 RNA capping A transcription factor containing cold shock domain. cold shock domain transcription factor cell death GO:0008219 cell death The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. [GO:0008219] GO:0006410 transcription RNA-dependent transcription RNA-dependent The synthesis of DNA on a template of RNA. [GO:0006410] The function of binding to a specific DNA sequence in order to modulate transcription. [GO:0003700] binding of transcription factor to DNA enhancer binding transcription factor An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]). RNA polymerase binding of transcription activator to enhancer HMG-box transcription factor A transcription factor containing high mobility group protein (HMG) box. [PANTHER:MF00226] general transcription factor basal transcription factor A transcription factor that is required to initiate all transcription events independent of upstream regulatory elements.[PANTHER:MF00228] mutated protein binding to micro RNA miRNA binding microRNA binding insulator Prevents eukaryotic gene regulatory proteins from influencing distant genes / a trancriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. [] insulator element boundary element SO:0000627 insulator tissue DB domain of nuclear receptor function transcription initiation complex methylation The process by which a methyl group is covalently attached to a molecule. [GO:0032259] GO:0032259 methylation transcription factor binding site of DNA helix-turn-helix domain A transcription factor containing the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding domain, which plays a variety of roles throughout the plant life cycle. AP2-EREBP related transcription factor The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [GO:0016310] GO:0016310 phosphorylation phosphorylation The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. [GO:0006413] translation initiation GO:0006413 translational initiation Any process involved in the controlled movement of a cell. [GO:0006928] cell motility GO:0006928 cell motility translation regulator Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome (modified from [GO:0045182]). Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. [GO:0030528] GO:0030528 transcription regulator activity transcription regulator activity gene expression locus regulation of transcriptin by two component regulatory system The protein complex that initiates ribosome-mediated translation of mRNA into a polypeptide (modified from [GO:0003743]). GO:0003743 translation initiation factor activity; IMR:0000901 translation initiation factor translation initiation complex A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. [SO:0000140] attenuator SO:0000140 attenuator regulation of function direction SMAD NF 1 domain apoenzyme biomass RNA polymerase II holoenzyme 2 complex molecular entity A transcription factor containing paired box domain, found in several developmentally regulated proteins in fruit fly, mouse and human paired box transcription factor plant NCBI Taxonomy ID:3193 Embryophyta chromosomal DNA GO:0046907 intracellular transport intracellular transport The directed movement of substances within a cell. [GO:0046907] nucleosome fusion gene 2 GO:0006412 translation The chemical reactions and pathways resulting in the formation of a protein. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GO:0006412] translation instrument reporter gene A transfected gene that encodes an easily assayed product, such as GFP; it is used to monitor gene expression under different conditions; usually to test the activity of a promoter. binding of protein to protein binding site of DNA A transcription factor containing beta-barrel alpha-helix domain. beta-barrel alpha-helix domain transcription factor Any process that activates or increases the frequency, rate or extent of a biological process, function or phenomenon. positive regulation UpRegulation Interacting selectively with an RNA molecule or a portion thereof. [GO:0003723] RNA binding GO:0003723 RNA binding binding to RNA RNA polymerase III promoter type 2 A domain containing a basic region followed by a leucine zipper region, which is required for protein protein interaction. b ZIP transcription repressor activity GO:0016564 transcription repressor activity Any transcription regulator activity that prevents or downregulates transcription. [GO:0016564] A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [SO: 0000188, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] intron SO:0000188 intron heterocyclic base molecular function GO:0003674 molecular function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. [GO:0003674] SO:0000252 rRNA RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. [SO:0000252, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] rRNA The joining of transcription factors formation of transcription factor complex protein amplification SO:0000141 terminator The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. [SO:0000141, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] terminator sigma factor antagonist activity protein domain The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GO:0007155] cell adhesion GO:0007155 cell adhesion disease splice enhancer Region of a transcript that regulates splicing. [SO:0000344] SO:0000344 splice enhancer p 53 like This domain is found in a number of transcription factors, including p53, NFATC, TonEBP, STAT-1, and NFkappaB, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis; NFATC regulates the production of effector proteins involved in coordinating the immune response; TonEBP regulates gene expression induced by osmotic stress and helps regulate intracellular volume during cell growth; STAT-1 plays an important role in B lymphocyte growth and function; and NFkappaB is involved in the inflammatory response. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilize the protein-DNA complex. Protein interactions may also serve to stabilize the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coup! downstream regulatory sequence binding of translation initiation complex to RNA RNA binding of translation initiation complex gene product RNA region A chain of ribonucleotides that is part of a longer chain of ribunucleotides. living entity SO:0000178 operon A genetic regulatory system in which genes (structural genes) coding for functionally related proteins are clustered along the DNA. The expression of structural genes is controlled by the regulatory elements (operator genes) that respond to environmental cues. operon GO:0019725 cellular homeostasis cell homeostasis The processes involved in the maintenance of an internal equilibrium at the level of the cell. [GO:0019725] RNA molecule A chain of ribonucleotides as it occures at a whole. motif identification negative regulation down regulation packed DNA Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0017148] GO:0017148 negative regulation of protein biosynthetic process negative regulation of translation biofilm RNA polymerase II TEA domain upstream regulatory sequence grainy-head transcription factor SO:0000171 RNApol III promoter RNA polymerase III promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. [SO:0000171] exon on RNA A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GO:0005634] nucleus GO:0005634 nucleus physical interaction runt-like transcription factor runt-domain-like transcription factor GCM domain binding assay spacer Provides flexibility needed for communication between DNA bound proteins. Not recognized by gene regulatory proteins. DNA polymerase An enzyme that catalyses the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA/or RNA template or primer (modified from [GO:0003887, GO:0003964]) transcription of operon orientation A physical continuant is an entity that has spatial dimension. It can either have mass (such as a protein) or no mass (such as DNA minor groove). physical continuant SO:0000625 silencer Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes. [SO:0000625, http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm] silencer b HSH C6 zinc cluster RNA coding gene A chain of ribonucleotides. RNA histone A ligand-dependent receptor found in the nucleus of the cell. [GO:0004879] GO:0004879 ligand-dependent nuclear receptor activity nuclear receptor transcription factor GO:0003712 transcription cofactor activity transcription cofactor activity The function that links a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself. [GO:0003712] binding of molecular entity TF binding site of protein TATA box RNA metabolism GO:0016070 RNA metabolic process The chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [GO:0016070] grainyhead protein complex 2 activation of transcription regulator activity Any process that activates or increases the frequency, rate or extent of activity of a transcription regulator, any factor plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor (modified from [GO:0051091, GO:0030528]) negative regulation of gene expression Any process that stops, prevents or reduces the frequency, rate or extent of gene expression. Any process that activates or increases the frequency, rate or extent of gene expression. positive regulation of gene expression DNA A chain of deoxyribonucleotides. The chemical reactions and pathways resulting in the formation of proteins. protein biosynthesis GO:0019538 protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. [GO:0019538] protein metabolism The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). [GO:0006464] protein modification GO:0006464 protein modification process binding to binding site of protein T box domain complex regulation of transcription Any process that activates or increases the frequency, rate or extent of transcription. [GO:0045941] positive regulation of transcription GO:0045941 positive regulation of transcription binding of RNA polymerase to DNA carbohydrate CHEBI:23008 carbohydrate A class of organic compounds containing carbon, hydrogen and oxygen and having the general formula Cm(H2O)n. They usually serve as a major energy source in the diet of animals. Example: sugar or starch. IMR:0001657 carbohydrate transcription regulator Protein that has transcription regulator activity. RHR transcription factor catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GO:0003824] GO:0003824 catalytic activity tryptophan cluster transcription factor behavior The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GO:0007610] GO:0007610 behavior DNA binding site HMG binding of TF to TF binding site of DNA binding of transcription factor to operator NCBI Taxonomy ID: 562 Escherichia coli Escherichia coli E.coli The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GO:0008380] RNA splicing GO:0008380 RNA splicing GCM transcription factor GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3'. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. ! glia cell missing transcription factors The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix'. The fork head domain binds B-DNA as a monomer, but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [InterPro: IPR001766] forkhead/winged-helix domain regulation of process cell cycle GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. [GO:0007049] defect gene beta scaffold domain transcription factor with minor groove contacts polyadenylation at the 3' end 3' polyadenylation The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript. [GO:0006378] GO:0006378 mRNA polyadenylation RNA coding DNA region A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] sigma factor Transcriptionally inactive form of chromatin. heterochromatin The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways. bHLH proteins include MyoD, SREBPs (sterol regulatory element binding proteins), and yeast Pho4 (phosphatase system). In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf. [InterPro: IPR011598] b HLH Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. [InterPro: IPR001083] copper fist transcription factor histone acetylation The modification of histones by addition of acetyl groups. [GO:0016573] GO:0016573 histone acetylation 2 gene control region Any process that modulates the frequency, rate or extent of the synthesis of RNA on a template of DNA or DNA on a template of RNA. regulation of transcription of operon GO:0045449 regulation of transcription Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0045449] regulation of transcription polarity gene fusion 2 pocket domain pocket consists of two conserved 'boxes' (A and B) with a less conserved spacer region lying in between MADS transcription factor A transcription factor containing MADS domain. sequence protein maturation GO:0051604 protein maturation The process leading to the attainment of the full functional capacity of a protein. [GO:0051604] zinc-coordinating domain homodimerization GO:0042803 protein homodimerization activity Interacting selectively with an identical protein to form a homodimer. [GO:0042803] GO:0030163 protein catabolic process protein catabolism The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GO:0030163] CHEBI:24846 inositol phosphates inositol phosphate TF module transcription activator A transcription regulator activity required for initiation or upregulation of transcription. molecular binding microRNA miRNA Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. [SO:0000253, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] SO:0000253 tRNA t RNA primary structure (Wikipedia, en:) The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence. nucleic acid region agonist deoxynucleoside CHEBI:33696 nucleic acids nucleic acid Macromolecules, the major organic matter of the nuclei of biological cells, made up of nucleotide units, and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. [CHEBI:33696] Any of numerous microorganisms of the kingdom Fungi, which are characterized by the absence of chlorophyll and by the presence of a rigid cell wall composed of chitin, mannans and sometimes cellulose. The kingdom includes the yeasts, molds, smuts, and mushrooms. fungus NCBI Taxonomy ID: 4751 Fungi NCBI Taxonomy ID: 2759 Eukaryota eukaryote RNA modification The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. [GO:0009451] GO:0009451 RNA modification modification of molecular entity regulation of physical interaction This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans. In D. melanogaste the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences. The NMR analysis of the DSX DM domain revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence. [InterPro: IPR001275] DM domain dimerization GO:0046983 protein dimerization activity The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [GO:0046983] A complete and catalytically active enzyme consisting of all subunits. (i.e. Holoenzyme = Apoenzyme + Cofactor). holoenzyme GO:0015031 protein transport The directed movement of proteins into, out of, within or between cells. [GO:0015031] protein transport GO:0065004 protein-DNA complex assembly formation of protein DNA complex The aggregation and bonding together of proteins and DNA molecules to form a protein-DNA complex. [GO:0065004] intron on DNA GO:0046982 protein heterodimerization activity Interacting selectively with a nonidentical protein to form a heterodimer. [GO:0046982] heterodimerization cell differentiation The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO:0030154] GO:0030154 cell differentiation structural domain of transcription repressor A region that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205). [SO:0000147, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] SO:0000147 exon exon runt like domain Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. [GO:0006352] transcription initiation GO:0006352 transcription initiation DNA binding domain of transcription factor ligand IMR:0000002 ligand Binding to a specific receptor protein and activating intracellular signaling cascades that alter the behavior of the cell. [IMR:0000002, ISBN:0815340729] positive regulation of transcription by transcription activator Any process involving transcription activator activity that activates or increases the frequency, rate or extent of transcription (modified from [GO:0045941]). GO:0006350 transcription The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350] transcription of gene A transcription factor containing pocket domain (e.g. the RB protein). pocket domain transcription factor C6 zinc cluster transcription factor The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. [GO:0006304] DNA modification GO:0006304 DNA modification CHEBI:24870 ions ion IMR:0001658 ion An ion is a molecular entity having a net electric charge. [CHEBI:24870] The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins. By contrast, the N-terminal region varies in both length and sequence. [InterPro: IPR000814] TATA-binding protein TBP SO:1001284 regulon A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. [SO:1001284, ISBN:0198506732] regulon The synthesis of DNA from an RNA transposon intermediate. [GO:0032199] GO:0032199 transcription during RNA-mediated transposition transcription during RNA-mediated transposition CHEBI:18059 lipids lipid A loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. [CHEBI:18059] IMR:0000947 lipid SMAD NF-1 transcription factor temperature A transcription factor containing zinc coordinating domain. zinc coordinating domain transcription factor molecular structure NCBI Taxonomy ID: 2157 Archaea archaebacterium GO:0044237 cellular metabolic process cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. [GO:0044237] CHEBI:28816 2-deoxy-D-ribose deoxyribose A transcription cofactor that represses transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003714]) transcription corepressor protein coding ORF sequence homology analysis double strand DNA bidirectional promoter gene SO:0000704 gene A unit of inheritance; a working subunit of DNA that contributes to phenotype/function and carries a particular set of instructions, usually coding for a particular protein. translation factor Any of a group of proteins involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. STAT regulation of pathway transcription coactivator A transcription cofactor that activates transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003713]) Heat shock transcription factor HSF transcription factor NCBI Taxonomy ID: 38018 unidentified phage bacteriophage microorganism SO:0000167 promoter A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. [SO:0000167] promoter The directed movement of mRNA from the nucleus to the cytoplasm. [GO:0006406] GO:0006406 mRNA export from nucleus nuclear export of mRNA binding of protein to protein binding site of protein molecular entity helix-turn-helix domain transcription factor A transcription factor containing helix-turn-helix domain. unpacked DNA The DNA that is unpacked from the loosen chromatin and hence get easy access to various enzymes like DNA polymerase or RNA polymerase in replication or transcription of gene. protist protein function GO:0009987 cellular process cellular process Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. [GO:0009987] CHEBI:26564 riboses ribose molecular process An exact synonyms of the given ontology term. PAL-CONSTRAINT DIRECTED-BINARY-RELATION GRO definition explaining the meaning of a class or property. If the definition was taken from an external resource a reference is given in brackets. Reference to a similar term in an external database or terminological resource.