Comment[ArrayExpressAccession] E-GEOD-39126 MAGE-TAB Version 1.1 Public Release Date 2013-12-01 Investigation Title The human AlkB homologue 4 interacts with proteins associated with transcription (methylation) Comment[Submitted Name] The human AlkB homologue 4 interacts with proteins associated with transcription (methylation) Experiment Description The Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from E. coli is a demethylase which repairs alkyl lesions in DNA, as well as RNA, through a direct reversal mechanism. Humans possess nine AlkB homologues (ALKBH1-8 and FTO). ALKBH2 and ALKBH3 display demethylase activities corresponding to that of AlkB, and both ALKBH8 and FTO are RNA modification enzymes. The biochemical functions of the rest of the homologues are still unknown. To increase our knowledge on the functions of ALKBH4 and ALKBH7 we have here performed yeast two-hybrid screens to identify interaction partners of the two proteins. While no high-confidence hits were detected in the case of ALKBH7, several proteins associated with chromatin and/or involved in transcription were found to interact with ALKBH4. For all interaction partners, the regions mediating binding to ALKBH4 comprised domains previously reported to be involved in interaction with DNA or chromatin. Furthermore, some of these partners showed nuclear co-localization with ALKBH4. However, the global gene expression pattern was only marginally altered upon ALKBH4 over-expression, and larger effects were observed in the case of ALKBH7. Although the molecular function of both proteins remains to be revealed, our findings suggest a role for ALKBH4 in regulation of gene expression or chromatin state and support the previous association of ALKBH7 with spermatogenesis. Comparison of DNA methylation patterns in cells over expressing ALKBH4 and ALKBH7 Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Meza-Zepeda Bjornstad Meza Otterlei Olafsrud Meza-Zepeda Falnes Person First Name Leonardo Linn Trine Marit Solveig Leonardo Pal Person Mid Initials A. G J M A O Person Email leonardm@rr-research.no Person Affiliation The Norwegian Radium Hospital Person Address Dept. of Tumor Biology, The Norwegian Radium Hospital, Ullernchausseen 70, Oslo, Norway Person Roles submitter Protocol Name P-GSE39126-1 P-GSE39126-4 P-GSE39126-5 P-GSE39126-2 P-GSE39126-3 P-GSE39126-6 Protocol Description Data extraction and initial quality control of the bead summary raw data were performed using BeadStudio v3.1.0.0 and the Methylation module v1.9, both provided by Illumina. ID_REF = VALUE = Average Beta or normalized (provide the normalization method) Average Beta DETECTION PVAL = Standard Ilumina label protocol Standard Ilumina hyb protocol HEL293 were grown in DulbeccoM-bM-^@M-^Ys modified EagleM-bM-^@M-^Ys medium (DMEM) (Lonza) supplemented with 10 % tetracycline-free fetal bovine serum (FBS) (Clontech), 100 U/ml penicillin (Lonza), 100 U/ml streptomycin (Lonza), 2 mM L-glutamine (Lonza), 15 M-NM-