Comment[ArrayExpressAccession]	E-GEOD-57039
MAGE-TAB Version	1.1							
Public Release Date	2014-05-15
Investigation Title	Genome Rearrangements and Pervasive Meiotic Drive Cause Hybrid Infertility in Fission Yeast							
Comment[Submitted Name]	Genome Rearrangements and Pervasive Meiotic Drive Cause Hybrid Infertility in Fission Yeast
Experiment Description	Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Uncovering the mechanisms of hybrid sterilitynot only provides insight into the origins of species but also potentially revealsnovel causes of intra-species infertility.Here we identify causes underlying hybrid infertilityofSchizosaccharomyces pombeand S. kambucha, two fission yeast species that are 99.5% identical at the nucleotide level.These yeasts mate to form viable diploids that efficiently complete meiosis. However,S. kambucha/S. pombe hybrids generate few viable gametes, most of which are either aneuploid or diploid.We find that chromosomal rearrangements and related recombination defectsare major causes of hybrid infertility. Surprisingly, using experiments in which we eliminate meiotic recombination, we find thatrecombination defects cannot completely explain the hybrid infertility. Instead, we find that a significant fraction of hybrid infertility is caused by the action of at least three distinct meiotic drive alleles, one on each S. kambucha chromosome,that M-bM-^@M-^\cheatM-bM-^@M-^] to be transmitted to more than half (up to 90%) of viable gametes.Two of these driving lociare linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. We find that all three S. kambuchadrive loci independently contribute to hybrid infertility by causing nonrandom spore death. This study reveals how quickly multiple barriers to fertility can arise.In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. Meiotic DNA double-strand break analysis of Schizosaccharomyces kambucha by immunoprecipitating accumulated Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following nitrogen starvation .							
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	Fowler	Zanders	Eickbush	Yu	Kang	Fowler	Smith	Malik
Person First Name	Kyle	SaraH	Michael	Jonathan	Ji-Won	Kyle	Gerald	Harmit
Person Mid Initials		E	T	S		R	R	S
Person Email	krfowler@fhcrc.org							
Person Affiliation	Fred Hutchinson Cancer Research Center							
Person Phone	206-667-4431							
Person Address	Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington, USA							
Person Roles	submitter							
Protocol Name	P-GSE57039-1	P-GSE57039-4	P-GSE57039-5	P-GSE57039-2	P-GSE57039-3	P-GSE57039-6		
Protocol Description	In addition to dark spot and control probes, custom probes for repetitive S. pombe DNA were also removed.  Due to the sequence divergence of the S. kambucha genome, some probes may not have efficiently hybridized to the immunoprecipitates.  To identify potentially incompatible probes, the whole-cell input channel was compared with that of a previously published S. pombe DSB array (Fowler et al., 2013).  When log-transformed and plotted, the dye-intensities of >99% of probes were generally linear, indicating efficient hybridization; a small subpopulation exhibited significantly reduced dye signal.  Probes whose dye-intensity was < 1.5 (on a log scale) in either input channel were removed. ID_REF =  VALUE = Median normalized log10 ratios of Rec12-IP/Input (Cy5/Cy3)	Immunoprecipitated material and whole-cell extracts were PCR amplified to increase signal and Cy3/Cy5-labeled dUTPs were incorporated.	Oligoarray controlM- targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus)M- were added, and samples were applied to microarrays enclosed in AgilentM- SureHyb-enabled hybridization chambers. After hybridization, slides wereM- washed.	Using S. kambucha diploids homozygous for rad50S and rec12-FLAG, 10 mL YEL cultures were started from single colonies and grown overnight at 30 degrees. These cultures were diluted the next day (1:100 or 1:50) into 100 mL PM medium and grown overnight (~16 hours) at 30 degrees to an OD600 ~1. Cells from 50 mL were then pelleted and resuspended in 500 mL PM minus nitrogen medium to induce sporulation. The cells sporulated at 30 degrees.	Cells were collected after 8.5 hours and lysed without exogenous crosslinking agents. Cells were first treated with protease inhibitors and then broken with a bead beater, chromatin was sonicated to ~500-1000 bp, and Rec12-FLAG immunoprecipitated.	Slides were imaged on anM- Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.7.3.1).		
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol		
Comment[SecondaryAccession]	GSE57039							
Comment[GEOReleaseDate]	2014-05-15							
Comment[ArrayExpressSubmissionDate]	2014-04-24							
Comment[GEOLastUpdateDate]	2014-05-17							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-57039.sdrf.txt