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Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (MNase-seq)

ABSTRACT: Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (MNase-seq)

PROVIDER: PRJEB15184 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1590154_1.fastq.gz	Fastqsanger.gz
	ERR1590154_2.fastq.gz	Fastqsanger.gz
	ERR1590155_1.fastq.gz	Fastqsanger.gz
	ERR1590155_2.fastq.gz	Fastqsanger.gz
	ERR1590156_1.fastq.gz	Fastqsanger.gz

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Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (SPO11-1-oligonucleotides-seq)

Project description:To determine meiotic recombination initiation sites in Arabidopsis thaliana genome we purified and sequenced oligonucleotides (35-45 nt) bound to SPO11-1, meiosis specific transesterase that induces meiotic DSB formation. This reveals that SPO11-1-oligonucleotide hotspots occur at nucleosome depleted regions of gene promoters, introns, terminators and specific families of DNA transposons (recomposons). To investigate the influence of chromatin structure and epigenetic factors on meiotic DSB formation we performed sequencing of SPO11-1-oligonucleotides in arp6, met1 and suvh4 suvh5 suvh6.

2017-06-05 | E-MTAB-5041 | biostudies-arrayexpress

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (MNase-seq)

Project description:To analyse nucleosome positioning and occupancy we performed micrococcal nuclease digestion of Arabidopsis wild type (Col-0) chromatin and gel purified the resulting ~150 bp mononucleosomal DNA band. This DNA was used to generate a library and paired-end sequencing performed (MNase-seq). To further examine influence of SWR1 chromatin remodelling complex and DNA methylation on nucleosome occupancy, we repeated MNase-seq in Aarabidopsis arp6 and met1 mutant.

2017-06-05 | E-MTAB-5042 | biostudies-arrayexpress

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (H3K4m3 ChIP-seq)

Project description:To investigate the relationship between meiotic recombination initiation and H3K4m3 in Arabidopsis, we generated and sequenced H3K4m3 ChIP libraries from meiotic stage floral buds in wild type, arp6 and met1. To produce high-resolution of H3K4m3 mapping, we used micrococcal nuclease (MNase) to digest chromatins that were cross-linked by formaldehyde for ChIP. This experiment provides for H3K4m3 maps with the resolution of mononucleosomal DNA level (~150 bp).

2017-06-05 | E-MTAB-5048 | biostudies-arrayexpress

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (H3K4m3 ChIP-seq)

Project description:Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (H3K4m3 ChIP-seq)

| PRJEB15183 | ENA

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (SPO11-1-oligonucleotides-seq)

Project description:Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (SPO11-1-oligonucleotides-seq)

| PRJEB15185 | ENA

Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination. Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.

2015-12-07 | E-GEOD-59004 | biostudies-arrayexpress

Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.

2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress

Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

2013-03-07 | GSE31648 | GEO

Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

2015-12-07 | GSE59004 | GEO

Functional roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hotspots (expression)

Project description:Meiotic recombination is initiated by the Spo11 endonuclease, which directs DNA double strand breaks at discrete regions in the genome coined hotspots. Here we report the profiles and dynamics of histone modifications at the cores of mouse recombination hotspots in early meiotic prophase. To define the spectrum of possible regulators of histone methylation and acetylation at all stages of meiosis I, expression analyses of histone acetylases/deacetylases (HATs/HDACs) and and HMTs/HDMTs genes when comparing those expressed in spermatogonia, pre-leptotene and leptotene/zygotene versus pachytene meiotic stages.

2016-11-04 | GSE57197 | GEO

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