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Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface [ChIP-Seq]

ABSTRACT: Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial-element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation nearby. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the highly structured axial element to promote recombination while easily adapting to changes in chromosome activity.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE69231 | GEO | 2015/08/06

SECONDARY ACCESSION(S): PRJNA284935

REPOSITORIES: GEO

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Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface [ChIP-Seq]

Project description:Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial-element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation nearby. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the highly structured axial element to promote recombination while easily adapting to changes in chromosome activity. ChIP-seq experiments were undertaken to understand the features of meiotic chromosomal axes assembly in meiosis. The genome-wide distribution of axis proteins including Hop1, Red1 as well as cohesin subunits Rec8 and Smc3 were measured. Axis protein binding pattern is also measured in rec8 mutant and pREC8-SCC1 in rec8 mutant.

2015-08-06 | E-GEOD-69231 | biostudies-arrayexpress

Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface

Project description:Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial-element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the axial element to promote recombination while easily adapting to changes in chromosome activity. 7 genome wide meiotic ChIP-seq sets: V5-Red1 DNA interaction (V5-Red1-ChIP), V5-Red1 DNA interaction in the absence of axis protein Hop1 (V5-Red1-ChIP, hop1delta), V5-Red1 DNA interaction in the absence of another two axis proteins Hop1 and Rec8 (V5-Red1-ChIP, hop1delta rec8delta), Rec8-HA DNA interaction (Rec8-HA-ChIP), Rec8-HA DNA interactionin the absence of Red1 (Rec8-HA-ChIP, red1delta), and 2 untagged control (V5-untagged-ChIP, HA-untagged-ChIP) (corresponding to the main Figure5)

2015-08-07 | E-GEOD-70112 | biostudies-arrayexpress

Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface [ChIP-chip]

Project description:Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial-element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation nearby. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the highly structured axial element to promote recombination while easily adapting to changes in chromosome activity. Two types of study were undertaken to understand the meiotic chromosomal axes assembly and its importance in DSB regulation in yeast. First, DSBs were mapped using ssDNA enrichment in strains isogenic for a dmc1 mutation, and also including rec8 deletion and pREC8-SCC1 in rec8 deletion. Second, the genome-wide distribution of meiotic or mitotic cohesin in meiosis was measured by ChIP-chip analysis in wild-type and pREC8-SCC1 in rec8 deletion.

2015-08-06 | E-GEOD-69230 | biostudies-arrayexpress

Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface

2015-08-07 | GSE70112 | GEO

Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface [ChIP-chip]

2015-08-06 | GSE69230 | GEO

Spo11-oligo mapping in S. cerevisiae red1, hop1, mek1 mutants

Project description:Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, the nonrandom distribution of meiotic DSBs along the genome can be attributed to the combined influence of multiple factors on Spo11 cleavage. One factor is higher-order chromatin structure, particularly the loop-axis organization of meiotic chromosomes. Axial element proteins Red1 and Hop1 provide the basis for meiotic loop-axis organization and are implicated in diverse aspects of meiotic recombination. Mek1 is a meiotic-specific kinase associated with Red1 and Hop1. Red1, Hop1, and Mek1 are required for normal DSB levels, but their effects on the DSB distribution has not been examined, and exactly how these proteins influence DSB levels and distribution is unknown. Here, we examined the contributions of Red1, Hop1, and Mek1 to the DSB distribution by deep sequencing and mapping Spo11-associated oligonucleotides from red1, hop1, and mek1 mutant strains, thereby generating genome-wide meiotic DSB maps.

2018-09-01 | GSE84859 | GEO

Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae

Project description:The DNA double strand breaks (DSBs) that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in budding yeast contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red are important for DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, only a small fraction of crossovers that formed at an insert locus required MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local DSB levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.

2022-07-12 | GSE201240 | GEO

Reduced dosage of the chromosome axis factor Red1 selectively disrupts the meiotic recombination checkpoint in Saccharomyces cerevisiae

Project description:Meiotic chromosomes assemble characteristic “axial element” structures that are essential for fertility and provide the chromosomal context for meiotic recombination, synapsis and checkpoint signaling. Whether these meiotic processes are equally dependent on axial element integrity has remained unclear. Here, we investigated this question in S. cerevisiae using the putative condensin allele ycs4S. We show that the severe axial element assembly defects of this allele are explained by a linked mutation in the promoter of the major axial element gene RED1 that reduces Red1 protein levels to 20-25% of wild type. Intriguingly, the Red1 levels of ycs4S mutants support meiotic processes linked to axis integrity, including DNA double-strand break formation and deposition of the synapsis protein Zip1, at levels that permit 70% gamete survival. By contrast, the ability to elicit a meiotic checkpoint arrest is completely eliminated. This selective loss of checkpoint function is supported by a RED1 dosage series and is associated with the loss of most of the cytologically detectable Red1 from the axial element. Our results indicate separable roles for Red1 in building the structural axis of meiotic chromosomes and mounting a sustained recombination checkpoint response.

2017-07-18 | GSE87060 | GEO

Spo11-accessory proteins link DNA double-strand break sites to the chromosome axis in early meiotic recombination

Project description:Meiotic recombination between homologous chromosomes initiates via programmed DNA double-strand breaks (DSBs), generated by complexes comprising Spo11 transesterase plus accessory proteins. DSBs arise concomitantly with the development of axial chromosome structures, where the coalescence of axis sites produces linear arrays of chromatin loops. Recombining DNA sequences map to loops, but are ultimately tethered to the underlying axis. How and when such tethering occurs is currently unclear. Using ChIPchip in yeast, we show that Spo11-accessory proteins Rec114, Mer2 and Mei4 stably interact with chromosome axis sequences, upon phosphorylation of Mer2 by S-phase Cdk. This axis tethering requires meiotic axis components (Red1/Hop1) and is modulated in a domain-specific fashion by cohesin. Loss of Rec114, Mer2 and Mei4 binding correlates with loss of DSBs. Our results strongly suggest that hotspot sequences become tethered to axis sites by the DSB machinery prior to DSB formation.

2011-08-28 | GSE29860 | GEO

Rec8 cohesin-mediated loop-axis chromatin architecture is required for meiotic recombination

Project description:During meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, functional correlation between these structure formation and cohesion remains elusive. Here we examined formation of the cohesin-dependent axial structure in fission yeast, which forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the central elements, and found that Rec8 cohesin is crucial for the formation of the loop-axis structure within the atypical SC. Furthermore, the Rec8-mediated loop-axis structure is formed in the absence of LinEs, and provides a structural platform for aligning homologous chromosomes. We also succeeded to identify a rec8 mutant that lost the ability of assembling the loop-axis structure without losing cohesion. Remarkably, this mutant showed defects in LinE assembly, resulting in great reduction of meiotic recombination. Collectively, our results demonstrate an essential role of the Rec8-dependent loop-axis structure in LinE assembly, facilitating meiotic recombination.

2022-04-27 | GSE192516 | GEO

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