Long-range effects of centromeres on the binding of the meiotic chromosome axis factor Red1
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ABSTRACT:
PROVIDER: PRJNA472390 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26353500_1.fastq.gz | Fastqsanger.gz | |||
| SRR26353500_2.fastq.gz | Fastqsanger.gz | |||
| SRR26353501.fastq.gz | Fastqsanger.gz | |||
| SRR26353502.fastq.gz | Fastqsanger.gz | |||
| SRR26353503.fastq.gz | Fastqsanger.gz |
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Project description:A chromosome size-dependent bias in meiotic recombination is in place to ensure that homologous chromosome pairing occurs for all chromosomes, including the smallest ones. This bias is clearly detectable during the assembly of the meiotic protein axis, the structure that compacts meiotic chromosomes and promotes recombination.To investigate the origin of the size bias, we mapped genome-wide occupancy of the meiotic axis protein Red1 in yeast strains containing chromosome fusions and synthetic chromosomes. Meiosis studies of the fusion and synthetic chromosomes further revealed that core centromeres influence the deposition of the axial element protein Red1 over distances >100kb, while pericentromeric regions co-evolved to reduce Red1 binding near centromeres and spread out Red1 along the chromosomes.
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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
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.
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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
Project description:Here we studied the budding yeast Lachancea kluyveri, a cousin of the model Saccharomyces cerevisiae, in order to try to understand the mechanism responsible for the absence of meiotic recombination on its almost entire sex chromosome (Brion et al. 2017). We performed protein-DNA interaction mapping of Rec8, Red1, Hop1 and Zip3 proteins by ChIP-seq. Briefly, we observed an enrichment of Zip3, a protein known as a marker of type I crossing-overs, where peaks of DSBs were detected by CC-seq and a virtual absence of Zip3 within Lakl0C-left. For Rec8, a meiotic specific protein part of the cohesin complex, we detected enriched peaks at centromeres and inside intergenic regions flanked by convergent ORFs everywhere in the genome Lakl0C-left included. Remarkably, Red1 and Hop1, known to form the lateral element of the synaptonemal complex and important for DSB formation, were enriched mainly at Rec8 peaks except at centromeres and particurlarly on Lakl0C-left where they are completely absent.
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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.
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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.
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Project description:Meiosis is a highly complex process that underpins recombination in sexually reproducing organisms. Recent genomics studies suggest that up to several thousand genes/proteins contribute to the meiotic pathway, yet relatively few have been functionally characterised. Our understanding of the physical interactions between meiotic proteins and how the meiotic machinery interacts with other components of the cell is also limited. In this study, we used affinity proteomics targeting the meiotic chromosome axis protein, ASY1, to enrich for axis-associated proteins in Brassica oleracea anthers or meiocytes in prophase I of meiosis. LC-MS/MS analysis identified 540 proteins which co-immunoprecipitated with ASY1 in a sample-specific manner. These correspond to 485 Arabidopsis orthologues, 90% of which form a coherent predicted protein-protein interaction network which includes known and novel meiotic proteins, based on mutant analysis, but also proteins more usually associated with other cellular processes including replication and proteolysis. Our data provided new insights into the role of the chromosome axis in plant meiosis. We identified a novel axis-associated protein and showed that during prophase I, ASY1 and its interacting partner, ASY3, are extensively phosphorylated. Further studies targeting other meiotic proteins may ultimately enable the construction of a comprehensive meiosis protein-protein interaction network for higher plants.
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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.
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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.
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