Hop1 and Red1 chip
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR727157.fastq.gz | Fastqsanger.gz | |||
| ERR727158.fastq.gz | Fastqsanger.gz | |||
| ERR727159.fastq.gz | Fastqsanger.gz | |||
| ERR727160.fastq.gz | Fastqsanger.gz | |||
| ERR727161.fastq.gz | Fastqsanger.gz |
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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: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.
2024-03-19 | GSE237707 | GEO
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: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
Project description:Crossover recombination is a hallmark of meiosis, which holds the paternal and maternal chromosomes (homologs) together for their faithful separation, meanwhile, it promotes genetic diversity of progenies. The pattern of crossover is mainly controlled by the architecture of meiotic chromosomes. Environmental factors, especially temperature, also play an important role in modulating crossovers. However, it is unclear how temperature affects crossovers. Here, we examined the distributions of budding yeast axis components (Red1, Hop1, and Rec8) and the CO-associated Zip3 foci in detail in different temperatures, and found that both increased and decreased temperatures result in shorter meiotic chromosome axes and more crossovers. Further investigations showed that altered temperature coordinately enhanced the hyperabundant accumulation of Hop1 and Red1 on chromosomes and the number of Zip3 foci. Most importantly, temperature-induced alterations in axis distribution and Zip3 foci depend on the changes in DNA negative supercoil. These findings suggest that yeast meiosis senses temperature changes by increasing the level of negative supercoil to increase crossovers and modulate chromosome organization. These findings provide a novel view in understanding the effect and mechanism of temperature on meiosis recombination and chromosome organization, and thus also have an important implication in evolution and breeding.
2024-07-30 | GSE246901 | GEO
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
Project description:Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific ‘licensing’ of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1 and Rec8). This suggests that although Pch2 is linked to axis/SC-directed recruitment and function, the chromosomal population of Pch2 described here is not directly associated with chromosomal axis sites. In line with this observation, interfering with the pool of Pch2 that associates with active RNAPII transcription does not lead to effects on the chromosomal abundance of Hop1, a known axial client of Pch2. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription.
2020-06-14 | GSE138429 | GEO
Project description:Polη-ChIP-seq analysis to investigate genome-wide distribution of Polη in budding yeast.
2021-08-16 | GSE179539 | GEO
Project description:SNP-ChIP is a novel method leveraging small-scale intra-species genetic polymorphisms, mainly SNPs, to allow quantitative spike-in normalization of ChIP-seq results. SNP-ChIP uses a different strain of the same organism as the spike-in material and can be applied to any organism for which genome assemblies are available for two different strains or individuals with sufficient genetic diversity. This ensures antibody cross-reactivity and thus extends the applicability of the method beyond the small number of highly conserved proteins. It also ensures complete physiological coherence between the test and the spike-in cells. In this work we develop and validate the method using test cases from budding yeast meiosis. We use strains with ~0.7% genomic sequence divergence as test strain background and the spike-in strain, respectively. Sequencing reads are mapped to a hybrid genome, with naturally occurring sequence polymorphisms allowing assignment of most reads to one of the two genomes. By targeting the yeast chromosomal protein Red1, we show that SNP-ChIP reliably identifies previously reported changes in overall protein levels, irrespective of changes in binding distribution. We also show that SNP-ChIP is robust to wide changes in sequencing depth, as well as the amount of spike-in material. SNP-ChIP allowed discovery of novel regulators of global Red1 protein accumulation and is also shown to allow quantitative analysis of the DNA-damage associated histone modification gamma-H2AX. SNP-ChIP is a robust and versatile spike-in normalization method that can be used with any target against which a ChIP-grade antibody is available and for any organisms with sufficient intra-species diversity, including most model organisms as well as human cells. Grant ID: FY16-208 Grant title: Meiotic segregation of small chromosomes Funding source: March of Dimes Grantee name: Andreas Hochwagen, New York University, New York, NY, United States
2018-11-21 | GSE115092 | GEO
Project description:Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast. Occupancy profiling of Red1, Mtl1, and Mmi1 proteins in fission yeast.
2016-01-05 | GSE74740 | GEO