Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

AbstractCohesin consists of the Smc1-Smc3-Rad21 tripartite ring and the SA protein that interacts with Rad21. The Nipped-B protein loads cohesin topologically around chromosomes to mediate sister chromatid cohesion and facilitate long-range control of gene transcription. It is largely unknown how Nipped-B and cohesin associate specifically with gene promoters and transcriptional enhancers, or how sister chromatid cohesion is established. Here we use genome-wide chromatin immunoprecipitation in Drosophila cells to show that SA and the Fs(1)h (BRD4) BET domain protein help recruit Nipped-B and cohesin to enhancers and DNA replication origins, while the MED30 subunit of the Mediator complex directs Nipped-B and Rad21 to promoters. All enhancers and their neighboring promoters are close to DNA replication origins and bind SA with proportional levels of cohesin subunits. Most promoters are far from origins and lack SA, but bind Nipped-B and Rad21 with sub-proportional amounts of Smc1, indicating that they bind SA-deficient cohesin part of the time. Genetic data confirm that Nipped-B and Rad21 function together with Fs(1)h in vivo to facilitate Drosophila development. These findings demonstrate that Nipped-B and cohesin are differentially targeted to enhancers and promoters and suggest models for how SA and DNA replication help establish sister chromatid cohesion and facilitate enhancer-promoter communication. They indicate that SA is not an obligatory cohesin subunit but a factor that controls cohesin location on chromosomes.

Download Full-text

The acetyltransferase Eco1 elicits cohesin dimerization during S phase

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.013102 ◽

2020 ◽

Vol 295 (22) ◽

pp. 7554-7565 ◽

Cited By ~ 3

Author(s):

Di Shi ◽

Shuaijun Zhao ◽

Mei-Qing Zuo ◽

Jingjing Zhang ◽

Wenya Hou ◽

...

Keyword(s):

Dna Replication ◽

Sister Chromatid ◽

Sister Chromatid Cohesion ◽

S Phase ◽

Cross Linking ◽

Temperature Sensitive ◽

Exact Nature ◽

Chromatid Cohesion ◽

Lysine Residues

Cohesin is a DNA-associated protein complex that forms a tripartite ring controlling sister chromatid cohesion, chromosome segregation and organization, DNA replication, and gene expression. Sister chromatid cohesion is established by the protein acetyltransferase Eco1, which acetylates two conserved lysine residues on the cohesin subunit Smc3 and thereby ensures correct chromatid separation in yeast (Saccharomyces cerevisiae) and other eukaryotes. However, the consequence of Eco1-catalyzed cohesin acetylation is unknown, and the exact nature of the cohesive state of chromatids remains controversial. Here, we show that self-interactions of the cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication–coupled manner in both yeast and human cells. Using cross-linking MS-based and in vivo disulfide cross-linking analyses of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, upon temperature-sensitive and auxin-induced degron-mediated Eco1 depletion, the cohesin-cohesin interactions became significantly compromised, whereas deleting either the deacetylase Hos1 or the Eco1 antagonist Wpl1/Rad61 increased cohesin dimer levels by ∼20%. These results indicate that cohesin dimerizes in the S phase and monomerizes in mitosis, processes that are controlled by Eco1, Wpl1, and Hos1 in the sister chromatid cohesion-dissolution cycle. These findings suggest that cohesin dimerization is controlled by the cohesion cycle and support the notion that a double-ring cohesin model operates in sister chromatid cohesion.

Download Full-text

The acetyltransferase Eco1 elicits cohesin dimerization during S phase

10.1101/2020.02.07.938530 ◽

2020 ◽

Author(s):

Di Shi ◽

Shuaijun Zhao ◽

Mei-Qing Zuo ◽

Jingjing Zhang ◽

Wenya Hou ◽

...

Keyword(s):

Dna Replication ◽

Sister Chromatid ◽

Sister Chromatid Cohesion ◽

S Phase ◽

Repair Gene ◽

Additional Layer ◽

Ring Model ◽

Dna Repair Gene ◽

Chromatid Cohesion

AbstractSister chromatid cohesion is established by Eco1 in S phase. Nevertheless, the exact consequence of Eco1-catalyzed acetylation is unknown, and the cohesive state remains highly controversial. Here we show that self-interactions of cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication-coupled manner in both yeast and human. Through cross-linking mass spectrometry and VivosX analysis of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, cohesin-cohesin interaction becomes significantly compromised when Eco1 is depleted. On the other hand, deleting either deacetylase Hos1 or Eco1 antagonist Wpl1/Rad61 results in an increase (e.g., from ∼20% to 40%) of cohesin dimers. These findings suggest that cohesin dimerization is controlled by common mechanisms as the cohesion cycle, thus providing an additional layer of regulation for cohesin to execute various functions such as sister chromatid cohesion, DNA repair, gene expression, chromatin looping and high-order organization.Author SummaryCohesin is a ring that tethers sister chromatids since their synthesis during S phase till their separation in anaphase. According to the single-ring model, one ring holds twin sisters. Here we show a conserved cohesin-cohesin interaction from yeast to human. A subpopulation of cohesin is dimerized concomitantly with DNA replication. Cohesin dimerization is dependent on the acetyltransferase Eco1 and counteracted by the anti-establishment factor Wpl1 and deacetylase Hos1. Approximately 20% of cellular cohesin complexes are measured to be dimers, close to the level of Smc3 acetylation by Eco1 in vivo. These findings provide evidence to support the double-ring model in sister chromatid cohesion.

Download Full-text

Faculty Opinions recommendation of DNA double-strand breaks trigger genome-wide sister-chromatid cohesion through Eco1 (Ctf7).

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1090512.545649 ◽

2007 ◽

Author(s):

Kerry Bloom

Keyword(s):

Sister Chromatid ◽

Sister Chromatid Cohesion ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Genome Wide ◽

Chromatid Cohesion

Download Full-text

Faculty Opinions recommendation of DNA double-strand breaks trigger genome-wide sister-chromatid cohesion through Eco1 (Ctf7).

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1090512.543783 ◽

2007 ◽

Author(s):

Antony Carr

Keyword(s):

Sister Chromatid ◽

Sister Chromatid Cohesion ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Genome Wide ◽

Chromatid Cohesion

Download Full-text

Faculty Opinions recommendation of Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717987460.793472434 ◽

2013 ◽

Author(s):

Susan Gerbi

Keyword(s):

Dna Replication ◽

Replication Timing ◽

Replication Origins ◽

Human Dna ◽

Genome Wide ◽

Dna Replication Origins

Download Full-text

Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe

EMBO Reports ◽

10.1038/sj.embor.embor7400008 ◽

2003 ◽

Vol 4 (11) ◽

pp. 1048-1053 ◽

Cited By ~ 3

Author(s):

Mónica Segurado ◽

Alberto de Luis ◽

Francisco Antequera

Keyword(s):

Dna Replication ◽

Schizosaccharomyces Pombe ◽

Wide Distribution ◽

Replication Origins ◽

Genome Wide ◽

Dna Replication Origins

Download Full-text

Cul4-Ddb1 ubiquitin ligases facilitate DNA replication-coupled sister chromatid cohesion through regulation of cohesin acetyltransferase Esco2

10.1101/414888 ◽

2018 ◽

Cited By ~ 1

Author(s):

Haitao Sun ◽

Jiaxin Zhang ◽

Jingjing Zhang ◽

Zhen Li ◽

Qinhong Cao ◽

...

Keyword(s):

Dna Replication ◽

Ubiquitin Ligase ◽

Sister Chromatid ◽

Critical Role ◽

E3 Ubiquitin Ligase ◽

Ubiquitin Ligases ◽

Sister Chromatid Cohesion ◽

Vital Role ◽

Chromatid Cohesion ◽

Evolutionarily Conserved

AbstractCohesin acetyltransferases Esco1 and Esco2 play a vital role in establishing sister chromatid cohesion. How Esco1 and Esco2 are controlled to achieve this in a DNA replication-coupled manner remains unclear in higher eukaryotes. Here we show that Cul4-RING ligases (CRL4s) play a critical role in sister chromatid cohesion in human cells. Depletion of Cul4A, Cul4B or Ddb1 subunits substantially reduces normal cohesion efficiency. We also show that Mms22L, a vertebrate ortholog of yeast Mms22, is one of Ddb1 and Cul4-associated factors (DCAFs) involved in cohesion. Several lines of evidence suggest a selective interaction of CRL4s with Esco2, but not Esco1. Depletion of either CRL4s or Esco2 causes a defect in Smc3 acetylation which can be rescued by HDAC8 inhibition. More importantly, both CRL4s and PCNA act as mediators for efficiently stabilizing Esco2 on chromatin and catalyzing Smc3 acetylation. Taken together, we propose an evolutionarily conserved mechanism in which CRL4s and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.Author summaryWe identified human Mms22L as a substrate specific adaptor of Cul4-Ddb1 E3 ubiquitin ligase. Downregulation of Cul4A, Cul4B or Ddb1 subunit causes reduction of acetylated Smc3, via interaction with Esco2 acetyltransferase, and then impairs sister chromatid cohesion in 293T cells. We found functional complementation between Cul4-Ddb1-Mms22L E3 ligase and Esco2 in Smc3 acetylation and sister chromatid cohesion. Interestingly, both Cul4-Ddb1 E3 ubiquitin ligase and PCNA contribute to Esco2 mediated Smc3 acetylation. To summarise, we demonstrated an evolutionarily conserved mechanism in which Cul4-Ddb1 E3 ubiquitin ligases and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.

Download Full-text