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Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE168803 | GEO | 2021/03/23

REPOSITORIES: GEO

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Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq)

Project description:Condensins are molecular motors that compact DNA for chromosome segregation and gene regulation. In vitro experiments have begun to elucidate the mechanics of condensin function but how condensin loading and translocation along DNA controls eukaryotic chromosome structure in vivo remains poorly understood. To address this question, we took advantage of a specialized condensin, which organizes the 3D conformation of X chromosomes to mediate dosage compensation (DC) in C. elegans. Condensin DC is recruited and spreads from a small number of recruitment elements on the X chromosome (rex). We found that ectopic insertion of rex sites on an autosome leads to bidirectional spreading of the complex over hundreds of kilobases. On the X chromosome, strong rex sites contain multiple copies of a 12-bp sequence motif and act as TAD borders. Inserting a strong rex and ectopically recruiting the complex on the X chromosome or an autosome creates a loop-anchored TAD. Unlike the CTCF system, which controls TAD formation by cohesin, direction of the 12-bp motif does not control the specificity of loops. In an X;V fusion chromosome, condensin DC linearly spreads into V and increases 3D DNA contacts, but fails to form TADs in the absence of rex sites. Finally, we provide in vivo evidence for the loop extrusion hypothesis by targeting multiple dCas9-Suntag complexes to an X chromosome repeat region. Consistent with linear translocation along DNA, condensin DC accumulates at the block site. Together, our results support a model whereby strong rex sites act as insulation elements through recruitment and bidirectional spreading of condensin DC molecules and form loop-anchored TADs.

2021-03-24 | GSE169250 | GEO

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (RNA-seq)

2021-03-24 | GSE168802 | GEO

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (Hi-C)

2021-03-24 | GSE169468 | GEO

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq and Hi-C data)

Project description:Inspection of Hi-C and ChIP-seq data suggests that condensin DC is an X-chromosome enriched loop extruder that stalls at rex sites. Insertion of rex site on X-chromosome suggests orientation independent barrier function of rex sites. Insertion of rex site on chromosome-II results in recruitment and spreading of condensin DC that coincides with TAD formation.

2022-06-14 | GSE206065 | GEO

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

Project description:Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

| PRJNA714064 | ENA

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (RNA-seq)

Project description:Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (RNA-seq)

| PRJNA714067 | ENA

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (Hi-C)

Project description:Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (Hi-C)

| PRJNA716654 | ENA

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq)

Project description:Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq)

| PRJNA716063 | ENA

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq and Hi-C data)

Project description:Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq and Hi-C data)

| PRJNA848997 | ENA

Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.

Project description:Despite recent advances in single-molecule and structural analysis of condensin activity in vitro, mechanisms of functional condensin loading and loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae, the most prominent condensin loading site is the rDNA locus on chromosome XII, but its repetitiveness deters rigorous analysis of individual genes. An equally prominent non-rDNA condensin site is located on chromosome III (chrIII). It lies in the promoter of a putative non-coding RNA gene called RDT1, which is in a segment of the recombination enhancer (RE) that dictates MATa-specific chrIII organization. Here, we unexpectedly find that condensin is recruited to the RDT1 promoter in MATa cells through hierarchical interactions with Fob1, Tof2, and cohibin (Lrs4/Csm1), a set of nucleolar factors that also recruit condensin to the rDNA. Fob1 directly binds to this locus in vitro, while its binding in vivo depends on an adjacent Mcm1/α2 binding site that provides MATa cell specificity. We also uncover evidence for condensin-driven loop extrusion anchored by Fob1 and cohibin at RDT1 that unidirectionally extends toward MATa on the right arm of chrIII, supporting donor preference during mating-type switching. S. cerevisiae chrIII therefore provides a new platform for the study of programmed condensin-mediated chromosome conformation.

| S-EPMC10132618 | biostudies-literature

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