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Mapping nucleolus-associated chromatin interactions by nucleolus-Hi-C reveals repression network

ABSTRACT: Nucleolus plays a key role in organizing global nuclear structure and facilitating gene regulation, but the three dimensional information within the nucleolus associated chromatins are still unknown, so here we development the Nucleolus Hi-C (NHi-C) experimental technique, which combines the nucleolus isolation with Hi-C experiment, and study the interactions within and surrounding nucleolus in human cells with a high resolution. With NHi-C experiment, we report how the nucleolus-associated chromatin regions interact at genome scale, and how these interactions organize the repressive nucleus architecture.

ORGANISM(S): Homo sapiens

PROVIDER: GSE90003 | GEO | 2021/02/01

SECONDARY ACCESSION(S): PRJNA354332

REPOSITORIES: GEO

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Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Project description:We develop Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables genome-wide detection of higher-order interactions that occur simultaneously within the nucleus in a proximity-ligation independent manner. We generated SPRITE maps in two mammalian cell types – mouse embryonic stem cells (mES) and human lymphoblastoid cells (GM12878). We generated ~1.5 billion sequencing reads from each sample and recapitulate known genome structures identified by Hi-C, including chromosome territories, compartments, topologically associated domains, and loop structures, and identify that many of these occur within higher-order structures in the nucleus. Because SPRITE does not rely on proximity-ligation, we find that SPRITE identifies interactions that occur across larger spatial distances than can be observed by Hi-C. These long-range interactions include two major hubs of inter-chromosomal interactions. We extended SPRITE to enable simultaneous measurements of RNA and DNA interactions and observe ribosomal RNA interactions across specific regions on the genome that correspond to DNA organization around the nucleolus. We show that gene-dense regions that are highly transcribed by PolII organize around nuclear speckles and gene poor, and therefore transcriptionally inactive, regions that are centromere-proximal organize around the nucleolus. In addition to the regions that directly associate around these nuclear bodies, we find that a substantial fraction of the genome exhibits preferential spatial positioning in the nucleus relative to each of these nuclear bodies and that the spatial preferences identified by SPRITE are highly correlated with 3D distances measured by microscopy.

2018-06-07 | GSE114242 | GEO

Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

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Homo sapiens

Project description:Mapping nucleolus-associated chromatin interactions by nucleolus-Hi-C reveals repression network

| PRJNA354332 | ENA

Mapping of nucleolus-associated chromosomal domains during replicative senescence.

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2017-06-18 | GSE78043 | GEO

Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

Project description:Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

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Comparative genomic hybridization of human genomic DNA and nucleolus-associated DNA in HeLa cell line.

Project description:The aim of the experiment was to identify nucleolus-associated chromosomal domains. HeLa exp samples represent DNA from isolated nucleoli, whereas HeLa ref samples total genomic DNA of HeLa cells. "exp" samples were Cy5 labeled and hybridized together with Cy3-labeled "ref" samples on a Nimblegen 385K WG CGH platform. The DNA samples were not amplified.

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Genome-wide mapping of promoter-enhancer interactions with HiCap [RNA-seq]

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The nucleolus functions as the compartment for histone 1 H2B protein degradation

Project description:Histones are the main components in chromatin organization, and the protein levels of histones significantly affect chromatin assembly. However, how the protein levels of histones are regulated, especially whether and how histones are degraded, is largely unclear. Here, we found that histone H2B is mainly degraded through the proteasome mediated pathway, and the lysine 120 site of H2B is essential for the K48-linked polyubiquitination and protein degradation of H2B. Moreover, our results further indicated that the degradation-impaired H2BK120R mutant shows an increased nucleolus localization, and inhibition of the proteasome results in an elevated nucleolus distribution of wild-type H2B, which is similar to that of H2BK120R mutants. More importantly, our in vitro data showed that only the nucleolus fractions can ubiquitinate and degrade the purified H2B, suggesting that the nucleolus, in addition to its canonical roles in the regulation of ribosome genesis and protein translation, is likely associated with H2B protein degradation. Therefore, these findings revealed a novel mechanism for the regulation of H2B protein degradation in which a nucleolus associated proteasome pathway is involved.

2021-09-09 | PXD023415 | Pride

A CTCF binding element regulates RA-induced early ESCs differentiation through orchestrating long-range chromatin interactions between its adjacent enhancers and HoxA

Project description:Proper Homeobox A (HoxA) cluster genes expression is essential for embryonic stem cells (ESCs) differentiation and individual development. However, the mechanisms controlling the precise spatiotemporal expression of HoxA cluster genes during early ESCs differentiation remain largely unknown. Here, we find a CTCF binding element (CBE+47kb) closest to the 3'-end of HoxA locus within a topologically associated domains (TAD) in ESCs. CRISPR-Cas9 mediated the CBE+47kb knockout significantly promotes expression of HoxA cluster genes and early ESCs differentiation induced by RA compared with wild type cells. In mechanism, we found that there was a significant differently long-range chromatin interactions between its adjacent enhancers and HoxA in CBE+47kb knockout cells through chromosome conformation capture assay (Capture-C), indicating that CBE+47kb can precisely organize interactions between its adjacent enhancers and HoxA chromatins. Furthermore, we also showed that its adjacent enhancers deletion shows significantly synthetic inhibition effect on HoxA genes expression, suggesting that these enhancers are required for RA-induced HoxA genes expression. Our study reveals that a new functional CBE+47 can regulate HoxA genes expression through orchestrating long-range chromatin interactions between its adjacent enhancers and HoxA, thus maintaining RA-induced early ESCs proper differentiation.

2020-07-16 | GSE154495 | GEO

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