Non-coding RNAs in chromatin folding and nuclear organization

Razin, Sergey V.; Гаврилов, А. В.

doi:10.1007/s00018-021-03876-w

Cited by 22 publications

(23 citation statements)

References 144 publications

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“…The nuclear matrix proteome 55 may form phase-separated droplets within the IC with the help of non-coding RNA sequences 56, 57 . Like assembled macromolecular machineries, such condensates are excluded by size from the INC and may serve as storage vesicles for the formation of functional machineries.…”

Section: Discussionmentioning

confidence: 99%

True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin

Gelléri

Chen

Szczurek

et al. 2022

Preprint

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Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggested only modest compaction differences (~2-10x) between active and inactive nuclear compartments (ANC and INC). Here, we present maps of nuclear landscapes with true-to-scale DNA-densities, ranging from <5 Mbp/μm3 to >300 Mbp/μm3. Maps were generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ~20 nm lateral and ~100 nm axial resolution and supplemented by electron spectroscopic imaging. Live cell microinjection experiments with 20 nm and 40 nm sized fluorescent beads, corresponding to macromolecular assemblies for transcription and replication, indicated movements within the ANC, but exclusion from the INC. In line with previous studies of transcription, pulse-chase labeling experiments of DNA demonstrated replication within the ANC, followed by re-location of replicated, inactive chromatin into the INC.

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Section: Discussionmentioning

confidence: 99%

True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin

Gelléri

Chen

Szczurek

et al. 2022

Preprint

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“…For example, cytosolic miRNAs and lncRNAs are thought to mainly regulate mRNA decay and translation, protein stability, as well as interfere with each other’s function. In contrast, nuclear ncRNAs have been shown to epigenetically regulate chromatin remodeling and structure as well as gene transcription through their interaction with chromatin modifying enzymes and transcription factors or by adopting an architectural role in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome [ 103 , 104 , 105 ]. Some of these nuclear functions of ncRNAs overlap with the aforementioned activities of the cohesin complex and its subunits.…”

Section: The Cohesin Complex and Its Interplay With Non-coding Rnasmentioning

confidence: 99%

The Cohesin Complex and Its Interplay with Non-Coding RNAs

Kuru-Schors

Haemmerle

Gutschner

2021

ncRNA

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The cohesin complex is a multi-subunit protein complex initially discovered for its role in sister chromatid cohesion. However, cohesin also has several other functions and plays important roles in transcriptional regulation, DNA double strand break repair, and chromosome architecture thereby influencing gene expression and development in organisms from yeast to man. While most of these functions rely on protein–protein interactions, post-translational protein, as well as DNA modifications, non-coding RNAs are emerging as additional players that facilitate and modulate the function or expression of cohesin and its individual components. This review provides a condensed overview about the architecture as well as the function of the cohesin complex and highlights its multifaceted interplay with both short and long non-coding RNAs.

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“…Non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and circular RNAs (circRNAs) as well as long ncRNAs (lncRNAs), have been reported to be functionally involved in various biological processes, such as cell proliferation, metabolism, stem cell differentiation, etc. 13 , 14 , 15 , 16 Accumulating studies have indicated that ncRNAs play crucial roles in bone development and regeneration. 14 , 15 , 17 MiRNAs are a class of short, single-stranded, and highly conserved endogenous ncRNAs and they mainly negatively regulate gene expression post-transcriptionally through interacting with its 3′-untranslated region (3′-UTR).…”

Section: Introductionmentioning

confidence: 99%