Long non-coding RNAs: the tentacles of chromatin remodeler complexes
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Cellular and Molecular Life Sciences
REVIEW
Long non‑coding RNAs: the tentacles of chromatin remodeler complexes Bernadette Neve1 · Nicolas Jonckheere1 · Audrey Vincent1 · Isabelle Van Seuningen1 Received: 10 June 2020 / Revised: 1 September 2020 / Accepted: 12 September 2020 © Springer Nature Switzerland AG 2020
Abstract Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long noncoding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved. Keywords ATP-dependent helicase · Nucleosome · Histone and epigenetic regulation
Introduction Long non-coding RNAs (lncRNAs) are a heterogeneous class of long RNAs without a large open reading frame encoding proteins. To better understand the role of lncRNAs in the formation and recruitment of chromatin remodeler complexes, we will briefly discuss the organization of DNA into chromatin, and then review the chromatin remodeler subfamilies with the involved subunit proteins. Chromatin is the state of organized DNA condensation in the nucleus. DNA is wrapped into nucleosome structures that are further packed into chromatin fibers and condensed into either “euchromatin” or highly condensed “heterochromatin”. Chromatin condensation is a dynamic process resulting in different nuclear sub‐compartments, including topologically lamina-associating domains, nucleoli, Cajal bodies, nuclear stress bodies, paraspeckles and non-chromatin bodies like nuclear speckles and PML bodies (reviewed by [1]). Audrey Vincent and Isabelle Van Seuningen are last co-auteurs. * Bernadette Neve [email protected] 1
UMR9020‑U1277 ‑ CANTHER ‑ Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000 Lille, France
In the fundamental nucleosome unit, ~ 146 base-pairs (bp) of the negatively charged DNA helix are folded ~ 1.7 times around an octamer of positively charged histone proteins. A tetramer consisting of two H3 and two H4 histones binds to the DNA, where after two H2A-H2B dimers join the complex. The first ~ 20 bp of DNA that sort the fold are hold together by the histone H1 protein and a “beads on a string” structure is formed with strings of ~ 15–70 bp free DNA (Fig. 1a, b, [2]). Nucleosome positioning is part of epigenetic regulation since the condensed DNA is inaccessibl
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