Literature DB >> 34117518

Non-coding RNAs in chromatin folding and nuclear organization.

Sergey V Razin1,2, Alexey A Gavrilov3,4.   

Abstract

One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.

Keywords:  3D genome; Liquid condensate; Non-coding RNA; Nucleus; Transcription

Year:  2021        PMID: 34117518     DOI: 10.1007/s00018-021-03876-w

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  116 in total

Review 1.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

Authors:  T Cremer; C Cremer
Journal:  Nat Rev Genet       Date:  2001-04       Impact factor: 53.242

2.  Unraveling the organization of the internal nuclear matrix: RNA-dependent anchoring of NuMA to a lamin scaffold.

Authors:  Paola Barboro; Cristina D'Arrigo; Alberto Diaspro; Michele Mormino; Ingles Alberti; Silvio Parodi; Eligio Patrone; Cecilia Balbi
Journal:  Exp Cell Res       Date:  2002-10-01       Impact factor: 3.905

3.  Localization of heterogeneous nuclear ribonucleoprotein in the interphase nuclear matrix core filaments and on perichromosomal filaments at mitosis.

Authors:  D C He; T Martin; S Penman
Journal:  Proc Natl Acad Sci U S A       Date:  1991-09-01       Impact factor: 11.205

4.  Role of chromosome territories in the functional compartmentalization of the cell nucleus.

Authors:  T Cremer; A Kurz; R Zirbel; S Dietzel; B Rinke; E Schröck; M R Speicher; U Mathieu; A Jauch; P Emmerich; H Scherthan; T Ried; C Cremer; P Lichter
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1993

Review 5.  A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus.

Authors:  S V Razin; O V Iarovaia; Y S Vassetzky
Journal:  Chromosoma       Date:  2014-03-25       Impact factor: 4.316

6.  Chromatin architecture and nuclear RNA.

Authors:  J A Nickerson; G Krochmalnic; K M Wan; S Penman
Journal:  Proc Natl Acad Sci U S A       Date:  1989-01       Impact factor: 11.205

7.  Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries.

Authors:  R M Zirbel; U R Mathieu; A Kurz; T Cremer; P Lichter
Journal:  Chromosome Res       Date:  1993-07       Impact factor: 5.239

8.  RNA-dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes.

Authors:  Elena Ioudinkova; Sergey V Razin; Victoria Borunova; Flora De Conto; Alla Rynditch; Klaus Scherrer
Journal:  J Cell Biochem       Date:  2005-02-15       Impact factor: 4.429

9.  Core filaments of the nuclear matrix.

Authors:  D C He; J A Nickerson; S Penman
Journal:  J Cell Biol       Date:  1990-03       Impact factor: 10.539

10.  Landscape of transcription in human cells.

Authors:  Sarah Djebali; Carrie A Davis; Angelika Merkel; Alex Dobin; Timo Lassmann; Ali Mortazavi; Andrea Tanzer; Julien Lagarde; Wei Lin; Felix Schlesinger; Chenghai Xue; Georgi K Marinov; Jainab Khatun; Brian A Williams; Chris Zaleski; Joel Rozowsky; Maik Röder; Felix Kokocinski; Rehab F Abdelhamid; Tyler Alioto; Igor Antoshechkin; Michael T Baer; Nadav S Bar; Philippe Batut; Kimberly Bell; Ian Bell; Sudipto Chakrabortty; Xian Chen; Jacqueline Chrast; Joao Curado; Thomas Derrien; Jorg Drenkow; Erica Dumais; Jacqueline Dumais; Radha Duttagupta; Emilie Falconnet; Meagan Fastuca; Kata Fejes-Toth; Pedro Ferreira; Sylvain Foissac; Melissa J Fullwood; Hui Gao; David Gonzalez; Assaf Gordon; Harsha Gunawardena; Cedric Howald; Sonali Jha; Rory Johnson; Philipp Kapranov; Brandon King; Colin Kingswood; Oscar J Luo; Eddie Park; Kimberly Persaud; Jonathan B Preall; Paolo Ribeca; Brian Risk; Daniel Robyr; Michael Sammeth; Lorian Schaffer; Lei-Hoon See; Atif Shahab; Jorgen Skancke; Ana Maria Suzuki; Hazuki Takahashi; Hagen Tilgner; Diane Trout; Nathalie Walters; Huaien Wang; John Wrobel; Yanbao Yu; Xiaoan Ruan; Yoshihide Hayashizaki; Jennifer Harrow; Mark Gerstein; Tim Hubbard; Alexandre Reymond; Stylianos E Antonarakis; Gregory Hannon; Morgan C Giddings; Yijun Ruan; Barbara Wold; Piero Carninci; Roderic Guigó; Thomas R Gingeras
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

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  5 in total

1.  Genome-Directed Cell Nucleus Assembly.

Authors:  Sergey V Razin; Sergey V Ulianov
Journal:  Biology (Basel)       Date:  2022-05-05

2.  RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.

Authors:  Alexey A Gavrilov; Rinat I Sultanov; Mikhail D Magnitov; Aleksandra A Galitsyna; Erdem B Dashinimaev; Erez Lieberman Aiden; Sergey V Razin
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-04       Impact factor: 11.205

Review 3.  Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus.

Authors:  Zaur M Kachaev; Sergey D Ivashchenko; Eugene N Kozlov; Lyubov A Lebedeva; Yulii V Shidlovskii
Journal:  Cells       Date:  2021-11-19       Impact factor: 6.600

4.  CircHGF suppressed cell proliferation and osteogenic differentiation of BMSCs in ONFH via inhibiting miR-25-3p binding to SMAD7.

Authors:  Xiaobo Feng; Qian Xiang; Jie Jia; Tingting Guo; Zhiwei Liao; Shuhua Yang; Xianyi Cai; Xianzhe Liu
Journal:  Mol Ther Nucleic Acids       Date:  2022-03-01       Impact factor: 8.886

Review 5.  Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities.

Authors:  Jianjian Li; Zhe Ming; Liuyi Yang; Tingxuan Wang; Gaowen Liu; Qing Ma
Journal:  Genes Dis       Date:  2022-04-29
  5 in total

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