Literature DB >> 31965996

Recent advances in the spatial organization of the mammalian genome.

Yatendra Kumar1, Dipta Sengupta, Wendya Bickmore.   

Abstract

The mammalian genome is complex and presents a dynamic structural organization that reflects function. Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but not limited to transcription, replication and repair, and in many biological contexts such as early development, differentiation and physiological adaptations. However, there is limited understating of how 3D organization of the mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad of genomics methods -- ropelled by next-generation sequencing -- have advanced our knowledge of genome organization to a great extent. In this review, we discuss nuclear compartments in general and recent advances in the understanding of how mammalian genome is organized in these compartments with an emphasis on dynamics at the nuclear periphery.

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Year:  2020        PMID: 31965996

Source DB:  PubMed          Journal:  J Biosci        ISSN: 0250-5991            Impact factor:   1.826


  108 in total

Review 1.  The Cajal body.

Authors:  Glenn E Morris
Journal:  Biochim Biophys Acta       Date:  2008-08-03

Review 2.  The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments.

Authors:  Thomas Cremer; Marion Cremer; Barbara Hübner; Hilmar Strickfaden; Daniel Smeets; Jens Popken; Michael Sterr; Yolanda Markaki; Karsten Rippe; Christoph Cremer
Journal:  FEBS Lett       Date:  2015-05-28       Impact factor: 4.124

3.  Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery.

Authors:  Benjamin D Towbin; Cristina González-Aguilera; Ragna Sack; Dimos Gaidatzis; Véronique Kalck; Peter Meister; Peter Askjaer; Susan M Gasser
Journal:  Cell       Date:  2012-08-31       Impact factor: 41.582

4.  A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.

Authors:  Shiwei Chen; Teresa Romeo Luperchio; Xianrong Wong; Europe B Doan; Aaron T Byrd; Kingshuk Roy Choudhury; Karen L Reddy; Michael S Krangel
Journal:  Cell Rep       Date:  2018-11-13       Impact factor: 9.423

5.  Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells.

Authors:  Youngjo Kim; Alexei A Sharov; Katie McDole; Melody Cheng; Haiping Hao; Chen-Ming Fan; Nicholas Gaiano; Minoru S H Ko; Yixian Zheng
Journal:  Science       Date:  2011-11-24       Impact factor: 47.728

6.  Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion.

Authors:  Sandra Krull; Julia Dörries; Björn Boysen; Sonja Reidenbach; Lars Magnius; Helene Norder; Johan Thyberg; Volker C Cordes
Journal:  EMBO J       Date:  2010-04-20       Impact factor: 11.598

7.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

8.  Identification of lamin B-regulated chromatin regions based on chromatin landscapes.

Authors:  Xiaobin Zheng; Youngjo Kim; Yixian Zheng
Journal:  Mol Biol Cell       Date:  2015-05-20       Impact factor: 4.138

9.  Nuclear position dictates DNA repair pathway choice.

Authors:  Charlène Lemaître; Anastazja Grabarz; Katerina Tsouroula; Leonid Andronov; Audrey Furst; Tibor Pankotai; Vincent Heyer; Mélanie Rogier; Kathleen M Attwood; Pascal Kessler; Graham Dellaire; Bruno Klaholz; Bernardo Reina-San-Martin; Evi Soutoglou
Journal:  Genes Dev       Date:  2014-11-03       Impact factor: 11.361

10.  Tissue-specific NETs alter genome organization and regulation even in a heterologous system.

Authors:  Jose I de Las Heras; Nikolaj Zuleger; Dzmitry G Batrakou; Rafal Czapiewski; Alastair R W Kerr; Eric C Schirmer
Journal:  Nucleus       Date:  2017-01-03       Impact factor: 4.197

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  3 in total

1.  Depletion of HP1α alters the mechanical properties of MCF7 nuclei.

Authors:  Susav Pradhan; Raoul Solomon; Ankita Gangotra; Gleb E Yakubov; Geoff R Willmott; Catherine P Whitby; Tracy K Hale; Martin A K Williams
Journal:  Biophys J       Date:  2021-06-02       Impact factor: 3.699

Review 2.  The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk".

Authors:  Giorgio Bernardi
Journal:  Life (Basel)       Date:  2021-04-13

3.  Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization.

Authors:  Daria Amiad-Pavlov; Dana Lorber; Gaurav Bajpai; Adriana Reuveny; Francesco Roncato; Ronen Alon; Samuel Safran; Talila Volk
Journal:  Sci Adv       Date:  2021-06-02       Impact factor: 14.136

  3 in total

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