Literature DB >> 30238154

Blank spots on the map: some current questions on nuclear organization and genome architecture.

Carmen Adriaens1,2, Leonid A Serebryannyy1, Marina Feric1, Andria Schibler1, Karen J Meaburn1, Nard Kubben1, Pawel Trzaskoma1,3, Sigal Shachar1, Sandra Vidak1, Elizabeth H Finn1, Varun Sood1, Gianluca Pegoraro1, Tom Misteli4.   

Abstract

The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.

Entities:  

Keywords:  Genome organization; Nuclear architecture; Nuclear lamina; Phase separation

Mesh:

Year:  2018        PMID: 30238154      PMCID: PMC6290477          DOI: 10.1007/s00418-018-1726-1

Source DB:  PubMed          Journal:  Histochem Cell Biol        ISSN: 0948-6143            Impact factor:   4.304


  182 in total

1.  Lamin a truncation in Hutchinson-Gilford progeria.

Authors:  Annachiara De Sandre-Giovannoli; Rafaëlle Bernard; Pierre Cau; Claire Navarro; Jeanne Amiel; Irène Boccaccio; Stanislas Lyonnet; Colin L Stewart; Arnold Munnich; Martine Le Merrer; Nicolas Lévy
Journal:  Science       Date:  2003-04-17       Impact factor: 47.728

Review 2.  Long-Range Chromatin Interactions.

Authors:  Job Dekker; Tom Misteli
Journal:  Cold Spring Harb Perspect Biol       Date:  2015-10-01       Impact factor: 10.005

Review 3.  Nuclear organization: taking a position on gene expression.

Authors:  Pamela K Geyer; Michael W Vitalini; Lori L Wallrath
Journal:  Curr Opin Cell Biol       Date:  2011-03-28       Impact factor: 8.382

Review 4.  TAD disruption as oncogenic driver.

Authors:  Anne-Laure Valton; Job Dekker
Journal:  Curr Opin Genet Dev       Date:  2016-04-22       Impact factor: 5.578

5.  Coactivator condensation at super-enhancers links phase separation and gene control.

Authors:  Benjamin R Sabari; Alessandra Dall'Agnese; Ann Boija; Isaac A Klein; Eliot L Coffey; Krishna Shrinivas; Brian J Abraham; Nancy M Hannett; Alicia V Zamudio; John C Manteiga; Charles H Li; Yang E Guo; Daniel S Day; Jurian Schuijers; Eliza Vasile; Sohail Malik; Denes Hnisz; Tong Ihn Lee; Ibrahim I Cisse; Robert G Roeder; Phillip A Sharp; Arup K Chakraborty; Richard A Young
Journal:  Science       Date:  2018-06-21       Impact factor: 47.728

6.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Authors:  Britt Adamson; Thomas M Norman; Marco Jost; Min Y Cho; James K Nuñez; Yuwen Chen; Jacqueline E Villalta; Luke A Gilbert; Max A Horlbeck; Marco Y Hein; Ryan A Pak; Andrew N Gray; Carol A Gross; Atray Dixit; Oren Parnas; Aviv Regev; Jonathan S Weissman
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

7.  The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Authors:  Stefan Schoenfelder; Mayra Furlan-Magaril; Borbala Mifsud; Filipe Tavares-Cadete; Robert Sugar; Biola-Maria Javierre; Takashi Nagano; Yulia Katsman; Moorthy Sakthidevi; Steven W Wingett; Emilia Dimitrova; Andrew Dimond; Lucas B Edelman; Sarah Elderkin; Kristina Tabbada; Elodie Darbo; Simon Andrews; Bram Herman; Andy Higgs; Emily LeProust; Cameron S Osborne; Jennifer A Mitchell; Nicholas M Luscombe; Peter Fraser
Journal:  Genome Res       Date:  2015-03-09       Impact factor: 9.043

8.  Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

Authors:  Gil Ron; Yuval Globerson; Dror Moran; Tommy Kaplan
Journal:  Nat Commun       Date:  2017-12-21       Impact factor: 14.919

9.  Lipodystrophic laminopathy: Lamin A mutation relaxes chromatin architecture to impair adipogenesis.

Authors:  Eman Elzeneini; Sara A Wickström
Journal:  J Cell Biol       Date:  2017-08-15       Impact factor: 10.539

10.  Recruitment to the nuclear periphery can alter expression of genes in human cells.

Authors:  Lee E Finlan; Duncan Sproul; Inga Thomson; Shelagh Boyle; Elizabeth Kerr; Paul Perry; Bauke Ylstra; Jonathan R Chubb; Wendy A Bickmore
Journal:  PLoS Genet       Date:  2008-03-21       Impact factor: 5.917

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  10 in total

1.  Chromatin Is the Same in a Relative Way (But You're Older).

Authors:  Rosibel J Mason; Thomas M Vondriska
Journal:  Circ Res       Date:  2019-07-03       Impact factor: 17.367

2.  In focus in HCB.

Authors:  Douglas J Taatjes; Jürgen Roth
Journal:  Histochem Cell Biol       Date:  2018-11-16       Impact factor: 4.304

3.  Reorganization of the nuclear compartments involved in transcription and RNA processing in myonuclei of type I spinal muscular atrophy.

Authors:  María S Castillo-Iglesias; María T Berciano; J Oriol Narcis; J Fernando Val-Bernal; José C Rodriguez-Rey; Olga Tapia; Miguel Lafarga
Journal:  Histochem Cell Biol       Date:  2019-06-11       Impact factor: 4.304

4.  How Chromatin Stiffens Fibroblasts.

Authors:  Shuaishuai Hu; Thomas M Vondriska
Journal:  Curr Opin Physiol       Date:  2022-04-12

Review 5.  Metabolism, Epigenetics, and Causal Inference in Heart Failure.

Authors:  Todd H Kimball; Thomas M Vondriska
Journal:  Trends Endocrinol Metab       Date:  2019-12-19       Impact factor: 12.015

6.  Nucleolar Expression and Chromosomal Associations in Robertsonian Spermatocytes of Mus musculus domesticus.

Authors:  Fernanda López-Moncada; Daniel Tapia; Nolberto Zuñiga; Eliana Ayarza; Julio López-Fenner; Carlo Alberto Redi; Soledad Berríos
Journal:  Genes (Basel)       Date:  2019-02-06       Impact factor: 4.096

7.  Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.

Authors:  Alessandro Bertero; Paul A Fields; Alec S T Smith; Andrea Leonard; Kevin Beussman; Nathan J Sniadecki; Deok-Ho Kim; Hung-Fat Tse; Lil Pabon; Jay Shendure; William S Noble; Charles E Murry
Journal:  J Cell Biol       Date:  2019-08-08       Impact factor: 10.539

8.  Cell cycle dynamics of lamina-associated DNA.

Authors:  Tom van Schaik; Mabel Vos; Daan Peric-Hupkes; Patrick Hn Celie; Bas van Steensel
Journal:  EMBO Rep       Date:  2020-09-07       Impact factor: 8.807

9.  Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.

Authors:  Ezequiel Miron; Roel Oldenkamp; Jill M Brown; David M S Pinto; C Shan Xu; Ana R Faria; Haitham A Shaban; James D P Rhodes; Cassandravictoria Innocent; Sara de Ornellas; Harald F Hess; Veronica Buckle; Lothar Schermelleh
Journal:  Sci Adv       Date:  2020-09-23       Impact factor: 14.136

Review 10.  Cell organelles as targets of mammalian cadmium toxicity.

Authors:  Wing-Kee Lee; Frank Thévenod
Journal:  Arch Toxicol       Date:  2020-03-23       Impact factor: 5.153

  10 in total

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