Literature DB >> 27111547

Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation.

Sergey V Razin1,2,3, Alexey A Gavrilov1, Yegor S Vassetzky2,3,4, Sergey V Ulianov1,2.   

Abstract

Structural-functional domains have long been hypothesized to occur in eukaryotic chromosomes, but their existence still remains controversial. Here, we discuss the current state of studies of 3D genome folding and the relation of this folding to the functional organization of the genome.

Keywords:  3D genome organization; Hi-C; chromatin; functional genomic domains; topologically-associating domains

Mesh：

Year:  2016        PMID： 27111547      PMCID： PMC4984688          DOI： 10.1080/21541264.2016.1181489

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  37 in total

1.  Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.

Authors:  Iouri Chepelev; Gang Wei; Dara Wangsa; Qingsong Tang; Keji Zhao
Journal:  Cell Res       Date:  2012-01-24       Impact factor: 25.617

Review 2.  The Hierarchy of Transcriptional Activation: From Enhancer to Promoter.

Authors:  Douglas Vernimmen; Wendy A Bickmore
Journal:  Trends Genet       Date:  2015-12       Impact factor: 11.639

3.  Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.

Authors:  Jessica Zuin; Jesse R Dixon; Michael I J A van der Reijden; Zhen Ye; Petros Kolovos; Rutger W W Brouwer; Mariëtte P C van de Corput; Harmen J G van de Werken; Tobias A Knoch; Wilfred F J van IJcken; Frank G Grosveld; Bing Ren; Kerstin S Wendt
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-13       Impact factor: 11.205

Review 4.  The 3D Genome as Moderator of Chromosomal Communication.

Authors:  Job Dekker; Leonid Mirny
Journal:  Cell       Date:  2016-03-10       Impact factor: 41.582

5.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

Authors:  Adrian L Sanborn; Suhas S P Rao; Su-Chen Huang; Neva C Durand; Miriam H Huntley; Andrew I Jewett; Ivan D Bochkov; Dharmaraj Chinnappan; Ashok Cutkosky; Jian Li; Kristopher P Geeting; Andreas Gnirke; Alexandre Melnikov; Doug McKenna; Elena K Stamenova; Eric S Lander; Erez Lieberman Aiden
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-23       Impact factor: 11.205

6.  Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes.

Authors:  Xiao-Tao Wang; Peng-Fei Dong; Hong-Yu Zhang; Cheng Peng
Journal:  Nucleic Acids Res       Date:  2015-07-06       Impact factor: 16.971

7.  Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Authors:  Fabian Grubert; Judith B Zaugg; Maya Kasowski; Oana Ursu; Damek V Spacek; Alicia R Martin; Peyton Greenside; Rohith Srivas; Doug H Phanstiel; Aleksandra Pekowska; Nastaran Heidari; Ghia Euskirchen; Wolfgang Huber; Jonathan K Pritchard; Carlos D Bustamante; Lars M Steinmetz; Anshul Kundaje; Michael Snyder
Journal:  Cell       Date:  2015-08-20       Impact factor: 41.582

Review 8.  Structural and functional diversity of Topologically Associating Domains.

Authors:  Job Dekker; Edith Heard
Journal:  FEBS Lett       Date:  2015-09-05       Impact factor: 4.124

9.  Formation of Chromosomal Domains by Loop Extrusion.

Authors:  Geoffrey Fudenberg; Maxim Imakaev; Carolyn Lu; Anton Goloborodko; Nezar Abdennur; Leonid A Mirny
Journal:  Cell Rep       Date:  2016-05-19       Impact factor: 9.423

10.  A high-resolution map of the three-dimensional chromatin interactome in human cells.

Authors:  Fulai Jin; Yan Li; Jesse R Dixon; Siddarth Selvaraj; Zhen Ye; Ah Young Lee; Chia-An Yen; Anthony D Schmitt; Celso A Espinoza; Bing Ren
Journal:  Nature       Date:  2013-10-20       Impact factor: 49.962
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  6 in total

1.  Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes.

Authors:  Tatiana Kulikova; Antonina Maslova; Polina Starshova; Juan Sebastian Rodriguez Ramos; Alla Krasikova
Journal:  Chromosoma       Date:  2022-08-29       Impact factor: 2.919

2.  C2H2 Zinc Finger Proteins: The Largest but Poorly Explored Family of Higher Eukaryotic Transcription Factors.

Authors:  A A Fedotova; A N Bonchuk; V A Mogila; P G Georgiev
Journal:  Acta Naturae       Date:  2017 Apr-Jun       Impact factor: 1.845

3.  Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes).

Authors:  Ezequiel Aguiar de Oliveira; Luiz Antonio Carlos Bertollo; Petr Rab; Tariq Ezaz; Cassia Fernanda Yano; Terumi Hatanaka; Oladele Ilesanmi Jegede; Alongklod Tanomtong; Thomas Liehr; Alexandr Sember; Sandra Regina Maruyama; Eliana Feldberg; Patrik Ferreira Viana; Marcelo de Bello Cioffi
Journal:  PLoS One       Date:  2019-03-25       Impact factor: 3.240

4.  Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae).

Authors:  Alexandr Sember; Šárka Pelikánová; Marcelo de Bello Cioffi; Vendula Šlechtová; Terumi Hatanaka; Hiep Do Doan; Martin Knytl; Petr Ráb
Journal:  Genes (Basel)       Date:  2020-04-28       Impact factor: 4.096

5.  Present and Future Salmonid Cytogenetics.

Authors:  Muhammet Gaffaroglu; Zuzana Majtánová; Radka Symonová; Šárka Pelikánová; Sevgi Unal; Zdeněk Lajbner; Petr Ráb
Journal:  Genes (Basel)       Date:  2020-12-06       Impact factor: 4.096

Review 6.  Gene functioning and storage within a folded genome.

Authors:  Sergey V Razin; Sergey V Ulianov
Journal:  Cell Mol Biol Lett       Date:  2017-08-29       Impact factor: 5.787
  6 in total

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