Literature DB >> 28551816

3D clustering of co-regulated genes and its effect on gene expression.

Manyu Du1,2, Lu Bai3,4,5.   

Abstract

There are extensive long-distance chromosomal interactions in eukaryotic genomes, but to what extent these interactions affect gene expression is not clear. Recent works have identified several cases where clustering of co-regulated genes leads to enhanced gene expression in budding yeast. Similar phenomenon was also observed in mammalian cells. These results challenge widely held views of gene regulation in yeast and further our understanding of how the 3D organization of the genome contribute to gene regulation in eukaryotes.

Entities:  

Keywords:  3D clustering; Chromosome configuration capture; Long-distance chromosomal interaction; Long-distance gene regulation

Mesh:

Substances:

Year:  2017        PMID: 28551816      PMCID: PMC5884626          DOI: 10.1007/s00294-017-0712-9

Source DB:  PubMed          Journal:  Curr Genet        ISSN: 0172-8083            Impact factor:   3.886


  38 in total

Review 1.  Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions.

Authors:  Christian Lanctôt; Thierry Cheutin; Marion Cremer; Giacomo Cavalli; Thomas Cremer
Journal:  Nat Rev Genet       Date:  2007-02       Impact factor: 53.242

2.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Authors:  Zhihu Zhao; Gholamreza Tavoosidana; Mikael Sjölinder; Anita Göndör; Piero Mariano; Sha Wang; Chandrasekhar Kanduri; Magda Lezcano; Kuljeet Singh Sandhu; Umashankar Singh; Vinod Pant; Vijay Tiwari; Sreenivasulu Kurukuti; Rolf Ohlsson
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

3.  Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression.

Authors:  Effie Apostolou; Dimitris Thanos
Journal:  Cell       Date:  2008-07-11       Impact factor: 41.582

4.  Interchromosomal associations between alternatively expressed loci.

Authors:  Charalampos G Spilianakis; Maria D Lalioti; Terrence Town; Gap Ryol Lee; Richard A Flavell
Journal:  Nature       Date:  2005-05-08       Impact factor: 49.962

5.  Chromosome conformation elucidates regulatory relationships in developing human brain.

Authors:  Hyejung Won; Luis de la Torre-Ubieta; Jason L Stein; Neelroop N Parikshak; Jerry Huang; Carli K Opland; Michael J Gandal; Gavin J Sutton; Farhad Hormozdiari; Daning Lu; Changhoon Lee; Eleazar Eskin; Irina Voineagu; Jason Ernst; Daniel H Geschwind
Journal:  Nature       Date:  2016-10-19       Impact factor: 49.962

Review 6.  Condensin-mediated chromosome organization in fission yeast.

Authors:  Osamu Iwasaki; Ken-Ichi Noma
Journal:  Curr Genet       Date:  2016-04-09       Impact factor: 3.886

7.  Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

Authors:  Ionas Erb; Erik van Nimwegen
Journal:  PLoS One       Date:  2011-09-09       Impact factor: 3.240

8.  Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms.

Authors:  Donna Garvey Brickner; Varun Sood; Evelina Tutucci; Robert Coukos; Kayla Viets; Robert H Singer; Jason H Brickner
Journal:  Mol Biol Cell       Date:  2016-08-03       Impact factor: 4.138

9.  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

10.  Large-scale functional organization of long-range chromatin interaction networks.

Authors:  Kuljeet Singh Sandhu; Guoliang Li; Huay Mei Poh; Yu Ling Kelly Quek; Yee Yen Sia; Su Qin Peh; Fabianus Hendriyan Mulawadi; Joanne Lim; Mile Sikic; Francesca Menghi; Anbupalam Thalamuthu; Wing Kin Sung; Xiaoan Ruan; Melissa Jane Fullwood; Edison Liu; Peter Csermely; Yijun Ruan
Journal:  Cell Rep       Date:  2012-10-25       Impact factor: 9.423

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  6 in total

1.  Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes.

Authors:  Christoforos Nikolaou
Journal:  Curr Genet       Date:  2017-08-05       Impact factor: 3.886

2.  Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin.

Authors:  Pierrick Moreau; Axel Cournac; Gianna Aurora Palumbo; Martial Marbouty; Shogofa Mortaza; Agnes Thierry; Stefano Cairo; Marc Lavigne; Romain Koszul; Christine Neuveut
Journal:  Nat Commun       Date:  2018-10-15       Impact factor: 14.919

3.  Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles.

Authors:  Manyu Du; Fan Zou; Yi Li; Yujie Yan; Lu Bai
Journal:  Nat Commun       Date:  2022-02-09       Impact factor: 17.694

Review 4.  Crosstalk between Hepatitis B Virus and the 3D Genome Structure.

Authors:  João Diogo Dias; Nazim Sarica; Axel Cournac; Romain Koszul; Christine Neuveut
Journal:  Viruses       Date:  2022-02-21       Impact factor: 5.048

Review 5.  Condensin action and compaction.

Authors:  Matthew Robert Paul; Andreas Hochwagen; Sevinç Ercan
Journal:  Curr Genet       Date:  2018-10-25       Impact factor: 3.886

6.  Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11.

Authors:  Congle Shen; Xiaoyu Feng; Tianhao Mao; Danli Yang; Jun Zou; Xiaobin Zao; Qiang Deng; Xiangmei Chen; Fengmin Lu
Journal:  Emerg Microbes Infect       Date:  2020-12       Impact factor: 7.163

  6 in total

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