Why the activity of a gene depends on its neighbors

被引：64

作者：

Feuerborn, Alexander ^{[1
]}

Cook, Peter R. ^{[1
]}

机构：

[1] Univ Oxford, Sir William Dunn Sch Pathol, Oxford OX1 3RE, England

来源：

TRENDS IN GENETICS | 2015年 / 31卷 / 09期

基金：

英国医学研究理事会;

关键词：

boundary; domain; enhancer; expression quantitative trait loci; position effect; silencer; GENOME ORGANIZATION; NUCLEAR LAMINA; TRANSCRIPTION; CHROMATIN; EXPRESSION; COHESIN; ARCHITECTURE; PROMOTERS; ENHANCERS; FACTORIES;

D O I：

10.1016/j.tig.2015.07.001

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Sixty years ago, the position of a gene on a chromosome was seen to be a major determinant of gene activity; however, position effects are rarely central to current discussions of gene expression. We describe a comprehensive and simplifying view of how position in 1D sequence and 3D nuclear space underlies expression. We suggest that apparently-different regulatory motifs including enhancers, silencers, insulators, barriers, and boundaries act similarly - they are active promoters that tether target genes close to, or distant from, appropriate transcription sites or 'factories'. We also suggest that any active transcription unit regulates the firing of its neighbors - and thus can be categorized as one or other type of motif; this is consistent with expression quantitative trait loci (eQTLs) being widely dispersed.

引用

页码：483 / 490

页数：8

共 75 条

[1] Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel [J].

Akhtar, Waseem ;

de Jong, Johann ;

Pindyurin, Alexey V. ;

Pagie, Ludo ;

Meuleman, Wouter ;

de Ridder, Jeroen ;

Berns, Anton ;

Wessels, Lodewyk F. A. ;

van Lohuizen, Maarten ;

van Steensel, Bas .

CELL, 2013, 154 (04) :914-927

[2] Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model [J].

Andersson, Robin .

BIOESSAYS, 2015, 37 (03) :314-323

[3] An atlas of active enhancers across human cell types and tissues [J].

Andersson, Robin ;

Gebhard, Claudia ;

Miguel-Escalada, Irene ;

Hoof, Ilka ;

Bornholdt, Jette ;

Boyd, Mette ;

Chen, Yun ;

Zhao, Xiaobei ;

Schmidl, Christian ;

Suzuki, Takahiro ;

Ntini, Evgenia ;

Arner, Erik ;

Valen, Eivind ;

Li, Kang ;

Schwarzfischer, Lucia ;

Glatz, Dagmar ;

Raithel, Johanna ;

Lilje, Berit ;

Rapin, Nicolas ;

Bagger, Frederik Otzen ;

Jorgensen, Mette ;

Andersen, Peter Refsing ;

Bertin, Nicolas ;

Rackham, Owen ;

Burroughs, A. Maxwell ;

Baillie, J. Kenneth ;

Ishizu, Yuri ;

Shimizu, Yuri ;

Furuhata, Erina ;

Maeda, Shiori ;

Negishi, Yutaka ;

Mungall, Christopher J. ;

Meehan, Terrence F. ;

Lassmann, Timo ;

Itoh, Masayoshi ;

Kawaji, Hideya ;

Kondo, Naoto ;

Kawai, Jun ;

Lennartsson, Andreas ;

Daub, Carsten O. ;

Heutink, Peter ;

Hume, David A. ;

Jensen, Torben Heick ;

Suzuki, Harukazu ;

Hayashizaki, Yoshihide ;

Mueller, Ferenc ;

Forrest, Alistair R. R. ;

Carninci, Piero ;

Rehli, Michael ;

Sandelin, Albin .

NATURE, 2014, 507 (7493) :455-+

[4] The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans [J].

Ardlie, Kristin G. ;

DeLuca, David S. ;

Segre, Ayellet V. ;

Sullivan, Timothy J. ;

Young, Taylor R. ;

Gelfand, Ellen T. ;

Trowbridge, Casandra A. ;

Maller, Julian B. ;

Tukiainen, Taru ;

Lek, Monkol ;

Ward, Lucas D. ;

Kheradpour, Pouya ;

Iriarte, Benjamin ;

Meng, Yan ;

Palmer, Cameron D. ;

Esko, Tonu ;

Winckler, Wendy ;

Hirschhorn, Joel N. ;

Kellis, Manolis ;

MacArthur, Daniel G. ;

Getz, Gad ;

Shabalin, Andrey A. ;

Li, Gen ;

Zhou, Yi-Hui ;

Nobel, Andrew B. ;

Rusyn, Ivan ;

Wright, Fred A. ;

Lappalainen, Tuuli ;

Ferreira, Pedro G. ;

Ongen, Halit ;

Rivas, Manuel A. ;

Battle, Alexis ;

Mostafavi, Sara ;

Monlong, Jean ;

Sammeth, Michael ;

Mele, Marta ;

Reverter, Ferran ;

Goldmann, Jakob M. ;

Koller, Daphne ;

Guigo, Roderic ;

McCarthy, Mark I. ;

Dermitzakis, Emmanouil T. ;

Gamazon, Eric R. ;

Im, Hae Kyung ;

Konkashbaev, Anuar ;

Nicolae, Dan L. ;

Cox, Nancy J. ;

Flutre, Timothee ;

Wen, Xiaoquan ;

Stephens, Matthew .

SCIENCE, 2015, 348 (6235) :648-660

[5] Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells [J].

Arner, Erik ;

Daub, Carsten O. ;

Vitting-Seerup, Kristoffer ;

Andersson, Robin ;

Lilje, Berit ;

Drablos, Finn ;

Lennartsson, Andreas ;

Roennerblad, Michelle ;

Hrydziuszko, Olga ;

Vitezic, Morana ;

Freeman, Tom C. ;

Alhendi, Ahmad M. N. ;

Arner, Peter ;

Axton, Richard ;

Baillie, J. Kenneth ;

Beckhouse, Anthony ;

Bodega, Beatrice ;

Briggs, James ;

Brombacher, Frank ;

Davis, Margaret ;

Detmar, Michael ;

Ehrlund, Anna ;

Endoh, Mitsuhiro ;

Eslami, Afsaneh ;

Fagiolini, Michela ;

Fairbairn, Lynsey ;

Faulkner, Geoffrey J. ;

Ferrai, Carmelo ;

Fisher, Malcolm E. ;

Forrester, Lesley ;

Goldowitz, Daniel ;

Guler, Reto ;

Ha, Thomas ;

Hara, Mitsuko ;

Herlyn, Meenhard ;

Ikawa, Tomokatsu ;

Kai, Chieko ;

Kawamoto, Hiroshi ;

Khachigian, Levon M. ;

Klinken, S. Peter ;

Kojima, Soichi ;

Koseki, Haruhiko ;

Klein, Sarah ;

Mejhert, Niklas ;

Miyaguchi, Ken ;

Mizuno, Yosuke ;

Morimoto, Mitsuru ;

Morris, Kelly J. ;

Mummery, Christine ;

Nakachi, Yutaka .

SCIENCE, 2015, 347 (6225) :1010-1014

[6] Modeling a self-avoiding chromatin loop: Relation to the packing problem, action-at-a-distance, and nuclear context [J].

Bon, M ;

Marenduzzo, D ;

Cook, PR .

STRUCTURE, 2006, 14 (02) :197-204

[7] Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization [J].

Brackley, Chris A. ;

Taylor, Stephen ;

Papantonis, Argyris ;

Cook, Peter R. ;

Marenduzzo, Davide .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (38) :E3605-E3611

[8] Genetic dissection of transcriptional regulation in budding yeast [J].

Brem, RB ;

Yvert, G ;

Clinton, R ;

Kruglyak, L .

SCIENCE, 2002, 296 (5568) :752-755

[9] Chromosome position effects on gene expression in Escherichia coli K-12 [J].

Bryant, Jack A. ;

Sellars, Laura E. ;

Busby, Stephen J. W. ;

Lee, David J. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (18) :11383-11392

[10] Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories [J].

Caudron-Herger, Maiwen ;

Cook, Peter R. ;

Rippe, Karsten ;

Papantonis, Argyris .

NUCLEIC ACIDS RESEARCH, 2015, 43 (14)

← 1 2 3 4 5 6 7 8 →