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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

by Saxena, Alka , Kai, Chieko , Lilje, Berit , Kawashima, Tsugumi , Ferrai, Carmelo , Bertin, Nicolas , Patrikakis, Margaret , Ishikawa-Kato, Sachi , Suzuki, Harukazu , Pombo, Ana , Beckhouse, Anthony , Orlando, Valerio , Tanaka, Hiroshi , Passier, Robert , Kojima, Miki , Okazaki, Yasushi , Rönnerblad, Michelle , Sugiyama, Daisuke , Faulkner, Geoffrey J. , Severin, Jessica , Fairbairn, Lynsey , Hara, Mitsuko , Koseki, Haruhiko , Bodega, Beatrice , Roy, Sugata , Lizio, Marina , Sato, Hiroki , Forrest, Alistair R. R. , Schwegmann, Anita , Qin, Xian-Yang , Mizuno, Yosuke , Zhang, Peter , Hori, Fumi , Okada-Hatakeyama, Mariko , Eslami, Afsaneh , Winteringham, Louise N. , Kawai, Jun , Forrester, Lesley , Hayashizaki, Yoshihide , Savvi, Suzana , Wells, Christine , Morris, Kelly J. , de Hoon, Michiel J. L. , Fukuda, Shiro , Sahin, Serkan , Ishizu, Yuri , Itoh, Masayoshi , Ehrlund, Anna , Fagiolini, Michela , Summers, Kim M. , Arner, Peter , Endoh, Mitsuhiro , Khachigian, Levon M. , Carninci, Piero , Lennartsson, Andreas , Kawamoto, Hiroshi , Vitezic, Morana , Klein, Sarah , Mummery, Christine , Tomoiu, Andru , Hrydziuszko, Olga , Abugessaisa, Imad , Drabløs, Finn , Murata, Mitsuyo

in Animals / Binding Sites / Cattle / Cell Differentiation - genetics / Cellular / Cellular biology / Differentiation / Dogs / Dynamic tests / Enhancer Elements, Genetic / Gene expression / Gene Expression Regulation, Developmental / Genes / Individualized Instruction / Mammals / Mathematical models / Mice / Rats / Ribonucleic acid / Ribonucleic acids / RNA / RNA, Messenger - genetics / RNA, Messenger - metabolism / Rodents / Stem Cells - cytology / Stem Cells - metabolism / Transcription Factors - metabolism / Transcription, Genetic

2015

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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

2015

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2015

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Journal Article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Saxena, Alka,

Kai, Chieko,

Lilje, Berit,

Kawashima, Tsugumi,

Ferrai, Carmelo,

Bertin, Nicolas,

Patrikakis, Margaret,

Ishikawa-Kato, Sachi,

Suzuki, Harukazu,

Pombo, Ana,

Beckhouse, Anthony,

Orlando, Valerio,

Tanaka, Hiroshi,

Passier, Robert,

Kojima, Miki,

Okazaki, Yasushi,

Rönnerblad, Michelle,

Sugiyama, Daisuke,

Faulkner, Geoffrey J.,

Severin, Jessica,

Fairbairn, Lynsey,

Hara, Mitsuko,

Koseki, Haruhiko,

Bodega, Beatrice,

Roy, Sugata,

Lizio, Marina,

Sato, Hiroki,

Forrest, Alistair R. R.,

Schwegmann, Anita,

Qin, Xian-Yang,

Mizuno, Yosuke,

Zhang, Peter,

Hori, Fumi,

Okada-Hatakeyama, Mariko,

Eslami, Afsaneh,

Winteringham, Louise N.,

Kawai, Jun,

Forrester, Lesley,

Hayashizaki, Yoshihide,

Savvi, Suzana,

Wells, Christine,

Morris, Kelly J.,

de Hoon, Michiel J. L.,

Fukuda, Shiro,

Sahin, Serkan,

Ishizu, Yuri,

Itoh, Masayoshi,

Ehrlund, Anna,

Fagiolini, Michela,

Summers, Kim M.,

Arner, Peter,

Endoh, Mitsuhiro,

Khachigian, Levon M.,

Carninci, Piero,

Lennartsson, Andreas,

Kawamoto, Hiroshi,

Vitezic, Morana,

Klein, Sarah,

Mummery, Christine,

Tomoiu, Andru,

Hrydziuszko, Olga,

Abugessaisa, Imad,

Drabløs, Finn,

Murata, Mitsuyo

2015

Overview

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

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Publisher

American Association for the Advancement of Science,The American Association for the Advancement of Science

Subject

Animals

/ Binding Sites

/ Cattle

/ Cell Differentiation - genetics

/ Cellular

/ Cellular biology

/ Differentiation