Long noncoding RNAs with enhancer-like function in human cells

Ulf Andersson Ørom; Thomas Derrien; Malte Beringer; Kiranmai Gumireddy; Alessandro Gardini; Giovanni Bussotti; Fan Lai; Matthias Zytnicki; Cedric Notredame; Qihong Huang; Roderic Guigo; Ramin Shiekhattar

doi:10.1016/j.cell.2010.09.001

Long noncoding RNAs with enhancer-like function in human cells

Ulf Andersson Ørom, Thomas Derrien, Malte Beringer, Kiranmai Gumireddy, Alessandro Gardini, Giovanni Bussotti, Fan Lai, Matthias Zytnicki, Cedric Notredame, Qihong Huang, Roderic Guigo, Ramin Shiekhattar

Human Genetics

Research output: Contribution to journal › Article › peer-review

1263 Scopus citations

Abstract

While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation. PaperClip:

Original language	English (US)
Pages (from-to)	46-58
Number of pages	13
Journal	Cell
Volume	143
Issue number	1
DOIs	https://doi.org/10.1016/j.cell.2010.09.001
State	Published - Oct 2010

Keywords

DNA
RNA

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

Access to Document

10.1016/j.cell.2010.09.001

Fingerprint Dive into the research topics of 'Long noncoding RNAs with enhancer-like function in human cells'. Together they form a unique fingerprint.

Cite this

Long noncoding RNAs with enhancer-like function in human cells. / Ørom, Ulf Andersson; Derrien, Thomas; Beringer, Malte; Gumireddy, Kiranmai; Gardini, Alessandro; Bussotti, Giovanni; Lai, Fan; Zytnicki, Matthias; Notredame, Cedric; Huang, Qihong; Guigo, Roderic; Shiekhattar, Ramin.

In: Cell, Vol. 143, No. 1, 10.2010, p. 46-58.

Research output: Contribution to journal › Article › peer-review

@article{35fbc79192ec45c481d2e08eab33ef19,

title = "Long noncoding RNAs with enhancer-like function in human cells",

abstract = "While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation. PaperClip:",

keywords = "DNA, RNA",

author = "{\O}rom, {Ulf Andersson} and Thomas Derrien and Malte Beringer and Kiranmai Gumireddy and Alessandro Gardini and Giovanni Bussotti and Fan Lai and Matthias Zytnicki and Cedric Notredame and Qihong Huang and Roderic Guigo and Ramin Shiekhattar",

year = "2010",

month = oct,

doi = "10.1016/j.cell.2010.09.001",

language = "English (US)",

volume = "143",

pages = "46--58",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "1",

}

TY - JOUR

T1 - Long noncoding RNAs with enhancer-like function in human cells

AU - Ørom, Ulf Andersson

AU - Derrien, Thomas

AU - Beringer, Malte

AU - Gumireddy, Kiranmai

AU - Gardini, Alessandro

AU - Bussotti, Giovanni

AU - Lai, Fan

AU - Zytnicki, Matthias

AU - Notredame, Cedric

AU - Huang, Qihong

AU - Guigo, Roderic

AU - Shiekhattar, Ramin

PY - 2010/10

Y1 - 2010/10

N2 - While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation. PaperClip:

AB - While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation. PaperClip:

KW - DNA

KW - RNA

UR - http://www.scopus.com/inward/record.url?scp=77957243921&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77957243921&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2010.09.001

DO - 10.1016/j.cell.2010.09.001

M3 - Article

C2 - 20887892

AN - SCOPUS:77957243921

VL - 143

SP - 46

EP - 58

JO - Cell

JF - Cell

SN - 0092-8674

IS - 1

ER -