Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells

Sophie A. Hanina, William Mifsud, Thomas A. Down, Katsuhiko Hayashi, Dónal O'Carroll, Kaiqin Lao, Eric A. Miska, M. Azim Surani

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes and upregulating pluripotency-associated genes such as Lin28.

Original languageEnglish
Article numbere1001163
Pages (from-to)1-13
Number of pages13
JournalPLoS genetics
Volume6
Issue number10
DOIs
Publication statusPublished - Jan 1 2010

Fingerprint

embryonic stem cells
MicroRNAs
microRNA
genome
stem
Genome
RNA
mice
Embryonic Stem Cells
RNA-Induced Silencing Complex
gene
metazoan
complementarity
RNA Sequence Analysis
myc Genes
Gene Expression Profiling
transcriptomics
seed
protein
Mouse Embryonic Stem Cells

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Hanina, S. A., Mifsud, W., Down, T. A., Hayashi, K., O'Carroll, D., Lao, K., ... Azim Surani, M. (2010). Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells. PLoS genetics, 6(10), 1-13. [e1001163]. https://doi.org/10.1371/journal.pgen.1001163

Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells. / Hanina, Sophie A.; Mifsud, William; Down, Thomas A.; Hayashi, Katsuhiko; O'Carroll, Dónal; Lao, Kaiqin; Miska, Eric A.; Azim Surani, M.

In: PLoS genetics, Vol. 6, No. 10, e1001163, 01.01.2010, p. 1-13.

Research output: Contribution to journalArticle

Hanina, SA, Mifsud, W, Down, TA, Hayashi, K, O'Carroll, D, Lao, K, Miska, EA & Azim Surani, M 2010, 'Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells', PLoS genetics, vol. 6, no. 10, e1001163, pp. 1-13. https://doi.org/10.1371/journal.pgen.1001163
Hanina, Sophie A. ; Mifsud, William ; Down, Thomas A. ; Hayashi, Katsuhiko ; O'Carroll, Dónal ; Lao, Kaiqin ; Miska, Eric A. ; Azim Surani, M. / Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells. In: PLoS genetics. 2010 ; Vol. 6, No. 10. pp. 1-13.
@article{61ffe5f0ab4e4cd2beba32af635028e2,
title = "Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells",
abstract = "Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes and upregulating pluripotency-associated genes such as Lin28.",
author = "Hanina, {Sophie A.} and William Mifsud and Down, {Thomas A.} and Katsuhiko Hayashi and D{\'o}nal O'Carroll and Kaiqin Lao and Miska, {Eric A.} and {Azim Surani}, M.",
year = "2010",
month = "1",
day = "1",
doi = "10.1371/journal.pgen.1001163",
language = "English",
volume = "6",
pages = "1--13",
journal = "PLoS Genetics",
issn = "1553-7390",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells

AU - Hanina, Sophie A.

AU - Mifsud, William

AU - Down, Thomas A.

AU - Hayashi, Katsuhiko

AU - O'Carroll, Dónal

AU - Lao, Kaiqin

AU - Miska, Eric A.

AU - Azim Surani, M.

PY - 2010/1/1

Y1 - 2010/1/1

N2 - Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes and upregulating pluripotency-associated genes such as Lin28.

AB - Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes and upregulating pluripotency-associated genes such as Lin28.

UR - http://www.scopus.com/inward/record.url?scp=78449254310&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78449254310&partnerID=8YFLogxK

U2 - 10.1371/journal.pgen.1001163

DO - 10.1371/journal.pgen.1001163

M3 - Article

VL - 6

SP - 1

EP - 13

JO - PLoS Genetics

JF - PLoS Genetics

SN - 1553-7390

IS - 10

M1 - e1001163

ER -