Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis on nuclear and retrotransposon-derived transcripts. We have performed deep profiling of the nuclear and cytoplasmic transcriptomes of human and mouse stem cells, identifying a class of previously undetected stem cell-specific transcripts. We show that long terminal repeat (LTR)-derived transcripts contribute extensively to the complexity of the stem cell nuclear transcriptome. Some LTR-derived transcripts are associated with enhancer regions and are likely to be involved in the maintenance of pluripotency.
1] Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan. [2].
Alexandre
A
Fort
1] Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan. [2].
Kosuke
K
Hashimoto
Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Daisuke
D
Yamada
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Md
M
Salimullah
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Chaman A
CA
Keya
1] Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan. [2].
Alka
A
Saxena
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Alessandro
A
Bonetti
1] Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan. [2].
Irina
I
Voineagu
1] Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan. [2].
Nicolas
0000000298359606
N
Bertin
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Anton
A
Kratz
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Yukihiko
Y
Noro
Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, USA.
Chee-Hong
CH
Wong
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Michiel
M
de Hoon
Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
Robin
000000031516879X
R
Andersson
Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
Albin
A
Sandelin
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Harukazu
H
Suzuki
Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, USA.
Chia-Lin
CL
Wei
Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Haruhiko
H
Koseki
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Yuki
Y
Hasegawa
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Alistair R R
AR
Forrest
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Piero
P
Carninci
D000818:Animals; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry; D003593:Cytoplasm / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D008214:Lymphocytes / Q000166:cytology; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D016376:Oligonucleotides, Antisense / Q000235:genetics; D039904:Pluripotent Stem Cells / Q000166:cytology*; D018626:Retroelements; D020079:Terminal Repeat Sequences; D059467:Transcriptome
D002843:Chromatin; D035683:MicroRNAs; D016376:Oligonucleotides, Antisense; D018626:Retroelements