Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
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Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. / Fort, Alexandre; Hashimoto, Kosuke; Yamada, Daisuke; Salimullah, Md; Keya, Chaman A.; Saxena, Alka; Bonetti, Alessandro; Voineagu, Irina; Bertin, Nicolas; Kratz, Anton; Noro, Yukihiko; Wong, Chee-Hong; de Hoon, Michiel; Andersson, Robin; Sandelin, Albin Gustav; Suzuki, Harukazu; Wei, Chia-Lin; Koseki, Haruhiko; Hasegawa, Yuki; Forrest, Alistair R R; Carninci, Piero; FANTOM Consortium.
In: Nature Genetics, Vol. 46, No. 6, 2014, p. 558-566.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
AU - Fort, Alexandre
AU - Hashimoto, Kosuke
AU - Yamada, Daisuke
AU - Salimullah, Md
AU - Keya, Chaman A.
AU - Saxena, Alka
AU - Bonetti, Alessandro
AU - Voineagu, Irina
AU - Bertin, Nicolas
AU - Kratz, Anton
AU - Noro, Yukihiko
AU - Wong, Chee-Hong
AU - de Hoon, Michiel
AU - Andersson, Robin
AU - Sandelin, Albin Gustav
AU - Suzuki, Harukazu
AU - Wei, Chia-Lin
AU - Koseki, Haruhiko
AU - Hasegawa, Yuki
AU - Forrest, Alistair R R
AU - Carninci, Piero
AU - FANTOM Consortium
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
U2 - 10.1038/ng.2965
DO - 10.1038/ng.2965
M3 - Journal article
C2 - 24777452
VL - 46
SP - 558
EP - 566
JO - Nature Genetics
JF - Nature Genetics
SN - 1061-4036
IS - 6
ER -
ID: 113242201