Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Alexandre Fort; Kosuke Hashimoto; Daisuke Yamada; Md Salimullah; Chaman A. Keya; Alka Saxena; Alessandro Bonetti; Irina Voineagu; Nicolas Bertin; Anton Kratz; Yukihiko Noro; Chee-Hong Wong; Michiel de Hoon; Robin Andersson; Albin Gustav Sandelin; Harukazu Suzuki; Chia-Lin Wei; Haruhiko Koseki; Yuki Hasegawa; Alistair R R Forrest; Piero Carninci; FANTOM Consortium

doi:10.1038/ng.2965

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A. Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz, Yukihiko Noro, Chee-Hong Wong, Michiel de Hoon, Robin Andersson, Albin Gustav Sandelin, Harukazu Suzuki, Chia-Lin Wei, Haruhiko Koseki, Yuki Hasegawa, Alistair R R ForrestPiero Carninci, FANTOM Consortium

Computational and RNA Biology

174 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Nature Genetics
Volume	46
Issue number	6
Pages (from-to)	558-566
Number of pages	9
ISSN	1061-4036
DOIs	https://doi.org/10.1038/ng.2965
Publication status	Published - Jun 2014

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Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C. A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C.-H., de Hoon, M., Andersson, R., Sandelin, A. G., Suzuki, H., Wei, C.-L., Koseki, H., Hasegawa, Y., ... FANTOM Consortium (2014). Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nature Genetics, 46(6), 558-566. https://doi.org/10.1038/ng.2965

Fort, A, Hashimoto, K, Yamada, D, Salimullah, M, Keya, CA, Saxena, A, Bonetti, A, Voineagu, I, Bertin, N, Kratz, A, Noro, Y, Wong, C-H, de Hoon, M, Andersson, R , Sandelin, AG, Suzuki, H, Wei, C-L, Koseki, H, Hasegawa, Y, Forrest, ARR, Carninci, P & FANTOM Consortium 2014, 'Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance', Nature Genetics, vol. 46, no. 6, pp. 558-566. https://doi.org/10.1038/ng.2965

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title = "Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance",

abstract = "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.",

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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 - 2014/6

Y1 - 2014/6

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

SN - 1061-4036

VL - 46

SP - 558

EP - 566

JO - Nature Genetics

JF - Nature Genetics

IS - 6

ER -

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Abstract

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