@article{0fa81fe251a14e7ab1c0c497ecb1ca83,
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.",
author = "Alexandre Fort and Kosuke Hashimoto and Daisuke Yamada and Md Salimullah and Keya, {Chaman A.} and Alka Saxena and Alessandro Bonetti and Irina Voineagu and Nicolas Bertin and Anton Kratz and Yukihiko Noro and Wong, {Chee Hong} and {De Hoon}, Michiel and Robin Andersson and Albin Sandelin and Harukazu Suzuki and Wei, {Chia Lin} and Haruhiko Koseki and Yuki Hasegawa and Forrest, {Alistair R.R.} and Piero Carninci",
note = "Funding Information: The authors thank the RIKEN GeNAS sequencing platform for sequencing of the libraries. This work was supported by a grant to P.C. from the Japan Society for the Promotion of Science (JSPS) through the Funding Program for Next-Generation World-Leading Researchers (NEXT) initiated by the Council for Science and Technology Policy (CSTP), by a grand-in-aid for scientific research from JSPS to P.C. and A.F., and by a research grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to the RIKEN Center for Life Science Technologies. FANTOM5 was made possible by a research grant for the RIKEN Omics Science Center from MEXT Japan to Y. Hayashizaki and by a grant for Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from MEXT to Y. Hayashizaki. A.F. was supported by a JSPS long-term fellowship (P10782) and by a Swiss National Science Foundation Fellowship for Advanced Researchers (PA00P3_142122). K.H. was supported by European Union Framework Programme 7 (MODHEP project) for P.C. A.B. was supported by the Sigrid Juselius Foundation Fellowship. D.Y. and H.K. were supported by the Japan Science and Technology Agency CREST. R.A. and A. Sandelin were supported by funds from FP7/2007-2013/ERC grant agreement 204135, the Novo Nordisk Foundation, the Lundbeck Foundation and the Danish Cancer Society.",
year = "2014",
month = jun,
doi = "10.1038/ng.2965",
language = "English (US)",
volume = "46",
pages = "558--566",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Research",
number = "6",
}