TY - JOUR
T1 - Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation
AU - Livyatan, Ilana
AU - Harikumar, Arigela
AU - Nissim-Rafinia, Malka
AU - Duttagupta, Radharani
AU - Gingeras, Thomas R.
AU - Meshorer, Eran
N1 - Funding Information:
Funding for open access charge: Israel Science Foundation [ISF 1252/12 and 657/12 to E.M.]; the Israel Ministry of Science (infrastructure grant to E.M.); the Abisch-Frenkel Foundation (to E.M.) and the European Research Council [ERC-281781 to E.M.].
PY - 2013/7
Y1 - 2013/7
N2 - The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention, albeit mostly confined to the polyadenylated fraction of RNA, whereas the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in ESCs using a combination of whole-genome tiling arrays and deep sequencing technologies. In addition to identifying previously characterized and new non-coding RNA members, we describe a group of novel conserved RNAs (snacRNAs: small NPA conserved), some of which are differentially expressed between ESC and neuronal progenitor cells, providing the first evidence of a novel group of potentially functional NPA RNA involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal small nuclear RNAs, which are NPA, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that NPA RNA, both known and novel, play important roles in ESCs.
AB - The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention, albeit mostly confined to the polyadenylated fraction of RNA, whereas the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in ESCs using a combination of whole-genome tiling arrays and deep sequencing technologies. In addition to identifying previously characterized and new non-coding RNA members, we describe a group of novel conserved RNAs (snacRNAs: small NPA conserved), some of which are differentially expressed between ESC and neuronal progenitor cells, providing the first evidence of a novel group of potentially functional NPA RNA involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal small nuclear RNAs, which are NPA, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that NPA RNA, both known and novel, play important roles in ESCs.
UR - http://www.scopus.com/inward/record.url?scp=84880246505&partnerID=8YFLogxK
U2 - 10.1093/nar/gkt316
DO - 10.1093/nar/gkt316
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C2 - 23630323
AN - SCOPUS:84880246505
SN - 0305-1048
VL - 41
SP - 6300
EP - 6315
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 12
ER -