ArticleNucleic acids research2013
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion.RNA (New York, N.Y.) · 2020Article
- SMARTer single cell total RNA sequencing.Nucleic acids research · 2019Article
- Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.Nature communications · 2018Article
- DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism.BMC genomics · 2017Article
- Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease.Nucleic acids research · 2016Article
- Systematic identification of gene family regulators in mouse and human embryonic stem cells.Nucleic acids research · 2016Article
- Single-cell analysis of long non-coding RNAs in the developing human neocortex.Genome biology · 2016Article
- Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster.BMC genomics · 2016Article
- Using the ENCODE Resource for Functional Annotation of Genetic Variants.Cold Spring Harbor protocols · 2015Review
- Deciphering the RNA landscape by RNAome sequencing.RNA biology · 2015Article
- Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.Arteriosclerosis, thrombosis, and vascular biology · 2014Article
- ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.BMC bioinformatics · 2014Article
- Functional transcriptomics in the post-ENCODE era.Genome research · 2013Article
- Noncoding RNAs in cancer and cancer stem cells.Chinese journal of cancer · 2013Review
- SON sheds light on RNA splicing and pluripotency.Nature cell biology · 2013Article
- Extraction of Molecular Features through Exome to Transcriptome Alignment.Journal of metabolomics and systems biology · 2013Article
- The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.Genome biology · 2013Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.