RNA profiling in mouse haemopoiesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Ryan Taft
PROVIDER: E-GEOD-20683 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.
Taft Ryan J RJ Simons Cas C Nahkuri Satu S Oey Harald H Korbie Darren J DJ Mercer Timothy R TR Holst Jeff J Ritchie William W Wong Justin J-L JJ Rasko John E J JE Rokhsar Daniel S DS Degnan Bernard M BM Mattick John S JS
Nature structural & molecular biology 20100711 8
We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences immediately downstream of transcription start sites. Here, using cytoplasmic and nuclear small RNA high-throughput sequencing datasets, we report the identification of a second class of nuclear-specific approximately 17- to 18-nucleotide small RNAs whose 3' ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed gen ...[more]
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Project description:We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences downstream of transcription start sites. Here we report the identification of a second class of nuclear-specific ~17-18 nucleotide small RNA whose 3M-bM-^@M-^Y ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed genes, and show evidence of developmental stage- and region-specific expression. We also confirm that tiRNAs are nuclear localized, enriched at chromatin marks associated with transcription initiation, and possess a 3M-bM-^@M-^Y nucleotide bias. Additionally, we find that microRNA-offset RNAs (moRNAs), the oncogenic miR-15/16 cluster and most snoRNA-derived small RNAs (sdRNAs) are enriched in the nucleus, whereas most miRNAs and two H/ACA sdRNAs are cytoplasmically enriched. We propose that nuclear localized tiny RNAs are involved in epigenetic regulation of gene expression. Discovery and characterization of small RNA species through high-througput deep sequencing of nuclear, cytoplasmic and total small RNA fractions from THP-1 cells, a monocytic leukemia cell line. Additional files and information are available at http://matticklab.com/index.php?title=NuclearTinyRNAs
2010-07-01 | E-GEOD-20664 | biostudies-arrayexpress
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2017-05-01 | E-GEOD-78901 | biostudies-arrayexpress
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2014-01-06 | E-GEOD-51997 | biostudies-arrayexpress
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