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Deep sequencing of ...
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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2022-08-12
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Cold Spring Harbor Laboratory,2022
Numbers
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LIBRIS-ID:oai:prod.swepub.kib.ki.se:150859279
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http://kipublications.ki.se/Default.aspx?queryparsed=id:150859279URI
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https://doi.org/10.1101/gr.276647.122DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3′ ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
Added entries (persons, corporate bodies, meetings, titles ...)
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Bonetti, A
(author)
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Plessy, C
(author)
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Ando, Y
(author)
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Hon, CC
(author)
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Ishizu, Y
(author)
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Itoh, M
(author)
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Kato, S
(author)
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Lin, DY
(author)
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Maekawa, S
(author)
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Murata, M
(author)
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Nishiyori, H
(author)
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Shin, JW
(author)
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Stolte, J
(author)
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Suzuki, AM
(author)
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Tagami, M
(author)
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Takahashi, H
(author)
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Forrest, ARR
(author)
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Hayashizaki, Y
(author)
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Kere, JKarolinska Institutet
(author)
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Carninci, P
(author)
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Thongjuea, S
(author)
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Karolinska Institutet
(creator_code:org_t)
Related titles
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In:Genome research: Cold Spring Harbor Laboratory32:9, s. 1727-17351549-54691088-9051
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- By the author/editor
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de Hoon, M
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Bonetti, A
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Plessy, C
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Ando, Y
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Hon, CC
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Ishizu, Y
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show more...
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Itoh, M
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Kato, S
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Lin, DY
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Maekawa, S
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Murata, M
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Nishiyori, H
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Shin, JW
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Stolte, J
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Suzuki, AM
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Tagami, M
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Takahashi, H
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Forrest, ARR
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Hayashizaki, Y
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Kere, J
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Carninci, P
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Thongjuea, S
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show less...
- Articles in the publication
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Genome research
- By the university
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Karolinska Institutet