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Cited by 191Cancer-related molecular mechanisms researchRNA Research and SplicingChromosomal and Genetic Variations

Computational discovery of sense-antisense transcription in the human and mouse genomes

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Shendure, Jay, Church, George M·2002·Genome Biology
DOI 10.1186/gb-2002-3-9-research0044PMC PMC126869
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Abstract

BACKGROUND: Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples of mammalian gene-regulatory phenomena in which endogenous dsRNA duplexes have been proposed or demonstrated to participate has greatly increased. These include genomic imprinting, RNA interference, translational regulation, alternative splicing, X-inactivation and RNA editing. We computationally mined public mouse and human expressed sequence tag (EST) databases to search for additional examples of bidirectionally transcribed genomic regions. RESULTS: Our bioinformatics approach identified over 217 candidate overlapping transcriptional units, almost all of which are novel. From experimental validation of a subset of our predictions by orientation-specific RT-PCR, we estimate that our methodology has a specificity of 84% or greater. In many cases, regions of sense-antisense overlap within the 5'- or 3'-untranslated regions of a given transcript correlate with genomic patterns of mouse-human conservation. CONCLUSIONS: Our results, in conjunction with the literature, bring the total number of predicted and validated examples of overlapping but oppositely oriented transcripts to over 300. Several of these cases support the hypothesis that a subset of the instances of substantial mouse-human conservation in the 5' and 3' UTRs of transcripts might be explained in part by functionality of an overlapping transcriptional unit.

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  • Only a few of the 40 known sense/antisense pairs reviewed by Shendure and Church (2002) contain HCEs coinciding with regions of sense/antisense overlap.

    “Only a few of the 40 known sense/antisense pairs reviewed by Shendure and Church (2002) contain HCEs coinciding with regions of sense/antisense overlap.”

    From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Shendure and Church 2002

    The Background (page not provided) says Shendure and Church reviewed 40 known sense–antisense cases. The Discussion (page not provided) describes conservation coinciding with overlap in several candidate pairs, but does not establish that only a few of the 40 reviewed pairs contain HCEs at their overlap regions. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

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Authors
Shendure, J., & Church, G. M.
Affiliations
Harvard University (US)
Corresponding author
Church, George M
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2002-08-22
Volume
3
Issue
9
Pages
RESEARCH0044-RESEARCH0044
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2002-3-9-research0044
PMC
PMC126869
OpenAlex
W2142445831
Cited by
191
References
1
Citations by year
2026: 4 · 2024: 3 · 2023: 1 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 4 · 2017: 2 · 2016: 5 · 2014: 3 · 2013: 5 · 2012: 6
FWCI
9.55
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
bidirectional transcription, expressed sequence tags, 5' untranslated region, 3' untranslated region, RNA interference, genomic imprinting
MeSH terms
Animals, DNA, Exons, Gene Expression Regulation, Humans, Introns, RNA, Messenger, Transcription, Genetic, Gene Library, Genome, Human, DNA, Antisense, Genome, Alternative Splicing, Computational Biology, Expressed Sequence Tags, Mice

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