Journal article
Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types
Scientific reports, v 4(1), pp 5947-5947
08 Aug 2014
PMID: 25103560
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
To date, analyses of individual targets have provided evidence of a miRNA targetome that extends beyond the boundaries of messenger RNAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed region. Here we report our findings from analyzing 34 Argonaute HITS-CLIP datasets from several human and mouse cell types. Investigation of the architectural (i.e. bulge vs. contiguous pairs) and sequence (Watson-Crick vs. G:U pairs) preferences for human and mouse miRNAs revealed that many heteroduplexes are "non-canonical" i.e. their seed region comprises G:U and bulge combinations. The genomic distribution of miRNA targets differed distinctly across cell types but remained congruent across biological replicates of the same cell type. For some cell types intergenic and intronic targets were more frequent whereas in other cell types mRNA targets prevailed. The findings suggest an expanded model of miRNA targeting that is more frequent than the standard model currently in use. Lastly, our analyses of data from different cell types and laboratories revealed consistent Ago-loaded miRNA profiles across replicates whereas, unexpectedly, the Ago-loaded targets exhibited a much more dynamic behavior across biological replicates.
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Details
- Title
- Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types
- Creators
- Peter M Clark - Thomas Jefferson UniversityPhillipe Loher - Thomas Jefferson UniversityKevin Quann - Thomas Jefferson UniversityJonathan Brody - Thomas Jefferson UniversityEric R Londin - Thomas Jefferson UniversityIsidore Rigoutsos - Thomas Jefferson University
- Publication Details
- Scientific reports, v 4(1), pp 5947-5947
- Publisher
- Springer Nature
- Grant note
- P30CA056036 / NCI NIH HHS 2U19AI056363-06/2030984 / NIAID NIH HHS P30 CA056036 / NCI NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems; Drexel University
- Web of Science ID
- WOS:000340592700001
- Scopus ID
- 2-s2.0-84905862595
- Other Identifier
- 991019356497904721
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- Web of Science research areas
- Biochemistry & Molecular Biology