Evidence map›Paper›PMID 26975654›Full record

ArticleNucleic acids research2016

Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets.

Ashley A Cass, Jae Hoon Bahn, Jae-Hyung Lee, Christopher Greer, Xianzhi Lin, Yong Kim, Yun-Hua Esther Hsiao, Xinshu Xiao

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Ashley A CassBioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
Jae Hoon BahnDepartment of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA.
Jae-Hyung LeeDepartment of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA.
Christopher GreerDepartment of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA.
Xianzhi LinDepartment of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA.
Yong KimSchool of Dentistry, University of California Los Angeles, Los Angeles, CA, USA UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA UCLA Broad Stem Cell Research Center, Los Angeles, CA, USA.
Yun-Hua Esther HsiaoDepartment of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA.
Xinshu XiaoBioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA gxxiao@ucla.edu.

Funding

UCLA Dentist-Scientist and Oral Health-Researcher Training ProgramT90DE022734 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI WONG, DAVID T · 2012 to 2017
$2.3M
Functional genetic variations in splicing regulationR01HG006264 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI XIAO, XINSHU GRACE · 2012 to 2016
$1.5M
Analysis of causal genetic variants in pre-mRNA processing using ENCODE dataU01HG007013 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI XIAO, XINSHU GRACE · 2012 to 2015
$1.1M
NHGRI NIH HHS R01HG006264NHGRI NIH HHS U01HG007013NIDCR NIH HHS T90 DE022734NIDCR NIH HHS T90DE022734
6 · The paper itself

Abstract

In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. We report a systematic study of small RNA-mediated endonucleolytic cleavage in mouse through integrative analysis of small RNA and degradome sequencing data without imposing any bias toward known small RNAs. Hundreds of small cleavage-inducing RNAs and their cognate target genes were identified, significantly expanding the repertoire of known small RNA-guided cleavage events. Strikingly, both small RNAs and their target sites demonstrated significant overlap with retrotransposons, providing evidence for the long-standing speculation that retrotransposable elements in mRNAs are leveraged as signals for gene targeting. Furthermore, our analysis showed that the RNA cleavage pathway is also present in human cells but affecting a different repertoire of retrotransposons. These results show that small RNA-guided cleavage is more widespread than previously appreciated. Their impact on retrotransposons in non-coding regions shed light on important aspects of mammalian gene regulation.

Indexed as

RNA CleavageAnimalsCerebellumEmbryonic Stem CellsEndoribonucleasesGenomicsHumansMaleMice, Inbred BALB CRepetitive Sequences, Nucleic AcidRetroelementsRNA, Small UntranslatedTestisEndoribonucleasesRetroelementsRNA, Small Untranslated

Identifiers

PMID26975654
PMCPMC4838385

What OpenQuestion holds

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Registered trials

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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.