Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development

ELife
Li ZhouKatsutomo Okamura

Abstract

Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.

References

Apr 1, 1994·In Vitro Cellular & Developmental Biology. Animal·K UiT Miyake
Mar 1, 2003·Science·Anne F SimonSeymour Benzer
Jul 3, 2004·Genes & Development·Katsutomo OkamuraMikiko C Siomi
Jun 10, 2005·Nature·Jun LuTodd R Golub
Nov 26, 2005·Science·Kyle Kai-How FarhDavid P Bartel
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·A Aziz AboobakerEric C Lai
Oct 31, 2006·Nature Genetics·Kevin Chen, Nikolaus Rajewsky
Apr 3, 2007·Nature Genetics·Madhu S KumarTyler Jacks
Jun 15, 2007·Nature Structural & Molecular Biology·Sonia Guil, Javier F Cáceres
Jun 15, 2007·Nature Reviews. Genetics·Peter A LawrenceJosé Casal
Feb 23, 2008·Science·Srinivas R ViswanathanRichard I Gregory
Jun 13, 2008·Nature·Brandi N DavisAkiko Hata
Oct 28, 2008·Molecular Cell·Inha HeoV Narry Kim
Nov 29, 2008·Science·Julius BrenneckeGregory J Hannon
Jan 24, 2009·Nature Reviews. Molecular Cell Biology·V Narry KimMikiko C Siomi
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 22, 2009·Nature·Michele TrabucchiMichael G Rosenfeld
May 28, 2009·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Kevin J PetersonMark A McPeek
Jul 25, 2009·Nature·Hiroshi I SuzukiKohei Miyazono
Nov 12, 2009·Genes & Development·Madhu S KumarTyler Jacks
Nov 18, 2009·Molecular Cell·Benjamin CzechGregory J Hannon
Feb 2, 2010·Current Biology : CB·Nayoung SuhRobert Blelloch
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Apr 14, 2010·Nucleic Acids Research·Yusuke OhnishiHirohiko Hohjoh
Apr 17, 2010·Trends in Biochemical Sciences·Tomoko Kawamata, Yukihide Tomari
Jun 19, 2010·Science·Stefan L AmeresPhillip D Zamore
Dec 24, 2010·Science·UNKNOWN modENCODE ConsortiumManolis Kellis
Dec 24, 2010·Nature·Brenton R GraveleySusan E Celniker
Jul 21, 2011·BMC Genomics·Sergei S RyazanskyEugene Berezikov
Oct 1, 2011·RNA Biology·Steven G ChaulkJ N Mark Glover
Nov 17, 2011·Wiley Interdisciplinary Reviews. RNA·Katsutomo Okamura
Jan 10, 2012·EMBO Reports·Taeko WadaYusuke Furukawa
Feb 10, 2012·Nature·Trudy F C MackayRichard A Gibbs

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Citations

Jun 26, 2020·Frontiers in Cell and Developmental Biology·Philipp J Dexheimer, Luisa Cochella
May 5, 2021·Proceedings of the National Academy of Sciences of the United States of America·Yan WangSibao Wang
Nov 6, 2020·Current Opinion in Cell Biology·Himani Galagali, John K Kim

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Datasets Mentioned

BETA
M21017.1
SRP109269

Methods Mentioned

BETA
RNA-seq
transfection
ChIP-seq
AGO1-IP
transgenic
immunoprecipitation
PCR
Assay

Software Mentioned

UCSC Genome Browser
modENCODE
tuxedo
STAR
FASTX
TargetScan
Bowtie

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