Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control

BMC Biology
Wencheng LiBin Tian

Abstract

Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3' untranslated regions (3'UTRs) in testes. By deep sequencing of the 3' end region of poly(A) + transcripts, we report widespread shortening of 3'UTR through APA during the first wave of spermatogenesis in mouse, with 3'UTR size being the shortest in spermatids. Using genes without APA as a control, we show that shortening of 3'UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear highly potent during spermatogenesis. We additionally found widespread regulation of APA events in introns and exons that can affect the coding sequence of transcripts and global activation of antisense transcripts upstream of the transcription start site, suggesting modulation of splicing and initiation of transcription during spermatogenesis. Importantly, genes that display significant 3'UTR shortening tend to have functions critical for further sperm maturation, and testis-specific genes display greater 3'UTR shortening than ubiquitously expressed ones, indicating functional relevance of APA to spermatogenesis. Interestingly, genes with short...Continue Reading

References

Nov 14, 1997·Genes & Development·D F Colgan, J L Manley
Sep 21, 2002·Current Opinion in Genetics & Development·Julian P Venables
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gene Yeo, Christopher B Burge
Oct 6, 2004·Genome Biology·Gene YeoChristopher B Burge
Jan 14, 2005·Nucleic Acids Research·Bin TianCarol S Lutz
Apr 13, 2005·Trends in Molecular Medicine·David MillerStephen A Krawetz
Dec 17, 2005·Genome Biology·Haibo ZhangBin Tian
Nov 28, 2006·Reproduction : the Official Journal of the Society for the Study of Fertility·David J Elliott, Sushma N Grellscheid
Dec 13, 2006·Nucleic Acids Research·Donglin LiuJoel H Graber
Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Brinda DassClinton C Macdonald
Dec 26, 2007·Cellular and Molecular Life Sciences : CMLS·C R MandelL Tong
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Feb 17, 2009·Molecular Cell·Yongsheng ShiJames L Manley
Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Zhe JiBin Tian
Jul 15, 2009·Cell Cycle·Amy C SeilaPhillip A Sharp
Oct 1, 2010·Nature·Daisuke KaidaGideon Dreyfuss
Feb 1, 2011·Wiley Interdisciplinary Reviews. RNA·Carol S Lutz, Alexandra Moreira
Feb 19, 2011·Molecular Cell·Takashi NagaikeJames L Manley
Sep 8, 2011·Genes & Development·Nick J Proudfoot
Sep 29, 2011·Molecular Systems Biology·Zhe JiBin Tian
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Carol S Lutz, Alexandra Moreira
Oct 21, 2011·Wiley Interdisciplinary Reviews. RNA·Bin Tian, Joel H Graber
Feb 23, 2012·Scientific Reports·Akio MasudaKinji Ohno
Mar 29, 2012·Genome Research·Adnan DertiTomas Babak
Oct 31, 2012·PloS One·Wencheng LiClinton C MacDonald
Mar 23, 2013·Genome Research·Pedro MiuraEric C Lai
May 2, 2013·Trends in Biochemical Sciences·Bin Tian, James L Manley
Jun 19, 2013·Nature Reviews. Genetics·Ran ElkonReuven Agami
Jun 26, 2013·Cell Reports·Magali SoumillonHenrik Kaessmann
Jun 25, 2013·Nature·Albert E AlmadaPhillip A Sharp

❮ Previous
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Citations

Sep 7, 2017·Journal of Bioinformatics and Computational Biology·Guoli JiXiaohui Wu
Sep 11, 2019·Nucleic Acids Research·Eldad David Shulman, Ran Elkon
Aug 18, 2020·PLoS Genetics·Eldad David Shulman, Ran Elkon
Sep 26, 2020·Nucleic Acids Research·Federico MariniSven Danckwardt
Apr 30, 2017·RNA Biology·Jonathan NeveAndré Martin Furger
Apr 27, 2017·Biology of Reproduction·Clinton C MacDonald, Petar N Grozdanov
Mar 1, 2019·Wiley Interdisciplinary Reviews. RNA·Clinton C MacDonald
Feb 13, 2020·Cell Research·Chong TangWei Yan
Nov 4, 2016·Nature Reviews. Molecular Cell Biology·Bin Tian, James L Manley
Sep 15, 2020·The Journal of Biological Chemistry·Rebecca R Florke GeePatrick Ryan Potts
Mar 23, 2021·Frontiers in Cell and Developmental Biology·Adriana GeisingerRicardo Benavente
Apr 13, 2021·Wiley Interdisciplinary Reviews. RNA·Isabel Pereira-Castro, Alexandra Moreira
May 15, 2021·Trends in Molecular Medicine·Pia SommerkampAndreas Trumpp
Jun 27, 2021·Reproductive Toxicology·Enrica BianchiKathleen Hwang
Aug 28, 2021·Life·Marco BarchiPaola Grimaldi
Sep 29, 2021·Wiley Interdisciplinary Reviews. RNA·Neeraja K MohananRakesh S Laishram
Oct 15, 2021·Nature Communications·Yu H SunXin Zhiguo Li
Nov 5, 2021·Frontiers in Cell and Developmental Biology·Yinchuan LiFei Sun

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Datasets Mentioned

BETA
GSE43717
GSE42004
GSE45441
GSE49621
GSE73973

Methods Mentioned

BETA
RNA-seq
ubiquitination
deubiquitination
ChIP-seq
immunoprecipitation
PCR

Software Mentioned

RepeatMasker Genome Browser
READS
SAAP
MaxEntScan
GAAP
Bowtie

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