A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line

Scientific Reports
Nikolai GenovAngela Relógio

Abstract

The circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternat...Continue Reading

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Sep 6, 2002·Chemico-biological Interactions·Alvaro PugaCornelis Elferink
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Nov 3, 2004·Cancer Research·Julian P Venables
Nov 18, 2004·The Journal of Biological Chemistry·Angela RelógioJuan Valcárcel
Mar 9, 2005·Biochemical and Biophysical Research Communications·Hui-Chun HsuYi-Ren Hong
May 27, 2005·Molecular Cell·Anindita BhoumikZe'ev Ronai
Sep 20, 2005·Nature Structural & Molecular Biology·Lionel BallutHervé Le Hir
Dec 27, 2005·The Journal of Biological Chemistry·Ming-Chuan HsuWen-Chun Hung
Feb 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Shihoko KojimaHajime Tei
Feb 21, 2007·Nature Structural & Molecular Biology·Rotem KarniAdrian R Krainer
Apr 4, 2007·Genes & Development·Tae-Don KimKyong-Tai Kim
Apr 4, 2007·Annals of the New York Academy of Sciences·Marco SgarbantiAngela Battistini
Jan 4, 2008·Molecular Cancer Research : MCR·Beatrix A OlofssonJane Azizkhan-Clifford
Mar 21, 2008·Molecular & Cellular Proteomics : MCP·Kasper ThorsenTorben F Orntoft
Apr 22, 2008·Nature Structural & Molecular Biology·Rebecca MathewReinhard Lührmann
Oct 1, 2008·BMC Bioinformatics·Sabry RazickIan M Donaldson
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Jan 7, 2009·BMC Bioinformatics·Steffen DurinckSandrine Dudoit
Feb 26, 2009·Cell·Markus C WahlReinhard Lührmann
Apr 4, 2009·PLoS Genetics·Michael E HughesJohn B Hogenesch
May 19, 2009·Nature Structural & Molecular Biology·Julian P VenablesSherif Abou Elela
Jun 12, 2009·Current Genomics·Claudia GhignaGiuseppe Biamonti
Sep 24, 2009·Nature Reviews. Molecular Cell Biology·Mo Chen, James L Manley
Oct 7, 2009·British Journal of Haematology·Peter BroderickRichard Houlston
Oct 22, 2010·The Journal of Investigative Dermatology·Florian SpörlAchim Kramer
Dec 1, 2010·British Journal of Haematology·Donatella AldinucciAntonino Carbone
Sep 17, 2011·Human Mutation·Francesco PivaGiovanni Principato
Nov 11, 2011·BMC Bioinformatics·John H MorrisThomas E Ferrin
Nov 26, 2011·BMC Bioinformatics·Antonio Mora, Ian M Donaldson
Nov 30, 2011·Molecular and Cellular Biology·Kyung-Ha LeeKyong-Tai Kim
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Jun 12, 2012·Journal of Nucleic Acids·Didier AuboeufGiuseppe Biamonti

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Citations

Apr 22, 2020·The Plant Journal : for Cell and Molecular Biology·Andrés RomanowskiMarcelo J Yanovsky
Sep 20, 2019·International Journal of Molecular Sciences·Nikolai GenovGianluigi Mazzoccoli
Nov 13, 2020·Cell Communication and Signaling : CCS·Jacqueline F PelhamJennifer M Hurley
Oct 23, 2020·Clocks & Sleep·Monica N MorganKristina M Cook

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Datasets Mentioned

BETA
GSE11923
E-MTAB-6400
27
GSE25585
GSE11922
GSE13949

Methods Mentioned

BETA
PCA
nucleotide exchange
transfection
PCR
electrophoresis

Software Mentioned

Cytoscape
MetaCycle 59 R package
clusterProfiler
IntAct
EventPointer R package
ArrayExpress
ChronoStar 82
affymetrix R
iRefR R 88
Metacycle

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