Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development

Transcription factors organize gene expression profiles by regulating promoter activity. However, the role of transcription factors after transcription initiation is poorly understood. Here, we show that the homeoprotein Nkx2-5 and the 5’-3’ exonuclease Xrn2 are involved in the regulation of alternative polyadenylation (APA) during mouse heart development. Nkx2-5 occupied not only the transcription start sites (TSSs) but also the downstream regions of genes, serving to connect these regions in primary embryonic cardiomyocytes (eCMs). Nkx2-5 deficiency affected Xrn2 binding to target loci and resulted in increases in RNA polymerase II (RNAPII) occupancy and in the expression of mRNAs with long 3’untranslated regions (3’ UTRs) from genes related to heart development. siRNA-mediated suppression of Nkx2-5 and Xrn2 led to heart looping anomaly. Moreover, Nkx2-5 genetically interacts with Xrn2 because Nkx2-5+/-Xrn2+/-, but neither Nkx2-5+/-nor Xrn2+/-, newborns exhibited a defect in ventricular septum formation, suggesting that the association between Nkx2-5 and Xrn2 is essential for heart development. Our results indicate that Nkx2-5 regulates not only the initiation but also the usage of poly(A) sites during heart development. Our findings suggest that tissue-specific transcription factors is involved in the regulation of APA. DOI: http://dx.doi.org/10.7554/eLife.16030.001

[1]  Marcus Krüger,et al.  Genetic compensation induced by deleterious mutations but not gene knockdowns , 2015, Nature.

[2]  H. Kimura,et al.  Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing , 2015, Cell.

[3]  Axel Visel,et al.  Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease , 2014, Nature Communications.

[4]  Wei Li,et al.  CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression , 2014, Nature.

[5]  R. Elkon,et al.  Alternative cleavage and polyadenylation: extent, regulation and function , 2013, Nature Reviews Genetics.

[6]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[7]  E. Lai,et al.  Widespread and extensive lengthening of 3′ UTRs in the mammalian brain , 2013, Genome research.

[8]  Wei Yang,et al.  The Histone Mark H3K36me3 Regulates Human DNA Mismatch Repair through Its Interaction with MutSα , 2013, Cell.

[9]  Tom Misteli,et al.  Functional implications of genome topology , 2013, Nature Structural &Molecular Biology.

[10]  Judith B. Zaugg,et al.  Gene Loops Enhance Transcriptional Directionality , 2012, Science.

[11]  C. Weitz,et al.  Feedback Regulation of Transcriptional Termination by the Mammalian Circadian Clock PERIOD Complex , 2012, Science.

[12]  C. Bezzina,et al.  Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. , 2012, The Journal of clinical investigation.

[13]  D. Bentley,et al.  mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. , 2012, Molecular cell.

[14]  Y. Kaneda,et al.  Essential Role for miR-196a in Brown Adipogenesis of White Fat Progenitor Cells , 2012, PLoS biology.

[15]  C. Dean,et al.  Cotranscriptional Role for Arabidopsis DICER-LIKE 4 in Transcription Termination , 2012, Science.

[16]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[17]  E. Birney,et al.  A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History , 2012, Cell.

[18]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[19]  J. Seidman,et al.  Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis , 2011, Nature Genetics.

[20]  S. Ohki,et al.  The NMR structure of stomagen reveals the basis of stomatal density regulation by plant peptide hormones. , 2011, Nature communications.

[21]  Joshua D. Wythe,et al.  Tinman/Nkx2-5 acts via miR-1 and upstream of Cdc42 to regulate heart function across species , 2011, The Journal of cell biology.

[22]  C. Moore,et al.  Unravelling the means to an end: RNA polymerase II transcription termination , 2011, Nature Reviews Molecular Cell Biology.

[23]  Aibin He,et al.  Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart , 2011, Proceedings of the National Academy of Sciences.

[24]  C. Glass,et al.  Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.

[25]  Marcel Grunert,et al.  The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs , 2011, PLoS genetics.

[26]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[27]  B. Bruneau.  Chromatin remodeling in heart development. , 2010, Current opinion in genetics & development.

[28]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[29]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[30]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[31]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[32]  B. Blencowe,et al.  Regulation of Alternative Splicing by Histone Modifications , 2010, Science.

[33]  T. Enver,et al.  Forcing cells to change lineages , 2009, Nature.

[34]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[35]  Y. Kaneda,et al.  A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf–Hirschhorn syndrome , 2009, Nature.

[36]  Patricia Richard,et al.  Transcription termination by nuclear RNA polymerases. , 2009, Genes & development.

[37]  Benoit G. Bruneau,et al.  Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors , 2009, Nature.

[38]  D. Srivastava,et al.  Cardiac fibroblasts regulate myocardial proliferation through beta1 integrin signaling. , 2009, Developmental cell.

[39]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[40]  K. Nishii,et al.  Targeted disruption of the cardiac troponin T gene causes sarcomere disassembly and defects in heartbeat within the early mouse embryo. , 2008, Developmental biology.

[41]  Michael Q. Zhang,et al.  Combinatorial patterns of histone acetylations and methylations in the human genome , 2008, Nature Genetics.

[42]  B. Bruneau.  The developmental genetics of congenital heart disease , 2008, Nature.

[43]  Ping Chen,et al.  Carboxyl terminus of Nkx2.5 impairs its interaction with p300. , 2007, Journal of molecular biology.

[44]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[45]  Michael T. McManus,et al.  Dysregulation of Cardiogenesis, Cardiac Conduction, and Cell Cycle in Mice Lacking miRNA-1-2 , 2007, Cell.

[46]  Milena B. Furtado,et al.  An Nkx2-5/Bmp2/Smad1 Negative Feedback Loop Controls Heart Progenitor Specification and Proliferation , 2007, Cell.

[47]  Y. Kaneda,et al.  Dnmt3a2 targets endogenous Dnmt3L to ES cell chromatin and induces regional DNA methylation , 2006, Genes to cells : devoted to molecular & cellular mechanisms.

[48]  D. Srivastava.  Making or Breaking the Heart: From Lineage Determination to Morphogenesis , 2006, Cell.

[49]  Jun Song,et al.  CEAS: cis-regulatory element annotation system , 2006, Nucleic Acids Res..

[50]  W. Earnshaw,et al.  Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. , 2006, Molecular cell.

[51]  R. Harvey,et al.  T-box transcription factors and their roles in regulatory hierarchies in the developing heart , 2005, Development.

[52]  I. Komuro,et al.  Cardiac transcription factor Csx/Nkx2-5: Its role in cardiac development and diseases. , 2005, Pharmacology & therapeutics.

[53]  N. Proudfoot,et al.  Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites , 2004, Nature.

[54]  N. Krogan,et al.  The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II , 2004, Nature.

[55]  Jeffrey L. Wrana,et al.  Baf60c is essential for function of BAF chromatin remodelling complexes in heart development , 2004, Nature.

[56]  Y. Saijoh,et al.  Nodal antagonists regulate formation of the anteroposterior axis of the mouse embryo , 2004, Nature.

[57]  T. Peng,et al.  Development of Heart Failure and Congenital Septal Defects in Mice Lacking Endothelial Nitric Oxide Synthase , 2002, Circulation.

[58]  Hiroshi Hamada,et al.  Establishment of vertebrate left–right asymmetry , 2002, Nature Reviews Genetics.

[59]  R. Schwartz,et al.  Embryonic expression of an Nkx2‐5/Cre gene using ROSA26 reporter mice , 2001, Genesis.

[60]  J. Manley,et al.  Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination. , 2001, Molecular cell.

[61]  E. Stanley,et al.  Cardiac Septal and Valvular Dysmorphogenesis in Mice Heterozygous for Mutations in the Homeobox Gene Nkx2-5 , 2000, Circulation research.

[62]  T. Doetschman,et al.  Impaired Cardiac Performance in Heterozygous Mice with a Null Mutation in the Sarco(endo)plasmic Reticulum Ca2+-ATPase Isoform 2 (SERCA2) Gene* , 1999, The Journal of Biological Chemistry.

[63]  A. Copp,et al.  Versican expression is associated with chamber specification, septation, and valvulogenesis in the developing mouse heart. , 1998, Circulation research.

[64]  H. Hamada,et al.  Pitx2, a Bicoid-Type Homeobox Gene, Is Involved in a Lefty-Signaling Pathway in Determination of Left-Right Asymmetry , 1998, Cell.

[65]  S. Orkin,et al.  DNA-binding specificity of GATA family transcription factors , 1993, Molecular and cellular biology.

[66]  W. Claycomb,et al.  Preproenkephalin mRNA expression in developing rat heart and in cultured ventricular cardiac muscle cells. , 1989, The Biochemical journal.

[67]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[68]  윤호주.  전사인자(transcription factor)와 기관지천식 , 1999 .

[69]  D. Wilkinson.  In situ hybridization: a practical approach , 1998 .

[70]  M. Mckeown.  Regulation of alternative splicing. , 1990, Genetic engineering.