Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis

Abstract Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.

[1]  Sudipto Roy,et al.  Distinct requirements of E2f4 versus E2f5 activity for multiciliated cell development in the zebrafish embryo. , 2018, Developmental biology.

[2]  Ian Quigley,et al.  Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts , 2018, Scientific Reports.

[3]  O. Moskvin,et al.  Zebrafish Rfx4 controls dorsal and ventral midline formation in the neural tube , 2018, Developmental dynamics : an official publication of the American Association of Anatomists.

[4]  J. Kere,et al.  Characterization of the human RFX transcription factor family by regulatory and target gene analysis , 2018, BMC Genomics.

[5]  Q. Lu,et al.  IL-6/STAT3 pathway induced deficiency of RFX1 contributes to Th17-dependent autoimmune diseases via epigenetic regulation , 2018, Nature Communications.

[6]  J. Reiter,et al.  Genes and molecular pathways underpinning ciliopathies , 2017, Nature Reviews Molecular Cell Biology.

[7]  N. Spassky,et al.  The development and functions of multiciliated epithelia , 2017, Nature Reviews Molecular Cell Biology.

[8]  Anushya Muruganujan,et al.  PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements , 2016, Nucleic Acids Res..

[9]  J. Azimzadeh,et al.  Multiciliated Cells in Animals. , 2016, Cold Spring Harbor perspectives in biology.

[10]  Ian K Quigley,et al.  Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression , 2016, bioRxiv.

[11]  D. Schild,et al.  TAp73 is a central transcriptional regulator of airway multiciliogenesis , 2016, Genes & development.

[12]  Camille Stephan-Otto Attolini,et al.  GEMC1 is a critical regulator of multiciliated cell differentiation , 2016, The EMBO journal.

[13]  Bo Wang,et al.  RFX1 maintains testis cord integrity by regulating the expression of Itga6 in male mouse embryos , 2016, Molecular reproduction and development.

[14]  B. A. Hamilton,et al.  Zfp423 Regulates Sonic Hedgehog Signaling via Primary Cilium Function , 2016, bioRxiv.

[15]  L. Attardi,et al.  p73 and FoxJ1: Programming Multiciliated Epithelia. , 2016, Trends in cell biology.

[16]  Bryan J. Venters,et al.  p73 Is Required for Multiciliogenesis and Regulates the Foxj1-Associated Gene Network. , 2016, Cell reports.

[17]  S. Taraviras,et al.  GemC1 controls multiciliogenesis in the airway epithelium , 2016, EMBO reports.

[18]  K. O’Connell,et al.  The E2F-DP1 Transcription Factor Complex Regulates Centriole Duplication in Caenorhabditis elegans , 2016, G3: Genes, Genomes, Genetics.

[19]  Sudipto Roy,et al.  Gmnc Is a Master Regulator of the Multiciliated Cell Differentiation Program , 2015, Current Biology.

[20]  David J. Eisenman,et al.  RFX transcription factors are essential for hearing in mice , 2015, Nature Communications.

[21]  B. Durand,et al.  RFX2 Is a Major Transcriptional Regulator of Spermiogenesis , 2015, PLoS genetics.

[22]  B. Futcher,et al.  A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression , 2015, Nucleic acids research.

[23]  C. Janke,et al.  Ependymal cell differentiation, from monociliated to multiciliated cells. , 2015, Methods in cell biology.

[24]  R. Pierce,et al.  Myb Permits Multilineage Airway Epithelial Cell Differentiation , 2014, Stem cells.

[25]  H. Omran,et al.  Multicilin drives centriole biogenesis via E2f proteins , 2014, Genes & development.

[26]  E. Marcotte,et al.  Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement , 2014, Genomics data.

[27]  B. Stefanovic,et al.  RFX7 is required for the formation of cilia in the neural tube , 2014, Mechanisms of Development.

[28]  Sudipto Roy,et al.  Switching on cilia: transcriptional networks regulating ciliogenesis , 2014, Development.

[29]  Yin-Won Lee,et al.  Transcription Factor RFX1 Is Crucial for Maintenance of Genome Integrity in Fusarium graminearum , 2014, Eukaryotic Cell.

[30]  E. Marcotte,et al.  Coordinated genomic control of ciliogenesis and cell movement by RFX2 , 2014, eLife.

[31]  Tao Liu,et al.  Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells. , 2014, Methods in molecular biology.

[32]  M. Krasnow,et al.  Myb promotes centriole amplification and later steps of the multiciliogenesis program , 2013, Development.

[33]  Gabrielle Wheway,et al.  The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium , 2013, Cilia.

[34]  J. Henriksson,et al.  Finding ciliary genes: a computational approach. , 2013, Methods in enzymology.

[35]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[36]  Marc D. Perry,et al.  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.

[37]  M. Brueckner,et al.  RFX2 is essential in the ciliated organ of asymmetry and an RFX2 transgene identifies a population of ciliated cells sufficient for fluid flow. , 2012, Developmental biology.

[38]  Kriston L. McGary,et al.  RFX2 is broadly required for ciliogenesis during vertebrate development. , 2012, Developmental biology.

[39]  J. Armstrong,et al.  The Gene Regulatory Cascade Linking Proneural Specification with Differentiation in Drosophila Sensory Neurons , 2011, PLoS biology.

[40]  B. Durand,et al.  Transcriptional control of genes involved in ciliogenesis: a first step in making cilia , 2010, Biology of the cell.

[41]  P. Swoboda,et al.  Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals , 2010, Proceedings of the National Academy of Sciences.

[42]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[43]  Philipp Bucher,et al.  The Transcription Factor Rfx3 Regulates β-Cell Differentiation, Function, and Glucokinase Expression , 2010, Diabetes.

[44]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[45]  C. Orvain,et al.  Rfx6 is an Ngn3-dependent winged helix transcription factor required for pancreatic islet cell development , 2010, Development.

[46]  K. Dewar,et al.  Rfx6 Directs Islet Formation and Insulin Production in Mice and Humans , 2009, Nature.

[47]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[48]  P Piasecki Brian,et al.  動物における繊毛遺伝子の調節因子X(RFX)仲介転写再配線 , 2010 .

[49]  Nansheng Chen,et al.  Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans , 2010, BMC Evolutionary Biology.

[50]  Youngshik Choe,et al.  The Rfx4 Transcription Factor Modulates Shh Signaling by Regional Control of Ciliogenesis , 2009, Science Signaling.

[51]  Z. Zuo,et al.  Knockout of the regulatory factor X1 gene leads to early embryonic lethality. , 2009, Biochemical and biophysical research communications.

[52]  B. Durand,et al.  RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies , 2009, Journal of Cell Science.

[53]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[54]  Graziano Pesole,et al.  Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes , 2009, Nucleic Acids Res..

[55]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[56]  Sudipto Roy,et al.  Foxj1 transcription factors are master regulators of the motile ciliogenic program , 2008, Nature Genetics.

[57]  B. Durand,et al.  Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species , 2007, Genome Biology.

[58]  R. Bronson,et al.  E2f4 is required for normal development of the airway epithelium. , 2007, Developmental biology.

[59]  Carine Benadiba,et al.  Novel Function of the Ciliogenic Transcription Factor RFX3 in Development of the Endocrine Pancreas , 2007, Diabetes.

[60]  Sunduz Keles,et al.  Statistical Applications in Genetics and Molecular Biology Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo , 2011 .

[61]  S. Brody,et al.  A transgenic FOXJ1-Cre system for gene inactivation in ciliated epithelial cells. , 2007, American journal of respiratory cell and molecular biology.

[62]  William Stafford Noble,et al.  Quantifying similarity between motifs , 2007, Genome Biology.

[63]  B. Durand,et al.  A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells , 2006, The European journal of neuroscience.

[64]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Gary Ruvkun,et al.  Analysis of xbx genes in C. elegans , 2005, Development.

[66]  A. Kierzek,et al.  Identification of New Genes Regulated by the Crt1 Transcription Factor, an Effector of the DNA Damage Checkpoint Pathway in Saccharomyces cerevisiae* , 2005, Journal of Biological Chemistry.

[67]  W. Kistler,et al.  RFX2 Is a Potential Transcriptional Regulatory Factor for Histone H1t and Other Genes Expressed During the Meiotic Phase of Spermatogenesis1 , 2004, Biology of reproduction.

[68]  C. Ucla,et al.  The Transcription Factor RFX3 Directs Nodal Cilium Development and Left-Right Asymmetry Specification , 2004, Molecular and Cellular Biology.

[69]  B. Gomperts,et al.  Foxj1 regulates basal body anchoring to the cytoskeleton of ciliated pulmonary epithelial cells , 2004, Journal of Cell Science.

[70]  Wyeth W. Wasserman,et al.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..

[71]  S. Brody,et al.  Foxj1 is required for apical localization of ezrin in airway epithelial cells , 2003, Journal of Cell Science.

[72]  I. Cobos,et al.  Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4 , 2003, Development.

[73]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[74]  Maurice Kernan,et al.  Drosophila Regulatory factor X is necessary for ciliated sensory neuron differentiation , 2002, Development.

[75]  W. Reith,et al.  The bare lymphocyte syndrome and the regulation of MHC expression. , 2001, Annual review of immunology.

[76]  S. Shapiro,et al.  Ciliogenesis and left-right axis defects in forkhead factor HFH-4-null mice. , 2000, American journal of respiratory cell and molecular biology.

[77]  J. Thomas,et al.  The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. elegans. , 2000, Molecular cell.

[78]  Stephen K. Burley,et al.  Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding , 2000, Nature.

[79]  R. Aebersold,et al.  A gene encoding a novel RFX-associated transactivator is mutated in the majority of MHC class II deficiency patients , 1998, Nature Genetics.

[80]  S. Elledge,et al.  The DNA Replication and Damage Checkpoint Pathways Induce Transcription by Inhibition of the Crt1 Repressor , 1998, Cell.

[81]  P. Emery,et al.  RFX proteins, a novel family of DNA binding proteins conserved in the eukaryotic kingdom. , 1996, Nucleic acids research.

[82]  M. McLeod,et al.  The sak1+ gene of Schizosaccharomyces pombe encodes an RFX family DNA-binding protein that positively regulates cyclic AMP-dependent protein kinase-mediated exit from the mitotic cell cycle , 1995, Molecular and cellular biology.

[83]  K. Rajewsky,et al.  A cre-transgenic mouse strain for the ubiquitous deletion of loxP-flanked gene segments including deletion in germ cells. , 1995, Nucleic acids research.

[84]  C. Ucla,et al.  RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins , 1994, Molecular and cellular biology.

[85]  W. Reith,et al.  The DNA-binding defect observed in major histocompatibility complex class II regulatory mutants concerns only one member of a family of complexes binding to the X boxes of class II promoters , 1992, Molecular and cellular biology.

[86]  W. Reith,et al.  MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. , 1990, Genes & development.

[87]  W. Reith,et al.  Congenital immunodeficiency with a regulatory defect in MHC class II gene expression lacks a specific HLA-DR promoter binding protein, RF-X , 1988, Cell.