[en] Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRNs). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse engineer the GRNs of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types and inferred a coexpression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5,632 direct target genes through 24,926 enhancers. Using this network, we found network motifs, cis-regulatory codes, and regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions.
Disciplines :
Genetics & genetic processes
Author, co-author :
Potier, Delphine; University of Leuven > Center for Human Genetics > Laboratory of Computational Biology
Davie, Kristofer; University of Leuven > Center for Human Genetics > Laboratory of Computational Biology
Hulselmans, Gert; University of Leuven > Center for Human Genetics > Laboratory of Computational Biology
Naval Sanchez, Marina; Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology
Haagen, Lotte; Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology
Huynh-Thu, Vân Anh ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Koldere, Duygu; Bogazici University > Department of Molecular Biology and Genetics
Celik, Azu; Bogazici University > Department of Molecular Biology and Genetics
Geurts, Pierre ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique
Christiaens, Valérie; Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology
Aerts, Stein; Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology
Language :
English
Title :
Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference
Aerts S., Quan X.-J., Claeys A., Naval Sanchez M., Tate P., Yan J., Hassan B.A. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PLoS Biol. 2010, 8:e1000435.
Amore G., Casares F. Size matters: the contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network. Dev. Biol. 2010, 344:569-577.
Basso K., Margolin A.A., Stolovitzky G., Klein U., Dalla-Favera R., Califano A. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 2005, 37:382-390.
Bessa J., Gebelein B., Pichaud F., Casares F., Mann R.S. Combinatorial control of Drosophila eye development by eyeless, homothorax, and teashirt. Genes Dev. 2002, 16:2415-2427.
Blastyák A., Mishra R.K., Karch F., Gyurkovics H. Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between Grainyhead and Pleiohomeotic. Mol. Cell. Biol. 2006, 26:1434-1444.
Bonnet E., Michoel T., Van de Peer Y. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 2010, 26:i638-i644.
Calero-Nieto F.J., Ng F.S., Wilson N.K., Hannah R., Moignard V., Leal-Cervantes A.I., Jimenez-Madrid I., Diamanti E., Wernisch L., Göttgens B. Key regulators control distinct transcriptional programmes in blood progenitor and mast cells. EMBO J. 2014, 33:1212-1226.
Canon J., Banerjee U. Invivo analysis of a developmental circuit for direct transcriptional activation and repression in the same cell by a Runx protein. Genes Dev. 2003, 17:838-843.
Ciofani M., Madar A., Galan C., Sellars M., Mace K., Pauli F., Agarwal A., Huang W., Parkurst C.N., Muratet M., et al. A validated regulatory network for Th17 cell specification. Cell 2012, 151:289-303.
Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.-H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., et al. A genomic regulatory network for development. Science 2002, 295:1669-1678.
De Cegli R., Iacobacci S., Flore G., Gambardella G., Mao L., Cutillo L., Lauria M., Klose J., Illingworth E., Banfi S., di Bernardo D. Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. Nucleic Acids Res. 2013, 41:711-726.
Deplancke B., Mukhopadhyay A., Ao W., Elewa A.M., Grove C.A., Martinez N.J., Sequerra R., Doucette-Stamm L., Reece-Hoyes J.S., Hope I.A., et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125:1193-1205.
Ditch L.M., Shirangi T., Pitman J.L., Latham K.L., Finley K.D., Edeen P.T., Taylor B.J., McKeown M. Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors. Development 2005, 132:155-164.
Eden E., Navon R., Steinfeld I., Lipson D., Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009, 10:48.
Frankfort B.J., Nolo R., Zhang Z., Bellen H., Mardon G. senseless repression of rough is required for R8 photoreceptor differentiation in the developing Drosophila eye. Neuron 2001, 32:403-414.
Fuse N., Hirose S., Hayashi S. Diploidy of Drosophila imaginal cells is maintained by a transcriptional repressor encoded by escargot. Genes Dev. 1994, 8:2270-2281.
Gerstein M.B., Kundaje A., Hariharan M., Landt S.G., Yan K.-K., Cheng C., Mu X.J., Khurana E., Rozowsky J., Alexander R., et al. Architecture ofthe human regulatory network derived from ENCODE data. Nature 2012, 489:91-100.
Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., Hannett N.M., Tagne J.-B., Reynolds D.B., Yoo J., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
Herrmann C., Van de Sande B., Potier D., Aerts S. i-cisTarget: an integrative genomics method for the prediction of regulatory features andcis-regulatory modules. Nucleic Acids Res. 2012, 40:e114.
Huynh-Thu V.A., Irrthum A., Wehenkel L., Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 2010, 5:e12776.
Janky R., Verfaillie A., Imrichová H., Van de Sande B., Standaert L., Christiaens V., Hulselmans G., Herten K., Naval Sanchez M., Potier D., et al. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput. Biol. 2014, 10:e1003731.
Jenett A., Rubin G.M., Ngo T.-T.B., Shepherd D., Murphy C., Dionne H., Pfeiffer B.D., Cavallaro A., Hall D., Jeter J., et al. A GAL4-driver line resource for Drosophila neurobiology. Cell Rep 2012, 2:991-1001.
Jory A., Estella C., Giorgianni M.W., Slattery M., Laverty T.R., Rubin G.M., Mann R.S. A survey of 6,300 genomic fragments forcis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep 2012, 2:1014-1024.
Junion G., Spivakov M., Girardot C., Braun M., Gustafson E.H., Birney E., Furlong E.E.M. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 2012, 148:473-486.
Kemmeren P., Sameith K., van de Pasch L.A.L., Benschop J.J., Lenstra T.L., Margaritis T., O'Duibhir E., Apweiler E., van Wageningen S., Ko C.W., et al. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. Cell 2014, 157:740-752.
Le D.-H., Kwon Y.-K. A coherent feedforward loop design principle to sustain robustness of biological networks. Bioinformatics 2013, 29:630-637.
MacArthur S., Li X.-Y., Li J., Brown J.B., Chu H.C., Zeng L., Grondona B.P., Hechmer A., Simirenko L., Keränen S.V.E., et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009, 10:R80.
Mangan S., Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA 2003, 100:11980-11985.
Marbach D., Costello J.C., Küffner R., Vega N.M., Prill R.J., Camacho D.M., Allison K.R., Kellis M., Collins J.J., Stolovitzky G. Wisdom of crowds for robust gene network inference. Nat. Methods 2012, 9:796-804. DREAM5 Consortium.
McKay D.J., Lieb J.D. A common set of DNA regulatory elements shapes Drosophila appendages. Dev. Cell 2013, 27:306-318.
Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
Moses K., Ellis M.C., Rubin G.M. The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells. Nature 1989, 340:531-536.
Naval-Sánchez M., Potier D., Haagen L., Sánchez M., Munck S., Van de Sande B., Casares F., Christiaens V., Aerts S. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Res. 2013, 23:74-88.
Novershtern N., Subramanian A., Lawton L.N., Mak R.H., Haining W.N., McConkey M.E., Habib N., Yosef N., Chang C.Y., Shay T., et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 2011, 144:296-309.
Noyes M.B., Christensen R.G., Wakabayashi A., Stormo G.D., Brodsky M.H., Wolfe S.A. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008, 133:1277-1289.
Pavlidis P., Noble W.S. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2001, 2:H0042.
Pepple K.L., Atkins M., Venken K., Wellnitz K., Harding M., Frankfort B., Mardon G. Two-step selection of a single R8 photoreceptor: a bistable loop between senseless and rough locks in R8 fate. Development 2008, 135:4071-4079.
Pfreundt U., James D.P., Tweedie S., Wilson D., Teichmann S.A., Adryan B. FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res. 2010, 38(Database issue):D443-D447.
Quan X.J., Ramaekers A., Hassan B.A. Transcriptional control ofcell fate specification: lessons from the fly retina. Curr. Top. Dev. Biol. 2012, 98:259-276.
Roy S., Ernst J., Kharchenko P.V., Kheradpour P., Negre N., Eaton M.L., Landolin J.M., Bristow C.A., Ma L., Lin M.F., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797. modENCODE Consortium.
Sandmann T., Girardot C., Brehme M., Tongprasit W., Stolc V., Furlong E.E.M. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev. 2007, 21:436-449.
Schuettengruber B., Chourrout D., Vervoort M., Leblanc B., Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 2007, 128:735-745.
Spinelli L., Gambette P., Chapple C.E., Robisson B., Baudot A., Garreta H., Tichit L., Guénoche A., Brun C. Clust&See: a Cytoscape plugin for the identification, visualization and manipulation of network clusters. Biosystems 2013, 113:91-95.
Spokony, R., and White, K. (2012). Spokony insertions. http://flybase.org/reports/FBrf0220060.html.
St Pierre S.E., Ponting L., Stefancsik R., McQuilton P. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014, 42(Database issue):D780-D788. FlyBase Consortium.
Wang V.Y., Hassan B.A., Bellen H.J., Zoghbi H.Y. Drosophila atonal fully rescues the phenotype of Math1 null mice: new functions evolve in new cellular contexts. Curr. Biol. 2002, 12:1611-1616.
Warner J.B., Philippakis A.A., Jaeger S.A., He F.S., Lin J., Bulyk M.L. Systematic identification of mammalian regulatory motifs' target genes and functions. Nat. Methods 2008, 5:347-353.
Weirauch M.T., Yang A., Albu M., Cote A.G., Montenegro-Montero A., Drewe P., Najafabadi H.S., Lambert S.A., Mann I., Cook K., et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 2014, 158:1431-1443.
Yan H., Canon J., Banerjee U. A transcriptional chain linking eye specification to terminal determination of cone cells in the Drosophila eye. Dev. Biol. 2003, 263:323-329.
Yan J., Enge M., Whitington T., Dave K., Liu J., Sur I., Schmierer B., Jolma A., Kivioja T., Taipale M., Taipale J. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 2013, 154:801-813.
Yao L.-C., Blitz I.L., Peiffer D.A., Phin S., Wang Y., Ogata S., Cho K.W.Y., Arora K., Warrior R. Schnurri transcription factors from Drosophila and vertebrates can mediate Bmp signaling through a phylogenetically conserved mechanism. Development 2006, 133:4025-4034.
Yosef N., Shalek A.K., Gaublomme J.T., Jin H., Lee Y., Awasthi A., Wu C., Karwacz K., Xiao S., Jorgolli M., et al. Dynamic regulatory network controlling TH17 cell differentiation. Nature 2013, 496:461-468.
Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., Bernstein B.E., Nusbaum C., Myers R.M., Brown M., Li W., Liu X.S. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9:R137.
