Organization of developmental enhancers in the Drosophila embryo

Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory ‘grammar’ of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid–Bicoid, Hunchback–Hunchback, Bicoid–Dorsal, Bicoid–Caudal and Dorsal–Twist. Direct evidence is presented for the importance of Bicoid–Dorsal linkage in the integration of the anterior–posterior and dorsal–ventral patterning systems. Hunchback–Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo.

[1]  John R. ten Bosch,et al.  The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription , 2006, Development.

[2]  Johannes Jaeger,et al.  On the dynamic nature of positional information. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[3]  C. Napoli,et al.  Mediator complexes and eukaryotic transcription regulation: an overview. , 2007, Biochimie.

[4]  Michael Levine,et al.  Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo , 2002, Cell.

[5]  Marc S Halfon,et al.  A combinatorial code for pattern formation in Drosophila oogenesis. , 2008, Developmental cell.

[6]  M. Metzstein,et al.  The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila , 2008, Nature.

[7]  Robert P Zinzen,et al.  A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas , 2006, Nucleic acids research.

[8]  Victor G. Levitsky,et al.  NPRD: Nucleosome Positioning Region Database , 2004, Nucleic Acids Res..

[9]  M. Levine,et al.  Computational Models for Neurogenic Gene Expression in the Drosophila Embryo , 2006, Current Biology.

[10]  Jens C. Brüning,et al.  Single copy shRNA configuration for ubiquitous gene knockdown in mice , 2005, Nucleic acids research.

[11]  Dmitri Papatsenko,et al.  Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Haussler,et al.  UCSC genome browser tutorial. , 2008, Genomics.

[13]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[14]  Dmitri Papatsenko,et al.  The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Connelly,et al.  Polyamines eliminate an extreme size bias against transformation of large yeast artificial chromosome DNA. , 1991, Genomics.

[16]  Victor G. Levitsky,et al.  Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis , 2001, Bioinform..

[17]  M. Levine,et al.  Activation and repression of transcription by the gap proteins hunchback and Krüppel in cultured Drosophila cells. , 1991, Genes & development.

[18]  Dmitri A. Papatsenko,et al.  ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors , 2007, Bioinform..

[19]  Steven M. Gallo,et al.  REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila , 2007, Nucleic Acids Res..

[20]  Dmitri Papatsenko,et al.  A rationale for the enhanceosome and other evolutionarily constrained enhancers , 2007, Current Biology.

[21]  M. Levine,et al.  Short-range repression permits multiple enhancers to function autonomously within a complex promoter. , 1994, Genes & development.

[22]  E. Davidson,et al.  Gene regulatory networks for development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  M Ptashne,et al.  Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix. , 1986, Cell.

[24]  Michael Levine,et al.  Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen , 1993, Cell.

[25]  J. Fak,et al.  Transcriptional Control in the Segmentation Gene Network of Drosophila , 2004, PLoS biology.

[26]  Diethard Tautz,et al.  A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo , 1990, Nature.

[27]  M. Levine,et al.  Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo. , 2005, Developmental biology.

[28]  Inna Dubchak,et al.  Conservation patterns in different functional sequence categories of divergent Drosophila species. , 2005, Genomics.

[29]  John Reinitz,et al.  A database for management of gene expression data in situ , 2004, Bioinform..

[30]  David N. Arnosti,et al.  dCtBP-Dependent and -Independent Repression Activities of the Drosophila Knirps Protein , 2000, Molecular and Cellular Biology.

[31]  F. van Roy,et al.  Low nucleosome occupancy is encoded around functional human transcription factor binding sites , 2008, BMC Genomics.

[32]  S. Carroll,et al.  Control of a Genetic Regulatory Network by a Selector Gene , 2001, Science.

[33]  Boris Lenhard,et al.  Genomic regulatory blocks underlie extensive microsynteny conservation in insects. , 2007, Genome research.

[34]  Young-Joon Kim,et al.  Interactions between subunits of Drosophila Mediator and activator proteins. , 2005, Trends in biochemical sciences.

[35]  Peter W. Markstein,et al.  Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Levine,et al.  Multiple modes of dorsal‐bHLH transcriptional synergy in the Drosophila embryo. , 1995, The EMBO journal.

[37]  M. Fujioka,et al.  Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients. , 1999, Development.

[38]  Anna G. Nazina,et al.  Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. , 2002, Genome research.

[39]  Peter W. Markstein,et al.  A regulatory code for neurogenic gene expression in the Drosophila embryo , 2004, Development.

[40]  Michael Ashburner,et al.  Drosophila melanogaster: a case study of a model genomic sequence and its consequences. , 2005, Genome research.

[41]  D. Papatsenko,et al.  How the Dorsal gradient works: Insights from postgenome technologies , 2008, Proceedings of the National Academy of Sciences.

[42]  N. Patel,et al.  Evidence for stabilizing selection in a eukaryotic enhancer element , 2000, Nature.

[43]  P. V. von Hippel,et al.  Facilitated Target Location in Biological Systems* , 2022 .

[44]  W. Bialek,et al.  Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient , 2007, Cell.

[45]  M. Levine,et al.  Transcriptional regulation of a pair-rule stripe in Drosophila. , 1991, Genes & development.

[46]  Jun Ma,et al.  Interplay between positive and negative activities that influence the role of Bicoid in transcription , 2005, Nucleic acids research.

[47]  Dmitri Papatsenko,et al.  A self-organizing system of repressor gradients establishes segmental complexity in Drosophila , 2003, Nature.

[48]  M. Ptashne,et al.  Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix , 1986, Cell.

[49]  Michael Levine,et al.  Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Anna G. Nazina,et al.  Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. , 2003, Nucleic acids research.

[51]  Z. Weng,et al.  The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome , 2008, PLoS genetics.

[52]  John Reinitz,et al.  Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Levine,et al.  Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. , 1991, Science.

[54]  L. Mirny,et al.  How gene order is influenced by the biophysics of transcription regulation , 2007, Proceedings of the National Academy of Sciences.

[55]  Alan M. Moses,et al.  Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis , 2007, PloS one.

[56]  Mireille Régnier,et al.  Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression , 2006, Bioinform..

[57]  Chen Zhao,et al.  Target Selectivity of Bicoid Is Dependent on Nonconsensus Site Recognition and Protein-Protein Interaction , 2000, Molecular and Cellular Biology.

[58]  M. Q. Zhang,et al.  Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Michael Levine,et al.  Whole-genome analysis of Drosophila gastrulation. , 2004, Current opinion in genetics & development.

[60]  N. Barkai,et al.  Two strategies for gene regulation by promoter nucleosomes. , 2008, Genome research.

[61]  D. Thanos,et al.  Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression , 2008, Cell.

[62]  M. Levine,et al.  dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo. , 1992, Genes & development.

[63]  Anna G. Nazina,et al.  Homotypic regulatory clusters in Drosophila. , 2003, Genome research.

[64]  Colin N. Dewey,et al.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , 2007, Nature.

[65]  Claude Desplan,et al.  Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila , 1994, Cell.

[66]  L. Mirny,et al.  Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. , 2004, Biophysical journal.

[67]  P. Georgiev,et al.  Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus , 2008, Molecular and Cellular Biology.

[68]  Melanie A. Huntley,et al.  Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.

[69]  D. Papatsenko,et al.  Dual regulation by the Hunchback gradient in the Drosophila embryo , 2008, Proceedings of the National Academy of Sciences.