The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option

Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.

[1]  R. Dixit,et al.  Neurog2 simultaneously activates and represses alternative gene expression programs in the developing neocortex. , 2013, Cerebral cortex.

[2]  Cory Y. McLean,et al.  PRISM offers a comprehensive genomic approach to transcription factor function prediction , 2013, Genome research.

[3]  G. Bourque,et al.  The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements , 2013, PLoS genetics.

[4]  Hani Z. Girgis,et al.  A High-Resolution Enhancer Atlas of the Developing Telencephalon , 2013, Cell.

[5]  S. Mcconnell,et al.  A network of genetic repression and derepression specifies projection fates in the developing neocortex , 2012, Proceedings of the National Academy of Sciences.

[6]  E. Furlong,et al.  Transcription factors: from enhancer binding to developmental control , 2012, Nature Reviews Genetics.

[7]  Gill Bejerano,et al.  Human Developmental Enhancers Conserved between Deuterostomes and Protostomes , 2012, PLoS genetics.

[8]  N. Šestan,et al.  Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex , 2012, Development.

[9]  Veronique Lefebvre,et al.  Cis-regulatory control of corticospinal system development and evolution , 2012, Nature.

[10]  A. Visel,et al.  Large-Scale Discovery of Enhancers from Human Heart Tissue , 2011, Nature Genetics.

[11]  Alignmen t Gridding Correlation Unionizer.  ALLEN Developing Mouse Brain Atlas , 2012 .

[12]  V. Tarabykin,et al.  A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons , 2011, PloS one.

[13]  Michael P. Eichenlaub,et al.  De Novo Genesis of Enhancers in Vertebrates , 2011, PLoS biology.

[14]  Pasko Rakic,et al.  Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing , 2011, Proceedings of the National Academy of Sciences.

[15]  A. Kriegstein,et al.  Development and Evolution of the Human Neocortex , 2011, Cell.

[16]  Z. Molnár.  Evolution of Cerebral Cortical Development , 2011, Brain, Behavior and Evolution.

[17]  J. Rubenstein,et al.  Annual Research Review: Development of the cerebral cortex: implications for neurodevelopmental disorders. , 2011, Journal of child psychology and psychiatry, and allied disciplines.

[18]  Mingfeng Li,et al.  TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract , 2011, Proceedings of the National Academy of Sciences.

[19]  J. Rubenstein,et al.  Tbr1 and Fezf2 Regulate Alternate Corticofugal Neuronal Identities during Neocortical Development , 2011, The Journal of Neuroscience.

[20]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2011 update , 2010, Nucleic Acids Res..

[21]  Jacques P. Bothma,et al.  Shadow Enhancers Foster Robustness of Drosophila Gastrulation , 2010, Current Biology.

[22]  A. Visel,et al.  ChIP-Seq identification of weakly conserved heart enhancers , 2010, Nature Genetics.

[23]  Tomomi Shimogori,et al.  Emergence of mammals by emergency: exaptation , 2010, Genes to cells : devoted to molecular & cellular mechanisms.

[24]  Rebecca D Hodge,et al.  Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex , 2010, Proceedings of the National Academy of Sciences.

[25]  G. K. Davis,et al.  Phenotypic robustness conferred by apparently redundant transcriptional enhancers , 2010, Nature.

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

[27]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[28]  Su Guo,et al.  A systematic approach to identify functional motifs within vertebrate developmental enhancers. , 2010, Developmental biology.

[29]  L. Richards,et al.  Multiple non-cell-autonomous defects underlie neocortical callosal dysgenesis in Nfib-deficient mice , 2009, Neural Development.

[30]  Ole Winther,et al.  Discovery of Regulatory Elements is Improved by a Discriminatory Approach , 2009, PLoS Comput. Biol..

[31]  L. Holland.  Chordate roots of the vertebrate nervous system: expanding the molecular toolkit , 2009, Nature Reviews Neuroscience.

[32]  A. Sharov,et al.  Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[33]  A. Visel,et al.  ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.

[34]  Ron Shamir,et al.  Allegro: Analyzing expression and sequence in concert to discover regulatory programs , 2009, Nucleic acids research.

[35]  B. Molyneaux,et al.  Bhlhb5 Regulates the Postmitotic Acquisition of Area Identities in Layers II-V of the Developing Neocortex , 2008, Neuron.

[36]  Qiang Li,et al.  cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation , 2008, Bioinform..

[37]  E. Zwarthoff,et al.  MN1 affects expression of genes involved in hematopoiesis and can enhance as well as inhibit RAR/RXR-induced gene expression. , 2008, Carcinogenesis.

[38]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[39]  N. Saitou,et al.  Possible involvement of SINEs in mammalian-specific brain formation , 2008, Proceedings of the National Academy of Sciences.

[40]  Tim J. P. Hubbard,et al.  NestedMICA as an ab initio protein motif discovery tool , 2008, BMC Bioinformatics.

[41]  P. Blackshear,et al.  Regulatory factor X4 variant 3: A transcription factor involved in brain development and disease , 2007, Journal of neuroscience research.

[42]  P. Arlotta,et al.  Neuronal subtype specification in the cerebral cortex , 2007, Nature Reviews Neuroscience.

[43]  David Haussler,et al.  Thousands of human mobile element fragments undergo strong purifying selection near developmental genes , 2007, Proceedings of the National Academy of Sciences.

[44]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[45]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[46]  D. Haussler,et al.  A distal enhancer and an ultraconserved exon are derived from a novel retroposon , 2006, Nature.

[47]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[48]  E. Lander,et al.  A large family of ancient repeat elements in the human genome is under strong selection. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[49]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[50]  Gerald E. Hough,et al.  Avian brains and a new understanding of vertebrate brain evolution , 2005, Nature Reviews Neuroscience.

[51]  L. Richards,et al.  The Transcription Factor Gene Nfib Is Essential for both Lung Maturation and Brain Development , 2005, Molecular and Cellular Biology.

[52]  Webb Miller,et al.  Evolution and functional classification of vertebrate gene deserts. , 2005, Genome research.

[53]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[54]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[55]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[56]  Jun S. Liu,et al.  An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments , 2002, Nature Biotechnology.

[57]  Alexander E. Kel,et al.  MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..

[58]  Graziano Pesole,et al.  An algorithm for finding signals of unknown length in DNA sequences , 2001, ISMB.

[59]  Kathleen Marchal,et al.  A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes , 2001, RECOMB.

[60]  Douglas L. Brutlag,et al.  BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes , 2000, Pacific Symposium on Biocomputing.

[61]  R. Gronostajski,et al.  Disruption of the murine nuclear factor I-A gene (Nfia) results in perinatal lethality, hydrocephalus, and agenesis of the corpus callosum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[62]  G. Church,et al.  Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation , 1998, Nature Biotechnology.

[63]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[64]  Matthew H. Kaufman,et al.  The Atlas of Mouse Development , 1992 .

[65]  R. Gronostajski.  Site-specific DNA binding of nuclear factor I: effect of the spacer region. , 1987, Nucleic acids research.

[66]  R. Britten,et al.  Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty , 1971, The Quarterly Review of Biology.