Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain

BackgroundThe basic/helix-loop-helix (bHLH) proteins are important components of the transcriptional regulatory network, controlling a variety of biological processes, especially the development of the central nervous system. Until now, reports describing the regulatory network of the bHLH transcription factor (TF) family have been scarce. In order to understand the regulatory mechanisms of bHLH TFs in mouse brain, we inferred their regulatory network from genome-wide gene expression profiles with the module networks method.ResultsA regulatory network comprising 15 important bHLH TFs and 153 target genes was constructed. The network was divided into 28 modules based on expression profiles. A regulatory-motif search shows the complexity and diversity of the network. In addition, 26 cooperative bHLH TF pairs were also detected in the network. This cooperation suggests possible physical interactions or genetic regulation between TFs. Interestingly, some TFs in the network regulate more than one module. A novel cross-repression between Neurod6 and Hey2 was identified, which may control various functions in different brain regions. The presence of TF binding sites (TFBSs) in the promoter regions of their target genes validates more than 70% of TF-target gene pairs of the network. Literature mining provides additional support for five modules. More importantly, the regulatory relationships among selected key components are all validated in mutant mice.ConclusionOur network is reliable and very informative for understanding the role of bHLH TFs in mouse brain development and function. It provides a framework for future experimental analyses.

[1]  T. Heinemeyer,et al.  Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms , 1999, Nucleic Acids Res..

[2]  Patrik D'haeseleer,et al.  Genetic network inference: from co-expression clustering to reverse engineering , 2000, Bioinform..

[3]  S. Pfaff,et al.  Transcriptional codes and the control of neuronal identity. , 2002, Annual review of neuroscience.

[4]  Thomas L Casavant,et al.  1274 full-open reading frames of transcripts expressed in the developing mouse nervous system. , 2004, Genome research.

[5]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[6]  W. Atchley,et al.  A natural classification of the basic helix-loop-helix class of transcription factors. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. Kessler,et al.  Interactions between ID and OLIG proteins mediate the inhibitory effects of BMP4 on oligodendroglial differentiation , 2004, Development.

[8]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[9]  S. Harrison,et al.  Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. , 1994, Genes & development.

[10]  M. Nakafuku,et al.  Dynamic expression of basic helix-loop-helix Olig family members: implication of Olig2 in neuron and oligodendrocyte differentiation and identification of a new member, Olig3 , 2000, Mechanisms of Development.

[11]  M. Uittenbogaard,et al.  Expression profiling upon Nex1/MATH‐2‐mediated neuritogenesis in PC12 cells and its implication in regeneration , 2004, Journal of neurochemistry.

[12]  M. Frotscher,et al.  Neuronal Basic Helix-Loop-Helix Proteins (NEX and BETA2/Neuro D) Regulate Terminal Granule Cell Differentiation in the Hippocampus , 2000, The Journal of Neuroscience.

[13]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[14]  Toshio Hakoshima,et al.  Structural basis for the diversity of DNA recognition by bZIP transcription factors , 2000, Nature Structural Biology.

[15]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[16]  Vladimir Batagelj,et al.  Pajek - Program for Large Network Analysis , 1999 .

[17]  Sergei Maslov,et al.  Detection of topological patterns in protein networks. , 2004, Genetic engineering.

[18]  Bing Zhang,et al.  GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies , 2004, BMC Bioinformatics.

[19]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[20]  M. Rosenfeld,et al.  Combinatorial codes in signaling and synergy: lessons from pituitary development. , 1999, Current opinion in genetics & development.

[21]  A. Blais,et al.  Constructing transcriptional regulatory networks. , 2005, Genes & development.

[22]  Ron Shamir,et al.  Computational expansion of genetic networks , 2001, ISMB.

[23]  M. Wegner,et al.  Induction of oligodendrocyte differentiation by Olig2 and Sox10: evidence for reciprocal interactions and dosage-dependent mechanisms. , 2007, Developmental biology.

[24]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[25]  R. Young,et al.  Transcription of eukaryotic protein-coding genes. , 2000, Annual review of genetics.

[26]  C. Goding,et al.  Single amino acid substitutions alter helix‐loop‐helix protein specificity for bases flanking the core CANNTG motif. , 1992, The EMBO journal.

[27]  M. Ishibashi.  Molecular mechanisms for morphogenesis of the central nervous system in mammals , 2004, Anatomical science international.

[28]  M. Vervoort,et al.  The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. , 2001, Genome research.

[29]  C. Bode,et al.  LE-PAS, a novel Arnt-dependent HLH-PAS protein, is expressed in limbic tissues and transactivates the CNS midline enhancer element. , 2004, Brain research. Molecular brain research.

[30]  J. Briscoe,et al.  Specification of neuronal fates in the ventral neural tube , 2001, Current Opinion in Neurobiology.

[31]  Nir Friedman,et al.  Inferring subnetworks from perturbed expression profiles , 2001, ISMB.

[32]  F. Corpet.  Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.

[33]  Daphne Koller,et al.  Genome-wide discovery of transcriptional modules from DNA sequence and gene expression , 2003, ISMB.

[34]  A. Simeone,et al.  Positioning the isthmic organizer where Otx2 and Gbx2meet. , 2000, Trends in genetics : TIG.

[35]  Joanne Chan,et al.  Sonic Hedgehog–Regulated Oligodendrocyte Lineage Genes Encoding bHLH Proteins in the Mammalian Central Nervous System , 2000, Neuron.

[36]  U. Francke,et al.  Molecular characterization of two mammalian bHLH-PAS domain proteins selectively expressed in the central nervous system. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Amos Tanay,et al.  Minreg: Inferring an active regulator set , 2002, ISMB.

[38]  Valérie Ledent,et al.  Phylogenetic analysis of the human basic helix-loop-helix proteins , 2002, Genome Biology.

[39]  Q. Lu,et al.  Myelinogenesis and Axonal Recognition by Oligodendrocytes in Brain Are Uncoupled in Olig1-Null Mice , 2005, The Journal of Neuroscience.

[40]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[41]  K. Ligon,et al.  Olig gene function in CNS development and disease , 2006, Glia.

[42]  J. Smith,et al.  Gradual refinement of activin-induced thresholds requires protein synthesis. , 2000, Developmental biology.

[43]  C. Garvie,et al.  Recognition of specific DNA sequences. , 2001, Molecular cell.

[44]  David J Anderson,et al.  Identification of a Novel Family of Oligodendrocyte Lineage-Specific Basic Helix–Loop–Helix Transcription Factors , 2000, Neuron.

[45]  Zhiping Weng,et al.  PromoSer: a large-scale mammalian promoter and transcription start site identification service , 2003, Nucleic Acids Res..

[46]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[47]  G. Stein,et al.  NeuroD: the predicted and the surprising. , 2004, Molecules and cells.

[48]  A. Ferré-D’Amaré,et al.  Structure and function of the b/HLH/Z domain of USF. , 1994, The EMBO journal.

[49]  H. Nakamura,et al.  Pax6 defines the di-mesencephalic boundary by repressing En1 and Pax2. , 2000, Development.

[50]  Yang Liu,et al.  Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis , 2004, Science.

[51]  Alfred L. Fisher,et al.  The function of hairy‐related bHLH repressor proteins in cell fate decisions , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[52]  K. Davis,et al.  Convergent evidence that oligodendrocyte lineage transcription factor 2 (OLIG2) and interacting genes influence susceptibility to schizophrenia , 2006, Proceedings of the National Academy of Sciences.

[53]  David J. Anderson,et al.  The bHLH Transcription Factors OLIG2 and OLIG1 Couple Neuronal and Glial Subtype Specification , 2002, Cell.

[54]  E. Dodou,et al.  N-twist, an evolutionarily conserved bHLH protein expressed in the developing CNS, functions as a transcriptional inhibitor. , 2002, Developmental biology.

[55]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[56]  A. Kho,et al.  Cerebellar ‘transcriptome’ reveals cell-type and stage-specific expression during postnatal development and tumorigenesis , 2006, Molecular and Cellular Neuroscience.

[57]  R. Milo,et al.  Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Peter A Lawrence,et al.  Morphogens, Compartments, and Pattern: Lessons from Drosophila? , 1996, Cell.

[59]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[60]  Y. Kyōgoku,et al.  Crystal structure of PHO4 bHLH domain–DNA complex: flanking base recognition , 1997, The EMBO journal.

[61]  Thomas Werner,et al.  LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts , 2005, Nucleic Acids Res..

[62]  Koichi Saito,et al.  Identification of a Novel Basic Helix-Loop-Helix-PAS Factor, NXF, Reveals a Sim2 Competitive, Positive Regulatory Role in Dendritic-Cytoskeleton Modulator Drebrin Gene Expression , 2004, Molecular and Cellular Biology.