2024
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
Pratt H, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal M, Geschwind D, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science Advances 2024, 10: eadj4452. PMID: 38781344, PMCID: PMC11114231, DOI: 10.1126/sciadv.adj4452.Peer-Reviewed Original ResearchConceptsEpigenetic dataCell-type-specific gene regulationCis-regulatory elementsComprehensive atlasGenetic variants associated with psychiatric disordersLineage-specific transcription factorsBrain cell typesMammalian elementsPsychENCODE ConsortiumNoncoding regionsEvolutionary historyGene regulationRegulatory elementsSequence mutationsTranscription factorsSequence syntaxRegulatory informationPrimate-specific sequencesBinding sitesHuman traitsCell typesFunctional implicationsPsychiatric disordersSequenceFetal brain developmentLess-is-more: selecting transcription factor binding regions informative for motif inference
Xu J, Gao J, Ni P, Gerstein M. Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic Acids Research 2024, 52: e20-e20. PMID: 38214231, PMCID: PMC10899791, DOI: 10.1093/nar/gkad1240.Peer-Reviewed Original ResearchConceptsChIP-seq signalsChIP-seqGenomic regionsMotif inferenceTranscription factorsTargeting motifTranscription factor binding regionsChIP-seq datasetsNon-specific interactionsC-scoreDNA motifsBinding regionMotifTranscriptionTF signalingAccurate inferenceStronger signalSignalDNARegionTargetInteraction
2012
Architecture of the human regulatory network derived from ENCODE data
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O’Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489: 91-100. PMID: 22955619, PMCID: PMC4154057, DOI: 10.1038/nature11245.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineDNAEncyclopedias as TopicGATA1 Transcription FactorGene Expression ProfilingGene Regulatory NetworksGenome, HumanGenomicsHumansK562 CellsMolecular Sequence AnnotationOrgan SpecificityPhosphorylationPolymorphism, Single NucleotideProtein Interaction MapsRegulatory Sequences, Nucleic AcidRNA, UntranslatedSelection, GeneticTranscription FactorsTranscription Initiation SiteConceptsTranscription factorsRegulatory networksHuman transcriptional regulatory networkHuman regulatory networkSpecific genomic locationsTranscription-related factorsState of genesTranscriptional regulatory networksAllele-specific activityPersonal genome sequencesGenomic locationStrong selectionGenome sequenceENCODE dataGenomic informationInformation-flow bottlenecksRegulatory informationConnected network componentsCombinatorial fashionInfluences expressionHuman biologyBinding informationNetwork motifsCo-associationGenes
2010
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Consortium M, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 2010, 330: 1775-1787. PMID: 21177976, PMCID: PMC3142569, DOI: 10.1126/science.1196914.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansCaenorhabditis elegans ProteinsChromatinChromosomesComputational BiologyConserved SequenceEvolution, MolecularGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksGenes, HelminthGenome, HelminthGenomicsHistonesModels, GeneticMolecular Sequence AnnotationRegulatory Sequences, Nucleic AcidRNA, HelminthRNA, UntranslatedTranscription FactorsConceptsAccurate gene modelsGenome-wide identificationTranscription factor-binding sitesKey model organismTranscription factor bindingAlternative splice formsFactor-binding sitesChromatin compositionModENCODE projectChromatin organizationHistone modificationsGenome annotationModel organismsNematode CaenorhabditisChromosomal locationPutative functionsGene modelsTranscriptome profilingChromosome armsTranscription factorsNoncoding RNAsFactor bindingSplice formsX chromosomeGene expression
2006
Genomic analysis of the hierarchical structure of regulatory networks
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 14724-14731. PMID: 17003135, PMCID: PMC1595419, DOI: 10.1073/pnas.0508637103.Peer-Reviewed Original ResearchConceptsTranscription factorsMaster transcription factorRegulatory networksRegulatory hierarchyProtein-protein interaction networkMost transcription factorsExpression of thousandsExpression level changesGenomic analysisProtein interactionsInteraction networksTarget genesDirect targetGenesEukaryotesProkaryotesCellsFundamental questionsBiologyTargetExpression
2004
Genomic analysis of regulatory network dynamics reveals large topological changes
Luscombe NM, Madan Babu M, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431: 308-312. PMID: 15372033, DOI: 10.1038/nature02782.Peer-Reviewed Original ResearchConceptsTranscription factorsActive transcription factorRegulatory network dynamicsBiological networksHigher eukaryotesLarge-scale topological changesGenomic scaleGenomic analysisCell cycleDiverse stimuliEnvironmental responsesMolecular biologyFast signal propagationTwo-tiered hierarchyNetwork analysisGlobal topological measuresLocal motifsSub-network structureEukaryotesTemporal progression