Featured Publications
Regulation of prefrontal patterning and connectivity by retinoic acid
Shibata M, Pattabiraman K, Lorente-Galdos B, Andrijevic D, Kim SK, Kaur N, Muchnik SK, Xing X, Santpere G, Sousa AMM, Sestan N. Regulation of prefrontal patterning and connectivity by retinoic acid. Nature 2021, 598: 483-488. PMID: 34599305, PMCID: PMC9018119, DOI: 10.1038/s41586-021-03953-x.Peer-Reviewed Original ResearchConceptsPrefrontal cortexRetinoic acidGranular layer 4Neocortex of humansRetinoic acid signalingCerebral cortexRetinoic acid receptorsMotor cortexMotor areaMediodorsal thalamusFetal developmentCortical expansionAcid receptorsGenetic deletionDendritic spinogenesisLayer 4Synthesizing enzymesCortexAcid signalingNeural developmentMiceCritical roleSignalingThalamusSpinogenesis
2023
Molecular and cellular mechanisms of human cortical connectivity
Luria V, Ma S, Shibata M, Pattabiraman K, Sestan N. Molecular and cellular mechanisms of human cortical connectivity. Current Opinion In Neurobiology 2023, 80: 102699. PMID: 36921362, DOI: 10.1016/j.conb.2023.102699.Peer-Reviewed Original Research
2021
Transcriptional network orchestrating regional patterning of cortical progenitors
Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2024795118. PMID: 34921112, PMCID: PMC8713794, DOI: 10.1073/pnas.2024795118.Peer-Reviewed Original ResearchConceptsRegional patterningEnhancer-gene interactionsTranscription factor networkTF ChIP-seqExpression of hundredsCortical progenitorsVentricular zoneRadial glial stem cellsMutant miceEpigenomic marksTF networksDNA accessibilityGenomic programmingTranscriptional networksGlial stem cellsFactor networkChIP-seqStem cellsVZ cellsPatterningProgenitorsEnhancerMouse cortexExpressionCellsHominini-specific regulation of CBLN2 increases prefrontal spinogenesis
Shibata M, Pattabiraman K, Muchnik SK, Kaur N, Morozov YM, Cheng X, Waxman SG, Sestan N. Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis. Nature 2021, 598: 489-494. PMID: 34599306, PMCID: PMC9018127, DOI: 10.1038/s41586-021-03952-y.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalcium-Binding ProteinsDendritesEnhancer Elements, GeneticFemaleHumansIntercellular Signaling Peptides and ProteinsMacacaMental DisordersMiceNerve Tissue ProteinsNervous System DiseasesNeural Cell Adhesion MoleculesPhylogenyPrefrontal CortexPromoter Regions, GeneticSOXD Transcription FactorsTranscriptomeUp-RegulationConceptsCerebellin 2Prefrontal cortexCerebral cortex regionsDendritic spine formationInitiation of synaptogenesisLaminar distributionDendritic spinesNervous systemNeuropsychiatric disordersSpine formationLevel of expressionCortex regionsGenetic humanizationCortical gradientsDisproportionate increaseSpecies differencesNeurexinsSpinogenesisDysfunctionMolecular basisPathogenesisExpressionCortexSynaptogenesisSpine
2020
The evolution of the human brain and disease susceptibility
Pattabiraman K, Muchnik SK, Sestan N. The evolution of the human brain and disease susceptibility. Current Opinion In Genetics & Development 2020, 65: 91-97. PMID: 32629339, DOI: 10.1016/j.gde.2020.05.004.Peer-Reviewed Original ResearchConceptsGene expression patternsField of evolutionDisease risk genesNervous system developmentExtant speciesGene regulationEvolutionary changeExtinct ancestorsExpression patternsGenetic studiesMetabolic processesHuman-specific aspectsRisk genesCell typesHuman biologyEvolutionary perspectiveDisease susceptibilityNeurodegenerative disease riskNeurodegenerative diseasesDifficult hypothesisComplex processGenomicsAncestorEvolutionGenes
2016
Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate
Silberberg SN, Taher L, Lindtner S, Sandberg M, Nord AS, Vogt D, Mckinsey GL, Hoch R, Pattabiraman K, Zhang D, Ferran JL, Rajkovic A, Golonzhka O, Kim C, Zeng H, Puelles L, Visel A, Rubenstein JLR. Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. Neuron 2016, 92: 59-74. PMID: 27710791, PMCID: PMC5063253, DOI: 10.1016/j.neuron.2016.09.027.Peer-Reviewed Original ResearchConceptsGABAergic cell fateEnhancer activityTranscriptional regulationCell fateNovel molecular mechanismStable transgenic mouse linesTranscriptional circuitryTransgenic linesTranscription factorsTranscriptional mechanismsDifferent enhancer elementsFate mapEnhancer elementsMolecular mechanismsTransgenic mouse lineForebrain developmentDistinct domainsMouse linesRegulationAmygdala neuronsBasal gangliaFateSpecific subtypesMutantsUnique tool
2015
Genomic Perspectives of Transcriptional Regulation in Forebrain Development
Nord AS, Pattabiraman K, Visel A, Rubenstein JL. Genomic Perspectives of Transcriptional Regulation in Forebrain Development. Neuron 2015, 85: 27-47. PMID: 25569346, PMCID: PMC4438709, DOI: 10.1016/j.neuron.2014.11.011.Peer-Reviewed Original ResearchConceptsCis-acting genomic elementsForebrain developmentGene expression statesGene expression programsAnalysis of chromatinGenomic regulatory mechanismsGenetic circuitryGenomic perspectiveExpression programsGenomic elementsTranscriptional regulationExpression statesHigher-order brain functionsTranscription factorsDNA modificationsGene expressionRegulatory mechanismsHuman neuropsychiatric disordersGenetic defectsCurrent knowledgeChromatinRecent progressEnhancerNeuropsychiatric disordersRegulation
2014
Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex
Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JL. Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex. Neuron 2014, 82: 989-1003. PMID: 24814534, PMCID: PMC4104757, DOI: 10.1016/j.neuron.2014.04.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCerebral CortexCOUP Transcription Factor IEnhancer Elements, GeneticEye ProteinsGene Expression Regulation, DevelopmentalHippocampusHomeodomain ProteinsHumansMiceMice, TransgenicPaired Box Transcription FactorsPAX6 Transcription FactorPre-B-Cell Leukemia Transcription Factor 1Repressor ProteinsTranscription FactorsTranscription, Genetic
2013
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL. A High-Resolution Enhancer Atlas of the Developing Telencephalon. Cell 2013, 152: 895-908. PMID: 23375746, PMCID: PMC3660042, DOI: 10.1016/j.cell.2012.12.041.Peer-Reviewed Original ResearchConceptsForebrain enhancersDistant-acting enhancersGene regulatory mechanismsTransgenic mouse embryosEnhancer architectureVivo enhancerEpigenomic analysisRegulatory sequencesMouse embryosRegulatory mechanismsTelencephalon developmentMammalian telencephalonVivo expressionEnhancerCritical roleDeveloping TelencephalonSequenceNeurodevelopmental disordersTelencephalonCortex tissueVivo activityGenesEmbryosSpeciesAtlas