2025
A Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function
Jiménez-Jiménez V, Sánchez-Cabo F, Schwartz M, Sánchez-Álvarez M, del Pozo M. A Survey for Human Tissue-Level Determinants of CAV1 Regulation and Function. International Journal Of Molecular Sciences 2025, 26: 3789. PMID: 40332409, PMCID: PMC12027754, DOI: 10.3390/ijms26083789.Peer-Reviewed Original ResearchConceptsGenotype-Tissue ExpressionTranscript levelsProtein-coding genesRNA-seq datasetsUpstream regulatory networkCell type proportionsInter-species comparisonsTissue-specific correlationsChromatin modifiersRegulatory networksPRC2 complexTissue-specific influencesCav1Complexity of human tissuesPhysiological regulationHuman tissuesPhysiological conditionsRegulationMetabolic stimuliCAV1 levelsDisease statesTissue dataInfiltration of immune cellsCellsChromatin
2023
Mettl3-catalyzed m6A regulates histone modifier and modification expression in self-renewing somatic tissue
López A, Ko E, Huang S, Pacella G, Kuprasertkul N, D’souza C, Hueros R, Shen H, Stoute J, Elashal H, Sinkfield M, Anderson A, Prouty S, Li H, Seykora J, Liu K, Capell B. Mettl3-catalyzed m6A regulates histone modifier and modification expression in self-renewing somatic tissue. Science Advances 2023, 9: eadg5234. PMID: 37656787, PMCID: PMC10854438, DOI: 10.1126/sciadv.adg5234.Peer-Reviewed Original ResearchConceptsSomatic tissuesMessenger RNALayer of gene regulationHistone modifying enzymesImpaired cell adhesionChromatin modifiersGene regulationAbundant modificationGene expression abnormalitiesHistone modifiersSelf-RenewalMethyltransferase-like protein 3Gross phenotypic abnormalitiesModifying enzymesN6</i>-methyladenosineEpithelial developmentCell adhesionPhenotypic abnormalitiesHair follicle morphogenesisProgenitors in vivoProtein 3Expression abnormalitiesOral ulcersEpithelial tissuesFollicle morphogenesis
2021
Targeting the Atf7ip–Setdb1 Complex Augments Antitumor Immunity by Boosting Tumor Immunogenicity
Hu H, Khodadadi-Jamayran A, Dolgalev I, Cho H, Badri S, Chiriboga LA, Zeck B, De Rodas Gregorio M, Dowling CM, Labbe K, Deng J, Chen T, Zhang H, Zappile P, Chen Z, Ueberheide B, Karatza A, Han H, Ranieri M, Tang S, Jour G, Osman I, Sucker A, Schadendorf D, Tsirigos A, Schalper KA, Velcheti V, Huang HY, Jin Y, Ji H, Poirier JT, Li F, Wong KK. Targeting the Atf7ip–Setdb1 Complex Augments Antitumor Immunity by Boosting Tumor Immunogenicity. Cancer Immunology Research 2021, 9: 1298-1315. PMID: 34462284, PMCID: PMC9414288, DOI: 10.1158/2326-6066.cir-21-0543.Peer-Reviewed Original ResearchConceptsHistone lysine methyltransferase 1Common adaptive mechanismSuppressor screenChromatin modifiersIntron retentionSET domainEpigenetic regulatorsEpigenetic modificationsEpigenetic modifiersType I interferon responseMethyltransferase 1I interferon responseHuman cancersTranscription factor 7Immune invasionInterferon responseAdaptive mechanismsFactor 7GenesCritical roleExpressionImmune evasionRejection of cellsAntigen processingAntigen expressionAltered endocytosis in cellular senescence
Shin EY, Soung NK, Schwartz MA, Kim EG. Altered endocytosis in cellular senescence. Ageing Research Reviews 2021, 68: 101332. PMID: 33753287, PMCID: PMC8131247, DOI: 10.1016/j.arr.2021.101332.Peer-Reviewed Original ResearchTunable, division-independent control of gene activation timing by a polycomb switch
Pease N, Nguyen P, Woodworth M, Ng K, Irwin B, Vaughan J, Kueh H. Tunable, division-independent control of gene activation timing by a polycomb switch. Cell Reports 2021, 34: 108888. PMID: 33761349, PMCID: PMC8024876, DOI: 10.1016/j.celrep.2021.108888.Peer-Reviewed Original ResearchConceptsEpigenetic switchHistone H3 lysine-27 trimethylationCell generationMultiple cell generationsChromatin modifiersRepression mechanismGene Bcl11bPopulation size controlTranscription factorsCell divisionH3K27me3 levelsDemethylase activitySilent stateInactive stateLociH3K27me3BCL11BActive stateCellsChromatinHistoneDemethylaseMethyltransferaseSize controlGenes
2020
A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma
Hayashi A, Fan J, Chen R, Ho Y, Makohon-Moore A, Lecomte N, Zhong Y, Hong J, Huang J, Sakamoto H, Attiyeh M, Kohutek Z, Zhang L, Boumiza A, Kappagantula R, Baez P, Bai J, Lisi M, Chadalavada K, Melchor J, Wong W, Nanjangud G, Basturk O, O’Reilly E, Klimstra D, Hruban R, Wood L, Overholtzer M, Iacobuzio-Donahue C. A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma. Nature Cancer 2020, 1: 59-74. PMID: 35118421, PMCID: PMC8809486, DOI: 10.1038/s43018-019-0010-1.Peer-Reviewed Original ResearchConceptsExpression profilesSquamous featuresPancreatic cancerChromatin modifier genesCancer expression profilesMetastatic pancreatic cancerEvolution of pancreatic cancerBasal-like phenotypeBasal-like subtypePhylogenetic studiesChromatin modifiersEvolutionary analysisPancreatic ductal adenocarcinomaTranscriptional heterogeneityModifier genesIntercellular heterogeneitySubclonal populationsSquamous histologyMYC amplificationGlandular tumorsSomatic mutationsSquamous morphologyClonal mutationsDuctal adenocarcinomaHistologic correlation
2019
Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis
Timberlake AT, Jin SC, Nelson-Williams C, Wu R, Furey CG, Islam B, Haider S, Loring E, Galm A, Steinbacher D, Larysz D, Staffenberg D, Flores R, Rodriguez E, Boggon T, Persing J, Lifton R, Lifton RP, Gunel M, Mane S, Bilguvar K, Gerstein M, Loring E, Nelson-Williams C, Lopez F, Knight J. Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 15116-15121. PMID: 31292255, PMCID: PMC6660739, DOI: 10.1073/pnas.1902041116.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentalpha CateninChildChild, PreschoolCraniosynostosesExomeExome SequencingFemaleGene ExpressionGlypicansHistone AcetyltransferasesHumansMaleMutationNuclear ProteinsPedigreeRisk AssessmentSignal TransductionSkullSOXC Transcription FactorsTranscription Factor AP-2Zinc Finger Protein Gli2ConceptsRare damaging mutationsSyndromic craniosynostosisCongenital anomaliesDamaging mutationsSyndromic casesExome sequencingAdditional congenital anomaliesFrequent congenital anomaliesDamaging de novo mutationsNeural crest cell migrationDamaging de novoCrest cell migrationCS patientsMutation burdenChromatin modifiersSubsequent childrenTranscription factorsDe novo mutationsCS casesCS geneHedgehog pathwayDisease locusPremature fusionFunction mutationsCraniosynostosis
2018
Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation
Duran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, Kahle KT. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation. Neuron 2018, 101: 429-443.e4. PMID: 30578106, PMCID: PMC10292091, DOI: 10.1016/j.neuron.2018.11.041.Peer-Reviewed Original ResearchConceptsChromatin modifiersVascular developmentSpecification of arteriesDeep venous systemNormal vascular developmentParent-offspring triosSignaling GenesGalen malformationDamaging mutationsGenesMutationsEssential roleArterio-venous malformationsCutaneous vascular abnormalitiesNovo mutationsExome sequencingDisease biologyIncomplete penetranceVariable expressivityVascular abnormalitiesVenous systemMutation carriersArterial bloodMutation burdenClinical implicationsGenomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Network T, Caesar-Johnson S, Demchok J, Felau I, Kasapi M, Ferguson M, Hutter C, Sofia H, Tarnuzzer R, Wang Z, Yang L, Zenklusen J, Zhang J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Cho J, DeFreitas T, Frazer S, Gehlenborg N, Getz G, Heiman D, Kim J, Lawrence M, Lin P, Meier S, Noble M, Saksena G, Voet D, Zhang H, Bernard B, Chambwe N, Dhankani V, Knijnenburg T, Kramer R, Leinonen K, Liu Y, Miller M, Reynolds S, Shmulevich I, Thorsson V, Zhang W, Akbani R, Broom B, Hegde A, Ju Z, Kanchi R, Korkut A, Li J, Liang H, Ling S, Liu W, Lu Y, Mills G, Ng K, Rao A, Ryan M, Wang J, Weinstein J, Zhang J, Abeshouse A, Armenia J, Chakravarty D, Chatila W, de Bruijn I, Gao J, Gross B, Heins Z, Kundra R, La K, Ladanyi M, Luna A, Nissan M, Ochoa A, Phillips S, Reznik E, Sanchez-Vega F, Sander C, Schultz N, Sheridan R, Sumer S, Sun Y, Taylor B, Wang J, Zhang H, Anur P, Peto M, Spellman P, Benz C, Stuart J, Wong C, Yau C, Hayes D, Parker J, Wilkerson M, Ally A, Balasundaram M, Bowlby R, Brooks D, Carlsen R, Chuah E, Dhalla N, Holt R, Jones S, Kasaian K, Lee D, Ma Y, Marra M, Mayo M, Moore R, Mungall A, Mungall K, Robertson A, Sadeghi S, Schein J, Sipahimalani P, Tam A, Thiessen N, Tse K, Wong T, Berger A, Beroukhim R, Cherniack A, Cibulskis C, Gabriel S, Gao G, Ha G, Meyerson M, Schumacher S, Shih J, Kucherlapati M, Kucherlapati R, Baylin S, Cope L, Danilova L, Bootwalla M, Lai P, Maglinte D, Van Den Berg D, Weisenberger D, Auman J, Balu S, Bodenheimer T, Fan C, Hoadley K, Hoyle A, Jefferys S, Jones C, Meng S, Mieczkowski P, Mose L, Perou A, Perou C, Roach J, Shi Y, Simons J, Skelly T, Soloway M, Tan D, Veluvolu U, Fan H, Hinoue T, Laird P, Shen H, Zhou W, Bellair M, Chang K, Covington K, Creighton C, Dinh H, Doddapaneni H, Donehower L, Drummond J, Gibbs R, Glenn R, Hale W, Han Y, Hu J, Korchina V, Lee S, Lewis L, Li W, Liu X, Morgan M, Morton D, Muzny D, Santibanez J, Sheth M, Shinbrot E, Wang L, Wang M, Wheeler D, Xi L, Zhao F, Hess J, Appelbaum E, Bailey M, Cordes M, Ding L, Fronick C, Fulton L, Fulton R, Kandoth C, Mardis E, McLellan M, Miller C, Schmidt H, Wilson R, Crain D, Curley E, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Thompson E, Yena P, Bowen J, Gastier-Foster J, Gerken M, Leraas K, Lichtenberg T, Ramirez N, Wise L, Zmuda E, Corcoran N, Costello T, Hovens C, Carvalho A, de Carvalho A, Fregnani J, Longatto-Filho A, Reis R, Scapulatempo-Neto C, Silveira H, Vidal D, Burnette A, Eschbacher J, Hermes B, Noss A, Singh R, Anderson M, Castro P, Ittmann M, Huntsman D, Kohl B, Le X, Thorp R, Andry C, Duffy E, Lyadov V, Paklina O, Setdikova G, Shabunin A, Tavobilov M, McPherson C, Warnick R, Berkowitz R, Cramer D, Feltmate C, Horowitz N, Kibel A, Muto M, Raut C, Malykh A, Barnholtz-Sloan J, Barrett W, Devine K, Fulop J, Ostrom Q, Shimmel K, Wolinsky Y, Sloan A, De Rose A, Giuliante F, Goodman M, Karlan B, Hagedorn C, Eckman J, Harr J, Myers J, Tucker K, Zach L, Deyarmin B, Hu H, Kvecher L, Larson C, Mural R, Somiari S, Vicha A, Zelinka T, Bennett J, Iacocca M, Rabeno B, Swanson P, Latour M, Lacombe L, Têtu B, Bergeron A, McGraw M, Staugaitis S, Chabot J, Hibshoosh H, Sepulveda A, Su T, Wang T, Potapova O, Voronina O, Desjardins L, Mariani O, Roman-Roman S, Sastre X, Stern M, Cheng F, Signoretti S, Berchuck A, Bigner D, Lipp E, Marks J, McCall S, McLendon R, Secord A, Sharp A, Behera M, Brat D, Chen A, Delman K, Force S, Khuri F, Magliocca K, Maithel S, Olson J, Owonikoko T, Pickens A, Ramalingam S, Shin D, Sica G, Van Meir E, Zhang H, Eijckenboom W, Gillis A, Korpershoek E, Looijenga L, Oosterhuis W, Stoop H, van Kessel K, Zwarthoff E, Calatozzolo C, Cuppini L, Cuzzubbo S, DiMeco F, Finocchiaro G, Mattei L, Perin A, Pollo B, Chen C, Houck J, Lohavanichbutr P, Hartmann A, Stoehr C, Stoehr R, Taubert H, Wach S, Wullich B, Kycler W, Murawa D, Wiznerowicz M, Chung K, Edenfield W, Martin J, Baudin E, Bubley G, Bueno R, De Rienzo A, Richards W, Kalkanis S, Mikkelsen T, Noushmehr H, Scarpace L, Girard N, Aymerich M, Campo E, Giné E, Guillermo A, Van Bang N, Hanh P, Phu B, Tang Y, Colman H, Evason K, Dottino P, Martignetti J, Gabra H, Juhl H, Akeredolu T, Stepa S, Hoon D, Ahn K, Kang K, Beuschlein F, Breggia A, Birrer M, Bell D, Borad M, Bryce A, Castle E, Chandan V, Cheville J, Copland J, Farnell M, Flotte T, Giama N, Ho T, Kendrick M, Kocher J, Kopp K, Moser C, Nagorney D, O’Brien D, O’Neill B, Patel T, Petersen G, Que F, Rivera M, Roberts L, Smallridge R, Smyrk T, Stanton M, Thompson R, Torbenson M, Yang J, Zhang L, Brimo F, Ajani J, Gonzalez A, Behrens C, Bondaruk J, Broaddus R, Czerniak B, Esmaeli B, Fujimoto J, Gershenwald J, Guo C, Lazar A, Logothetis C, Meric-Bernstam F, Moran C, Ramondetta L, Rice D, Sood A, Tamboli P, Thompson T, Troncoso P, Tsao A, Wistuba I, Carter C, Haydu L, Hersey P, Jakrot V, Kakavand H, Kefford R, Lee K, Long G, Mann G, Quinn M, Saw R, Scolyer R, Shannon K, Spillane A, Stretch O, Synott M, Thompson J, Wilmott J, Al-Ahmadie H, Chan T, Ghossein R, Gopalan A, Levine D, Reuter V, Singer S, Singh B, Tien N, Broudy T, Mirsaidi C, Nair P, Drwiega P, Miller J, Smith J, Zaren H, Park J, Hung N, Kebebew E, Linehan W, Metwalli A, Pacak K, Pinto P, Schiffman M, Schmidt L, Vocke C, Wentzensen N, Worrell R, Yang H, Moncrieff M, Goparaju C, Melamed J, Pass H, Botnariuc N, Caraman I, Cernat M, Chemencedji I, Clipca A, Doruc S, Gorincioi G, Mura S, Pirtac M, Stancul I, Tcaciuc D, Albert M, Alexopoulou I, Arnaout A, Bartlett J, Engel J, Gilbert S, Parfitt J, Sekhon H, Thomas G, Rassl D, Rintoul R, Bifulco C, Tamakawa R, Urba W, Hayward N, Timmers H, Antenucci A, Facciolo F, Grazi G, Marino M, Merola R, de Krijger R, Gimenez-Roqueplo A, Piché A, Chevalier S, McKercher G, Birsoy K, Barnett G, Brewer C, Farver C, Naska T, Pennell N, Raymond D, Schilero C, Smolenski K, Williams F, Morrison C, Borgia J, Liptay M, Pool M, Seder C, Junker K, Omberg L, Dinkin M, Manikhas G, Alvaro D, Bragazzi M, Cardinale V, Carpino G, Gaudio E, Chesla D, Cottingham S, Dubina M, Moiseenko F, Dhanasekaran R, Becker K, Janssen K, Slotta-Huspenina J, Abdel-Rahman M, Aziz D, Bell S, Cebulla C, Davis A, Duell R, Elder J, Hilty J, Kumar B, Lang J, Lehman N, Mandt R, Nguyen P, Pilarski R, Rai K, Schoenfield L, Senecal K, Wakely P, Hansen P, Lechan R, Powers J, Tischler A, Grizzle W, Sexton K, Kastl A, Henderson J, Porten S, Waldmann J, Fassnacht M, L. S, Schadendorf D, Couce M, Graefen M, Huland H, Sauter G, Schlomm T, Simon R, Tennstedt P, Olabode O, Nelson M, Bathe O, Carroll P, Chan J, Disaia P, Glenn P, Kelley R, Landen C, Phillips J, Prados M, Simko J, Smith-McCune K, VandenBerg S, Roggin K, Fehrenbach A, Kendler A, Sifri S, Steele R, Jimeno A, Carey F, Forgie I, Mannelli M, Carney M, Hernandez B, Campos B, Herold-Mende C, Jungk C, Unterberg A, von Deimling A, Bossler A, Galbraith J, Jacobus L, Knudson M, Knutson T, Ma D, Milhem M, Sigmund R, Godwin A, Madan R, Rosenthal H, Adebamowo C, Adebamowo S, Boussioutas A, Beer D, Giordano T, Mes-Masson A, Saad F, Bocklage T, Landrum L, Mannel R, Moore K, Moxley K, Postier R, Walker J, Zuna R, Feldman M, Valdivieso F, Dhir R, Luketich J, Pinero E, Quintero-Aguilo M, Carlotti C, Dos Santos J, Kemp R, Sankarankuty A, Tirapelli D, Catto J, Agnew K, Swisher E, Creaney J, Robinson B, Shelley C, Godwin E, Kendall S, Shipman C, Bradford C, Carey T, Haddad A, Moyer J, Peterson L, Prince M, Rozek L, Wolf G, Bowman R, Fong K, Yang I, Korst R, Rathmell W, Fantacone-Campbell J, Hooke J, Kovatich A, Shriver C, DiPersio J, Drake B, Govindan R, Heath S, Ley T, Van Tine B, Westervelt P, Rubin M, Lee J, Aredes N, Mariamidze A, Stuart J, Laird P, Hoadley K, Weinstein J, Peto M, Pickering C, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports 2018, 23: 194-212.e6. PMID: 29617660, PMCID: PMC6002769, DOI: 10.1016/j.celrep.2018.03.063.Peer-Reviewed Original ResearchConceptsChromosomal copy number alterationsSquamous cell carcinomaRas-MAPK pathwayChromatin modifiersGenomic integrityCopy number alterationsAlternative promotersHuman papillomavirusDNA mutationsPathway networkAberrant methylationCell stemnessHarbor mutationsOxidative damageAtlas studyMesenchymal differentiationCell signatureMutationsMolecular featuresImmune checkpointsImmune therapySquamous carcinomaCell carcinomaImmunoregulatory moleculesTherapeutic approaches
2017
Coordinating Regulation of Gene Expression in Cardiovascular Disease: Interactions between Chromatin Modifiers and Transcription Factors
Bauer AJ, Martin KA. Coordinating Regulation of Gene Expression in Cardiovascular Disease: Interactions between Chromatin Modifiers and Transcription Factors. Frontiers In Cardiovascular Medicine 2017, 4: 19. PMID: 28428957, PMCID: PMC5382160, DOI: 10.3389/fcvm.2017.00019.Peer-Reviewed Original ResearchChromatin modifiersTranscription factorsGene expressionTranscriptional controlChromatin-modifying proteinsTranscription factor recruitmentDysregulated gene expressionNumerous cell typesChromatin structureFactor recruitmentHistone methylationGene accessibilityTranscriptional interactionsDNA methylationEpigenetic modifiersRegulatory regionsHistone acetylationVascular smooth muscle cellsCell typesSmooth muscle cellsMuscle cellsMethylationNovel therapeuticsExpressionDisease pathogenesis
2016
Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation
Grandy R, Whitfield T, Wu H, Fitzgerald M, VanOudenhove J, Zaidi S, Montecino M, Lian J, van Wijnen A, Stein J, Stein G. Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation. Molecular And Cellular Biology 2016, 36: 615-627. PMID: 26644406, PMCID: PMC4751694, DOI: 10.1128/mcb.00877-15.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell DifferentiationCell LineChromatinDNA MethylationDNA-Binding ProteinsEpigenesis, GeneticGene Expression Regulation, DevelopmentalGenome-Wide Association StudyHistone-Lysine N-MethyltransferaseHistonesHuman Embryonic Stem CellsHumansMyeloid-Lymphoid Leukemia ProteinNeoplasm ProteinsConceptsHuman embryonic stem cellsBivalent genesHistone modificationsCell cycleCell cycle-dependent fashionPluripotent cell cycleRepressive histone modificationsPosttranslational histone modificationsH3K4me3/H3K27me3Maintenance of pluripotencyHistone modification signaturesMethylation/demethylationLevels of H3K4me3Embryonic stem cellsInduction of differentiationChromatin regulationChromatin modifiersEpigenetic landscapeCell identityModification signaturesLineage commitmentGenomic enrichmentGene promoterProgeny cellsMolecular mechanisms
2015
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nature Communications 2015, 6: 6404. PMID: 25752243, PMCID: PMC4355952, DOI: 10.1038/ncomms7404.Peer-Reviewed Original ResearchConceptsASD risk genesRisk genesRegulatory networksAncient gene regulatory networksHuman neural stem cellsLoss of CHD8Specific regulatory networksGene regulatory networksCo-expression networkAutism risk genesEmbryonic mouse cortexChromatin modifiersIdentification of recurrentChromodomain-HelicaseChd8 knockdownNeural stem cellsMouse neurodevelopmentCHD8Human brain developmentFunction mutationsGenesStem cellsHuman neurodevelopmentNovo lossBrain development
2014
The contribution of de novo coding mutations to autism spectrum disorder
Iossifov I, O’Roak B, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The contribution of de novo coding mutations to autism spectrum disorder. Nature 2014, 515: 216-221. PMID: 25363768, PMCID: PMC4313871, DOI: 10.1038/nature13908.Peer-Reviewed Original ResearchConceptsLGD mutationsMissense mutationsWild-type alleleChromatin modifiersGene-disrupting mutationsGenetic architectureCopy number variantsDe novo mutationsDe novo missense mutationsWhole-exome sequencingHuman diseasesGenesNovo missense mutationNumber variantsLikely gene-disrupting mutationsMutationsDe novoNovo mutationsExome sequencingSimplex familiesTargetFMRPPowerful toolSimilar numberSequencing
2009
Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. Science 2009, 326: 257-263. PMID: 19729616, PMCID: PMC2879337, DOI: 10.1126/science.1179050.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteriaChromatin Assembly and DisassemblyDendritic CellsDNA, Single-StrandedFeedback, PhysiologicalGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksInflammationLipopeptidesLipopolysaccharidesMiceMice, Inbred C57BLPoly I-CRNA-Binding ProteinsToll-Like ReceptorsTranscription FactorsTranscription, GeneticVirusesConceptsTranscriptional responseRegulatory networksMajor transcriptional responsePrimary mammalian cellsCellular transcriptional responsesPathogen-sensing pathwaysChromatin modifiersPathogen responseCandidate regulatorsCore regulatorsMammalian cellsTranscription factorsGenomic dataGene expressionRegulatory functionsUnbiased approachUnbiased strategyRegulatorUnbiased reconstructionPrimary dendritic cellsCellsRNAProteinPathwayPathogens
2008
Failure of Terminal Erythroid Differentiation in EKLF-Deficient Mice Is Associated with Cell Cycle Perturbation and Reduced Expression of E2F2
Pilon AM, Arcasoy MO, Dressman HK, Vayda SE, Maksimova YD, Sangerman JI, Gallagher PG, Bodine DM. Failure of Terminal Erythroid Differentiation in EKLF-Deficient Mice Is Associated with Cell Cycle Perturbation and Reduced Expression of E2F2. Molecular And Cellular Biology 2008, 28: 7394-7401. PMID: 18852285, PMCID: PMC2593440, DOI: 10.1128/mcb.01087-08.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell CycleCell DifferentiationE2F2 Transcription FactorEmbryo, MammalianErythropoiesisGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksKruppel-Like Transcription FactorsLiverMiceMice, KnockoutOligonucleotide Array Sequence AnalysisPromoter Regions, GeneticStem CellsTranscription, GeneticConceptsErythroid Krüppel-like factorTerminal erythroid differentiationEarly erythroid progenitor cellsErythroid progenitor cellsErythroid differentiationChromatin modifiersProgenitor cellsKrüppel-like transcription factorsNetwork of genesCell cycle regulationChromatin immunoprecipitation analysisKrüppel-like factorCell cycle progressionFailure of erythropoiesisS phase transitionEarly progenitor cellsTranscriptional activatorCycle regulationTranscriptional profilingTranscription factorsTarget genesImmunoprecipitation analysisDNase IErythroid cellsCycle progression
2007
Drosophila PIWI associates with chromatin and interacts directly with HP1a
Brower-Toland B, Findley SD, Jiang L, Liu L, Yin H, Dus M, Zhou P, Elgin SC, Lin H. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes & Development 2007, 21: 2300-2311. PMID: 17875665, PMCID: PMC1973144, DOI: 10.1101/gad.1564307.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAnimalsArgonaute ProteinsBinding SitesChromatinChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDrosophila melanogasterDrosophila ProteinsEmbryo, NonmammalianFemaleGene SilencingMaleModels, MolecularNuclear ProteinsProtein BindingProteinsRNA-Induced Silencing ComplexConceptsHeterochromatin protein 1aPIWI-interacting RNAsEpigenetic changesChromatin-associated proteinsProtein family membersNormal silencingHeterochromatic genesFly genomeHeterochromatin componentsChromatin modifiersEpigenetic stateEpigenetic regulationRNA mechanismFruit flyPiwiTerminal domainProtein 1ACentral playerRNASpecific sequencesDirect interactionGenomeGenesMotifCellular systems
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