2023
Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome
Rahman S, Dong P, Apontes P, Fernando M, Kosoy R, Townsley K, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos S, Brennand K, Fullard J, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Research 2023, 51: 11142-11161. PMID: 37811875, PMCID: PMC10639075, DOI: 10.1093/nar/gkad798.Peer-Reviewed Original ResearchConceptsChromatin interactomeNeural developmentSpecific gene expressionEnhancer-promoter loopsDistinct cell typesGenome compartmentalizationRepressive compartmentGenome architectureFine-scale changesGenome structureChromatin loopsGWAS lociTAD boundariesTranscriptional inactivationActive promotersGene expressionInteractomeGenomeCell typesComplex organDisease mechanismsHuman brainAdult prefrontal cortexAdult human brainNeurodevelopmental processes
2022
Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation
Michieletto M, Tello-Cajiao J, Mowel W, Chandra A, Yoon S, Joannas L, Clark M, Jimenez M, Wright J, Lundgren P, Williams A, Thaiss C, Vahedi G, Henao-Mejia J. Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. Nature Immunology 2022, 24: 42-54. PMID: 36050414, PMCID: PMC10134076, DOI: 10.1038/s41590-022-01295-y.Peer-Reviewed Original ResearchConceptsGenome organizationThree-dimensional genome organizationDistal regulatory elementsId2 promoterChromatin accessibilityGenome structureFunction of ILCsTissue homeostasisRegulatory elementsId2 expressionGene expressionIntegrative analysisILC biologyTranscription factor GATA-3Innate lymphoid cellsFunctional differentiationHost defenseAllergic airway inflammationMultiple interactionsMature ILCGATA-3Key roleExpressionAirway inflammationOntogenesis
2020
Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.Peer-Reviewed Original ResearchTriple-negative breast cancer cellsCancer cellsBreast cancer cellsStress response genesMulti-omics landscapeCell population compositionDrug-induced cell deathMulti-omics investigationsCell linesBCL2 family inhibitorsSingle-cell analysisChromatin accessibilityGenome structureMDA-MB-231 triple-negative breast cancer cellsChromatin structureMethylation stateResponse genesFamily inhibitorsCell deathTNBC cell linesNumber variationsDefense mechanismsResistance mechanismsNew therapeutic strategiesGenes
2019
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Zhou B, Ho S, Greer S, Spies N, Bell J, Zhang X, Zhu X, Arthur J, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong W, Ji H, Abyzov A, Urban A. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research 2019, 47: 3846-3861. PMID: 30864654, PMCID: PMC6486628, DOI: 10.1093/nar/gkz169.Peer-Reviewed Original ResearchConceptsGenome sequenceStructural variantsGenomic structural featuresSomatic genomic rearrangementsFunctional genomics dataAllele-specific expressionEntire chromosome armsIntegrated genome analysisCRISPR/Cas9Cell linesMain cell linesGenome structureEpigenomic characteristicsChromosome armsGenome analysisDNA methylationGenome characteristicsRetrotransposon insertionChromosomal segmentsGenomic rearrangementsGenomic dataRegulatory complexityCell line HepG2Copy numberLoss of heterozygosity
2009
Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis
Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, DeSalle R. Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis. PLOS Biology 2009, 7: e1000020. PMID: 19175291, PMCID: PMC2631068, DOI: 10.1371/journal.pbio.1000020.Peer-Reviewed Original ResearchConceptsMetazoan animalsBase of MetazoaPlacozoan Trichoplax adhaerensMitochondrial ribosomal genesMolecular sequence dataEarly metazoan evolutionGene expression patternsNuclear genesConcatenated analysisMetazoan evolutionTrichoplax adhaerensGenome structurePhylogenetic relationshipsRibosomal genesPhylogenetic scenariosSequence dataInformative charactersExpression patternsBasal positionSequence analysisSecondary structureIntriguing modelPlacozoaMorphological evidenceGenes
1980
ANALYSIS OF VSV GLYCOPROTEIN STRUCTURE AND GENOME STRUCTURE USING CLONED DNA11This work was supported by Public Health Service Grant No. AI 15481 from NIAID, National Science Foundation Grant No. PCM 77974, NCI Grant No. CA 14195
Rose J, Welch W, Sefton B, Iverson L. ANALYSIS OF VSV GLYCOPROTEIN STRUCTURE AND GENOME STRUCTURE USING CLONED DNA11This work was supported by Public Health Service Grant No. AI 15481 from NIAID, National Science Foundation Grant No. PCM 77974, NCI Grant No. CA 14195. 1980, 81-93. DOI: 10.1016/b978-0-12-255850-4.50012-3.Peer-Reviewed Original ResearchNH2-terminal sequenceVSV genomeCOOH terminusSite of polyadenylationDNA primersVesicular stomatitis virus glycoproteinGenome structureIntergenic regionTranscription eventsCDNA clonesDNA insertsDNA sequencesL geneU residuesRepetitive copyingM geneTerminal sequenceHydrophobic domainCOOH-terminalG geneGenesFunctional significanceLipid bilayersGenomePolyadenylation
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply