A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS
Boddu P, Roy R, Baumgartner F, Hutter S, Haferlach T, Pillai M. A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS. Blood 2024, 144: 2732-2732. DOI: 10.1182/blood-2024-211458.Peer-Reviewed Original ResearchRNA-binding proteinsIntron retentionAlternative splicing patternsPost-transcriptional mechanismsIR eventsSF mutationsSR proteinsSF3B1 mutantsAnalyzed RNA-seq datasetsMyelodysplastic syndromeCo-transcriptional splicingCo-transcriptional mechanismsRNA-seq datasetsPost-transcriptional splicingWild-typeSub-compartmentsNuclear sub-compartmentsHEK293T cellsGene expression analysisWild-type K562 cellsRNA processingMutant cellsPhospho-proteomicsExon featuresAS eventsTet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts
Roy R, Pillai M, Boddu P. Tet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts. Blood 2024, 144: 1812. DOI: 10.1182/blood-2024-211494.Peer-Reviewed Original ResearchTopologically associating domainsDisruption of TAD boundariesTopologically associating domains boundariesTAD boundariesMutant cellsChromatin organizationChromatin compartmentsDNA methylationLT-HSCsKO cellsEnhancer-promoterHigher-order chromatin organizationTet2 lossStudy of chromatin organizationGene expressionMethyl-seq dataHypermethylated differentially methylated regionsPaired-end readsWT cellsGene regulatory networksConversion of 5-methylcytosineDifferentially methylated regionsMyelodysplastic syndromeCompartment shiftsChanges to DNA methylationSF3B1 Mutations Lead to Changes in Fine-Scale Chromatin Organization through Impaired Transcription
Roy R, Gupta A, Pillai M, Boddu P. SF3B1 Mutations Lead to Changes in Fine-Scale Chromatin Organization through Impaired Transcription. Blood 2024, 144: 1813. DOI: 10.1182/blood-2024-211548.Peer-Reviewed Original ResearchPol II densityPol IIGenome binsGenome organizationMutant cellsSplicing factorsEnhancer-promoterEP pairsH3K27ac ChIP-seq dataHi-C protocolPol II distributionChIP-seq dataChIP-seq datasetsEnhancer-promoter interactionsPol II transcriptionRNA polymerase IIPromoter chromatin architecturePol II pausingSF3B1-mutant cellsPaused Pol IIChromatin organization changesFine-scalePutative enhancer regionsGene promoter regionChIP-seq