2024
Cytoplasmic Intron Retention As a Regulatory Mechanism of Mitochondrial Homeostasis in Erythroid Cells
Roy R, Boddu P, Pillai M. Cytoplasmic Intron Retention As a Regulatory Mechanism of Mitochondrial Homeostasis in Erythroid Cells. Blood 2024, 144: 1075-1075. DOI: 10.1182/blood-2024-211280.Peer-Reviewed Original ResearchNonsense-mediated decayIntron retentionRetained intronsCry transcriptsSplicing factorsRI transcriptionFunctional genomics dataLong-read sequencingAbsence of intronsErythroid cellsENCODE consortiumPolyadenylated RNAGenomic dataRNA-seqHUDEP-2 cellsMRNA processingNuclear exportCRISPR deletionMitochondrial homeostasisProtein isoformsRNA abundanceUnspliced RNAIntronStages of erythropoiesisPeptide translationSF3B1 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
2023
Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E
Boddu P, Gupta A, Roy R, De La Pena Avalos B, Herrero A, Zimmer J, Simon M, Chandhok N, King D, Neuenkirchen N, Dray E, Lin H, Kupfer G, Verma A, Neugebauer K, Pillai M. Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E. Blood 2023, 142: 714. DOI: 10.1182/blood-2023-187303.Peer-Reviewed Original ResearchSplicing factorsChIP-seqK562 cell lineKey regulatory genesCell linesSingle mutant alleleNon-denaturing gelsAlternative splicingTranscriptional kineticsRegulatory genesSpliceosome assemblySplicing efficiencyMRNA splicingCRISPR/Progenitor populationsNeomorphic functionsMolecular mechanismsMutant allelesIsoform changesGene editingNovel mechanismMutationsSF mutationsRecurrent mutationsAssembly kineticsTranscription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape
Boddu P, Gupta A, Roy R, Herrero A, Verma A, Neugebauer K, Pillai M. Transcription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape. Blood 2023, 142: 709. DOI: 10.1182/blood-2023-188083.Peer-Reviewed Original ResearchChromatin organizationSuch epigenetic changesGenome editing approachesRNA splicing factorsChromatin landscapeSingle mutant alleleEpigenetic landscapeGenomic integrityTranscription defectTranscription kineticsSplicing factorsChIP-seqEpigenetic regulatorsEpigenetic changesEpigenetic therapyMutant allelesEditing approachesFactor mutationsK562 cell lineDownstream effectsCell linesMyeloid disordersClonal myeloid disordersHDAC pathwayMutations