Karla M Neugebauer, PhD
Cards
Appointments
Additional Titles
Director, Yale Center for RNA Science and Medicine
Contact Info
Molecular Biophysics and Biochemistry
333 Cedar St, P.O. Box 208024
New Haven, Connecticut 06520
United States
Appointments
Additional Titles
Director, Yale Center for RNA Science and Medicine
Contact Info
Molecular Biophysics and Biochemistry
333 Cedar St, P.O. Box 208024
New Haven, Connecticut 06520
United States
Appointments
Additional Titles
Director, Yale Center for RNA Science and Medicine
Contact Info
Molecular Biophysics and Biochemistry
333 Cedar St, P.O. Box 208024
New Haven, Connecticut 06520
United States
About
Titles
R. Selden Rose Professor of Molecular Biophysics and Biochemistry and Professor of Cell Biology
Director, Yale Center for RNA Science and Medicine
Biography
Karla Neugebauer holds a BS in Biology from Cornell University and a PhD in Neuroscience from UCSF. She switched gears to RNA biology as a postdoc with Mark Roth at Fred Hutchinson Cancer Research Center. There she participated in the initial description of the SR protein family of splicing regulators and was inspired to study RNA metabolism in vivo by combining imaging, genomics, and sequencing strategies. From 2001-2013 she was a Research Group Leader at the Max Planck Institute of Cell biology and Genetics in Dresden Germany. In 2013, she moved to Yale as a Professor of Molecular Biophysics and Biochemistry and of Cell Biology. She has been the Director of the Yale Center for RNA Science and Biomedicine since 2018 and was recognized internationally for her work in RNA Biology by the RNA Society (2017 mid-career award). She has studied splicing in relation to nuclear speckles and discovered that most introns are removed during the process, or co-transcriptionally. Her lab has shown that snRNP assembly occurs in membraneless organelles called Cajal bodies (CBs) and that depletion of the CB scaffolding protein coilin is lethal in zebrafish embryos, due to a deficit in splicing. She is passionate about climate change, believing that everyone has something to contribute to meet its challenges. She is currently developing biochemistry curriculum to show the relevance of the discipline to meeting the current and future needs of our planet.
Appointments
Molecular Biophysics and Biochemistry
ProfessorPrimaryCell Biology
ProfessorSecondary
Other Departments & Organizations
- Biochemistry, Quantitative Biology, Biophysics and Structural Biology (BQBS)
- Cell Biology
- Cell Biology of RNA
- Cell Biology Research
- Center for Biomedical Data Science
- Center for RNA Science and Medicine
- Genomics, Genetics, and Epigenetics
- Molecular Biophysics and Biochemistry
- Molecular Cell Biology, Genetics and Development
- Yale Cancer Center
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Ventures
- YCCEH
Education & Training
- PhD
- University of California-San Francisco, Neuroscience (1990)
- BS
- Cornell University, Biology/Neuroscience (1984)
Research
Overview
Medical Subject Headings (MeSH)
ORCID
0000-0002-3835-6761- View Lab Website
Neugebauer Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Manoj M Pillai, MBBS
Matt Simon, PhD
Nils Neuenkirchen, PhD
Prajwal Boddu, MD
Haifan Lin, PhD
Joerg Bewersdorf, PhD
RNA Splicing
Transcription, Genetic
Zebrafish
Cell Nucleus
Alternative Splicing
Saccharomyces cerevisiae
Publications
2024
Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics
Gordon J, Phizicky D, Schärfen L, Brown C, Escayola D, Kanyo J, Lam T, Simon M, Neugebauer K. Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic Acids Research 2024, gkae562. PMID: 38943343, DOI: 10.1093/nar/gkae562.Peer-Reviewed Original ResearchAltmetricConceptsPoly(A)-binding proteinTranscriptome dynamicsNuclear poly(A) binding proteinPoly(A) binding proteinMode of gene regulationFunctional consequences of phosphorylationLong-read sequencingIncreased mRNA turnoverNucleo-cytoplasmic exportConsequences of phosphorylationRegulation of poly(ACohort of mRNAsGene expression programsMRNA biogenesisCytoplasmic mixingMRNA turnoverGene regulationShorter poly(ARNA stabilityMitotic kinasesPoly(ACell cycleMRNA synthesisIncreased transcriptionBinding proteinMultiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy
Podszywalow-Bartnicka P, Neugebauer K. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biology 2024, 21: 1-17. PMID: 38798162, PMCID: PMC11135835, DOI: 10.1080/15476286.2024.2346688.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsARE-binding proteinsRNA-binding proteinsAU-rich elementsStress granulesBinding proteinTranslational regulation of mRNAsImpact alternative splicingCytoplasmic stress granulesProtein-RNA bindingAdaptation to microenvironmentProtein-RNA networksBinding to AU-rich elementsCancer cell proteomePost-transcriptional regulationAU-rich RNA-binding proteinsRegulation of mRNAsChemotherapy resistanceGene expression levelsSequence motifsProtein-RNAMRNA structureMature mRNATranslational regulationAlternative splicingCell proteomeTranscription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape
Boddu P, Gupta A, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma A, Neugebauer K, Pillai M. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell 2024, 84: 1475-1495.e18. PMID: 38521065, PMCID: PMC11061666, DOI: 10.1016/j.molcel.2024.02.032.Peer-Reviewed Original ResearchCitationsAltmetricConceptsRate of RNA polymerase IIChromatin landscapeElongation defectsElongation rate of RNA polymerase IIImpaired protein-protein interactionsSplicing of pre-messenger RNATranscription elongation defectsRNA polymerase IIProtein-protein interactionsPre-messenger RNACancer-associated mutationsIsogenic cell linesSin3/HDAC complexGene bodiesPolymerase IIChromatin accessibilityH3K4me3 markChromatin changesMutant SF3B1ChromatinMutant mouse modelsEpigenetic disordersEpigenetic factorsHuman diseasesMutant stateCo-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer K. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology 2024, 25: 534-554. PMID: 38509203, PMCID: PMC11199108, DOI: 10.1038/s41580-024-00706-2.Peer-Reviewed Original ResearchCitationsAltmetricConceptsRNA polymeraseRNA biogenesisRNA processingGene regulationDevelopment of RNA sequencingTranscription to translationRNA processing intermediatesGene expression stepsCo-transcriptional activityCellular stress responseNascent RNATranscriptional readthroughNascent transcriptsTranscriptional coordinationIntron retentionRNA foldingEukaryotesProkaryotesExpression stepsRNA sequencingTransient transcriptionGene expressionTranscriptionStress responseRNAA correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context
Bao Y, Marin Z, Zhang C, Neugebauer K, Baddeley D, Shribak M, Bewersdorf J. A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context. Biophysical Journal 2024, 123: 290a. DOI: 10.1016/j.bpj.2023.11.1808.Peer-Reviewed Original ResearchHow cell biology can save the planet
Neugebauer K. How cell biology can save the planet. Nature Cell Biology 2024, 26: 4-4. PMID: 38228830, DOI: 10.1038/s41556-023-01305-7.Peer-Reviewed Original ResearchAltmetric
2023
Five questions on how biochemistry can combat climate change
Chen K, Guo Y, How K, Acosta A, Documet D, Liang C, Arul D, Wood S, Moon K, Oliver L, Fajardo E, Kopyto M, Shine M, Neugebauer K. Five questions on how biochemistry can combat climate change. BBA Advances 2023, 4: 100111. PMID: 38075469, PMCID: PMC10709155, DOI: 10.1016/j.bbadva.2023.100111.Peer-Reviewed Original ResearchCitationsAltmetricConceptsClimate changeCell biologyGreater ecosystemMolecular biophysicsEnvironmental changesEnvironmental conditionsOrganismsBiochemistryMolecular pointNew diseaseHuman activitiesDispersalMicrobesGeneticsBiologyEcosystemsPlantsGlobal warmingPathwayHigh levelsSalt concentrationBiophysicsCellsAccumulationWeather patternsSplicing under stress: A matter of time and place
Podszywalow-Bartnicka P, Neugebauer K. Splicing under stress: A matter of time and place. Journal Of Cell Biology 2023, 222: e202311014. PMID: 37988026, PMCID: PMC10660129, DOI: 10.1083/jcb.202311014.Peer-Reviewed Original ResearchAltmetricImpaired 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 ResearchConceptsSplicing 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 ResearchConceptsChromatin 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
Academic Achievements and Community Involvement
activity Committee on Admissions and Financial Aid (Yale College)
CommitteesCommittee MemberDetails09/01/2014 - Presentactivity Yale Center for RNA Science and Medicine
CommitteesDirectorDetails09/01/2017 - Presentactivity Faculty Committee on Athletics
CommitteesMemberDetails09/01/2017 - Presentactivity Biological Sciences Area Committee
CommitteesCommittee MemberDetails07/01/2022 - Presentactivity MB&B Graduate Studies (DGS)
CommitteesDirectorDetails2019 - 2021
Links & Media
Media
- Illustration of the nucleus and cytoplasm of a eukaryotic cell containing nonmembrane-bound cellular bodies, such as nucleoli, Cajal bodies, the histone locus bodies, and P-bodies. Cellular bodies promote molecular interactions by increasing the local concentration of factors. They are often linked to transcription of particular genes (nucleolus: rDNA genes; CB: snRNA genes; histone body locus: histone genes). Similarly, individual machines are rich in RNA polymerase, spliceosomes, RNA-binding proteins and other factors that communicate with one another during gene regulation.
News
- February 16, 2024
Saving the Planet Through Biochemistry
- July 25, 2023
Midsummer's RNA Dreams happy hour
- April 25, 2023
‘There is no textbook’: Biochem course confronts the climate challenge
- March 13, 2023Source: Nature Biotechnology
Super-resolution microscopy goes high-throughput
Get In Touch
Contacts
Molecular Biophysics and Biochemistry
333 Cedar St, P.O. Box 208024
New Haven, Connecticut 06520
United States
Locations
Sterling Hall of Medicine
Lab
333 Cedar Street, Rm C-111
New Haven, CT 06510
Sterling Hall of Medicine
Academic Office
333 Cedar Street, Rm C-123
New Haven, CT 06510