Karla M. Neugebauer

Molecular Biophysics and Biochemistry, Yale University

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2026

Other Publications

Article	Year
Good cap/bad cap: how the cap-binding complex determines RNA fate. Nature structural & molecular biology\| PubMed ID: 24389545	2014
The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies. Molecular cell\| PubMed ID: 25514182	2014
RNA: master or servant? RNA (New York, N.Y.)\| PubMed ID: 25780198	2015
Quantification of co-transcriptional splicing from RNA-Seq data. Methods (San Diego, Calif.)\| PubMed ID: 25929182	2015
Coilin: The first 25 years. RNA biology\| PubMed ID: 25970135	2015
Paraspeckles: paragons of functional aggregation. The Journal of cell biology\| PubMed ID: 26283795	2015
SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes & development\| PubMed ID: 26944680	2016
Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell\| PubMed ID: 27020755	2016
Droplet organelles? The EMBO journal\| PubMed ID: 27357569	2016
Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos. RNA biology\| PubMed ID: 27858508	2017
Perfect timing: splicing and transcription rates in living cells. Wiley interdisciplinary reviews. RNA\| PubMed ID: 27873472	2017
Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome research\| PubMed ID: 28381614	2017
Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 28456961	2017
Special focus on the Cajal Body. RNA biology\| PubMed ID: 28486008	2017
Cellular differentiation state modulates the mRNA export activity of SR proteins. The Journal of cell biology\| PubMed ID: 28592444	2017
Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches. Methods (San Diego, Calif.)\| PubMed ID: 28734934	2017
Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. Nature reviews. Molecular cell biology\| PubMed ID: 28792005	2017
Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm. Nucleic acids research\| PubMed ID: 28977534	2017
RNA tales - how embryos read and discard messages from mom. Journal of cell science\| PubMed ID: 29467249	2018
Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry\| PubMed ID: 29473743	2018
Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome research\| PubMed ID: 29903723	2018
Blood Relatives: Splicing Mechanisms underlying Erythropoiesis in Health and Disease. F1000Research\| PubMed ID: 30228869	2018
Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling. Developmental cell\| PubMed ID: 30713074	2019
Uncoupling of nucleo-cytoplasmic RNA export and localization during stress. Nucleic acids research\| PubMed ID: 30864659	2019
Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harbor perspectives in biology\| PubMed ID: 31371351	2019
Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis. Molecular biology of the cell\| PubMed ID: 32049586	2020
Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell\| PubMed ID: 32386545	2020
Pre-mRNA Splicing in the Nuclear Landscape. Cold Spring Harbor symposia on quantitative biology\| PubMed ID: 32493763	2019
Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. medRxiv : the preprint server for health sciences\| PubMed ID: 32511630	2020
Preparation of Mammalian Nascent RNA for Long Read Sequencing. Current protocols in molecular biology\| PubMed ID: 33085989	2020
Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns. Cell reports\| PubMed ID: 33113357	2020
Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision. Current opinion in genetics & development\| PubMed ID: 33291060	2021
Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Molecular cell\| PubMed ID: 33440169	2021
SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. medRxiv : the preprint server for health sciences\| PubMed ID: 33532791	2021
Transcription Regulation Through Nascent RNA Folding. Journal of molecular biology\| PubMed ID: 33811916	2021
Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Med (New York, N.Y.)\| PubMed ID: 33969332	2021
Calorimetric Heat Dissipation Measurements of Developing Zebrafish Embryos. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34085232	2021
DMA-tudor interaction modules control the specificity of in vivo condensates. Cell\| PubMed ID: 34115980	2021
Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase. Communications biology\| PubMed ID: 34645977	2021
Identification of Alternative Polyadenylation in Through Long-Read Sequencing of mRNA. Frontiers in genetics\| PubMed ID: 35154260	2021
Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Molecular cell\| PubMed ID: 35303483	2022
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2). NAR cancer\| PubMed ID: 35528200	2022
Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. PLoS biology\| PubMed ID: 35609439	2022
The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies. Nature communications\| PubMed ID: 36224177	2022
An integrated platform for high-throughput nanoscopy. Nature biotechnology\| PubMed ID: 36914886	2023
Tudor-dimethylarginine interactions: the condensed version. Trends in biochemical sciences\| PubMed ID: 37156649	2023
The promoter as a trip navigator: Guiding alternative polyadenylation site destinations. Molecular cell\| PubMed ID: 37478824	2023
Splicing under stress: A matter of time and place. The Journal of cell biology\| PubMed ID: 37988026	2023
Five questions on how biochemistry can combat climate change. BBA advances\| PubMed ID: 38075469	2023
How cell biology can save the planet. Nature cell biology\| PubMed ID: 38228830	2024
Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature reviews. Molecular cell biology\| PubMed ID: 38509203	2024
Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular cell\| PubMed ID: 38521065	2024
Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic acids research\| PubMed ID: 38943343	2024
Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Molecular cell\| PubMed ID: 39366353	2024
Steering research on mRNA splicing in cancer towards clinical translation. Nature reviews. Cancer\| PubMed ID: 39384951	2024
Identification of coilin interactors reveals coordinated control of Cajal body number and structure. The Journal of cell biology\| PubMed ID: 39602297	2025
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis. Molecular cell\| PubMed ID: 40139190	2025
Dynamic interaction of spliceosomal snRNPs with coilin explains Cajal body characteristics. The Journal of cell biology\| PubMed ID: 40560171	2025
The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons. Genes & development\| PubMed ID: 41102016	2026
A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context. bioRxiv : the preprint server for biology\| PubMed ID: 41278783	2025
Control of gene output by intron RNA structure. bioRxiv : the preprint server for biology\| PubMed ID: 41278789	2025
Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts. bioRxiv : the preprint server for biology\| PubMed ID: 41279293	2025
Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib. bioRxiv : the preprint server for biology\| PubMed ID: 41279586	2025