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Mutant NPM1 Directly Regulates Oncogenic Transcription in Acute Myeloid Leukemia

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Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci

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Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

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Transcriptomics in the era of long-read sequencing

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POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

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3′-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression

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Sites of Transcription Initiation Drive mRNA Isoform Selection

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Co-transcriptional gene regulation in eukaryotes and prokaryotes

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

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Pre-mRNA splicing and its cotranscriptional connections

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The regulation and function of post-transcriptional RNA splicing

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HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

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Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle

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A ubiquitous disordered protein interaction module orchestrates transcription elongation

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MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape

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HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock

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Profiling the epigenome using long-read sequencing

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Transcription Regulation Through Nascent RNA Folding

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Integrated Analysis of Whole Genome and Epigenome Data Using Machine Learning Technology: Toward the Establishment of Precision Oncology

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FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing

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STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

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Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing

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Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential

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Control of mammalian gene expression by modulation of polyA signal cleavage at 5′ UTR

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Introns: the “dark matter” of the eukaryotic genome

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Who let the DoGs out? – biogenesis of stress-induced readthrough transcripts

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Co-transcriptional genome surveillance by HUSH is coupled to termination machinery

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Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features

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Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing

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Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release

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From computational models of the splicing code to regulatory mechanisms and therapeutic implications

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Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing

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Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

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Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts

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Birth of a poly(A) tail: mechanisms and control of mRNA polyadenylation

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The control of polycomb repressive complexes by long noncoding RNAs

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Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data

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Rixosomal RNA degradation contributes to silencing of Polycomb target genes

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PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells

Iannone, C., Kainov, Y. A., Zhuravskaya, A., Hamid, F., Nojima, T., & Makeyev, E. V. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.12.014 · Cited by 34

Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation

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Regulation of bacterial gene expression by non-coding RNA: It is all about time!

Chauvier, A., & Walter, N. G. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2023.12.011 · Cited by 34

The upstream 5′ splice site remains associated to the transcription machinery during intron synthesis

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Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

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Nuclear mRNA decay: regulatory networks that control gene expression

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Cotranscriptional splicing efficiencies differ within genes and between cell types

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It’s a DoG-eat-DoG world—altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production

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RNA helicase-dependent gene looping impacts messenger RNA processing

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CTCF blocks antisense transcription initiation at divergent promoters

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RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis

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Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression

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Inherited blood cancer predisposition through altered transcription elongation

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miR-430 regulates zygotic mRNA during zebrafish embryogenesis

Amaral, D. B., Egidy, R., Perera, A. G., & Bazzini, A. (2024) · Genome biology · doi:10.1186/s13059-024-03197-8 · Cited by 23

Challenges in identifying mRNA transcript starts and ends from long-read sequencing dataPreprint

Calvo-Roitberg, E., Daniels, R. F., & Pai, A. A. (2024) · Genome Research · doi:10.1101/gr.279559.124 · Cited by 24

Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins

Lü, W., & Lai, E. C. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.848626 · Cited by 26

Regulation of gene expression by alternative polyadenylation in health and disease

Tian, B., Yu, S., & Zhang, Q. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-025-00928-w · Cited by 23

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Parker, M. T., Knop, K., Barton, G. J., & Simpson, G. G. (2021) · Genome biology · doi:10.1186/s13059-021-02296-0 · Cited by 23

SF3B1-targeted Splicing Inhibition Triggers Transcriptional Stress Response and Global Alterations in R-Loop LandscapePreprint

Castillo-Guzman, D., Hartono, S. R., Frederick, M. H., Sanz, L. A., Sereiva, T., & Chedin, F. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.08.130583 · Cited by 25

Regulation of alternative splicing and polyadenylation in neurons

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Modulation of mRNA 3′-End Processing and Transcription Termination in Virus-Infected Cells

Vijayakumar, A., Park, A., & STEITZ, J. A. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.828665 · Cited by 20

Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation

Zhang, X., Xu, J., Hu, J., Zhang, S., Hao, Y., Zhang, D., Qian, H., Wang, D., & Fu, X. (2024) · Nature Communications · doi:10.1038/s41467-024-50298-w · Cited by 19

Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis

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Elements at the 5′ end of Xist harbor SPEN-independent transcriptional antiterminator activity

Trotman, J. B., Lee, D. M., Cherney, R. E., Kim, S. O., Inoue, K., Schertzer, M. D., Bischoff, S. R., Cowley, D. O., & Calabrese, J. M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa789 · Cited by 18

Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ

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Transcription and splicing dynamics during early Drosophila development

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Post-transcriptional splicing can occur in a slow-moving zone around the genePreprint

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The quantitative impact of 3′UTRs on gene expression

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Widespread occurrence of hybrid internal-terminal exons in human transcriptomes

Fiszbein, A., McGurk, M. P., Calvo-Roitberg, E., Kim, G., Burge, C. B., & Pai, A. A. (2022) · Science Advances · doi:10.1126/sciadv.abk1752 · Cited by 16

Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders

Danckwardt, S., Trégouët, D., & Castoldi, E. (2023) · Cardiovascular Research · doi:10.1093/cvr/cvad046 · Cited by 17

CDK11, a splicing-associated kinase regulating gene expression

Hluchý, M., & Blažek, D. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.08.004 · Cited by 16

Measuring mRNA Decay with Roadblock‐qPCR

Watson, M. J., & Thoreen, C. C. (2022) · Current Protocols · doi:10.1002/cpz1.344 · Cited by 16

TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence

Wu, G., Yoshida, N., Liu, J., Zhang, X., Xiong, Y., Heavican, T. B., Mandato, E., Liu, H., Nelson, G. M., Yang, L., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.adi7244 · Cited by 15

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation

Pascal, C., Zonszain, J., Hameiri, O., Gargi-Levi, C., Lev-Maor, G., Tammer, L., Levy, T., Tarabeih, A., Roy, V. R., Ben-Salmon, S., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.003 · Cited by 17

Timing is everything: advances in quantifying splicing kinetics

Merens, H. E., Choquet, K., Baxter‐Koenigs, A. R., & Churchman, L. S. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.03.007 · Cited by 16

Long non-coding RNAs and splicing

Staněk, D. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200087 · Cited by 17

Interplay between splicing and transcriptional pausing exerts genome-wide control over alternative polyadenylation

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Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1st and 2nd chemical steps

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Multiomic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation

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