Nature Reviews Molecular Cell Biology, Published online: 06 October 2025; doi:10.1038/s41580-025-00895-4Co-transcriptional mRNA maturation is a complex, multistep process. This Review focuses on how the development of long-read sequencing methods enabled investigating the timing, coordination and outcomes of alternative uses of transcription start sites, splice sites and polyadenylation sites and their disease implications.

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Proteins operate through a few critical residues, yet most proteins remain uncharacterized at the deep molecular resolution, particularly within essential genes, where functional dissection is obstructed by lethality. Here, we establish a platform for mutational scanning of essential genes at their endogenous locus, combining a repressible complementation system with multiplexed CRISPR-based genome editing in budding yeast. Our approach provides a generalizable framework for dissecting essential protein function in vivo, expanding the capacity to map critical residues underlying essential cellular processes. We applied this strategy to NRD1, encoding an essential RNA Polymerase II (RNAPII) termination factor and performed a systematic alanine scanning with near-saturation coverage. We discovered novel and unexpected lethal mutations in the CTD-interacting domain (CID), thus revealing an unanticipated importance for this domain. Overall, our results demonstrate the power of our mutation scanning platform to map critical residues underlying essential cellular processes. ### Competing Interest Statement The authors have declared no competing interest. European Molecular Biology Organization, https://ror.org/04wfr2810, ALTF 889-2022

Vacancy at Department of Molecular Biology and Genetics - Protein Science, Aarhus University

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Vacancy at Department of Molecular Biology and Genetics - BiRC - Bioinformatics Research Center, Aarhus University