Global Run-On sequencing to measure nascent transcription in C. elegans

Quarato, Piergiuseppe; Cecere, Germano

doi:10.1016/j.xpro.2021.100991

Cited by 2 publications

(1 citation statement)

References 6 publications

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“…It has been demonstrated that CapSeq exhibits greater precision in identifying transcription start sites compared to GRO-seq specifically within the C. elegans model 48 . Both of these methods rely on nuclei isolation, which exhibits an efficiency of approximately 50% 50 . Consequently, they necessitate a substantial amount of initial material for analysis.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of transcription-coupled repair reveals novel transcription events inCaenorhabditis elegans

Kose,

Lindsey-Boltz,

Sancar

et al. 2023

Preprint

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We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. The integration of epigenetic markers, chromatin states, enhancer RNA and long intergenic non-coding RNA annotations supports the robust detection of intergenic nascent transcription by XR-seq. Overall, our results provide a comprehensive view of the transcription-coupled repair landscape in C. elegans, highlighting its potential contributions to our understanding of DNA repair mechanisms and non-coding RNA biology.

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Section: Discussionmentioning

confidence: 99%