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Gene-specific quantification of nascent transcription following targeted degradation of endogenous proteins in cultured cells.

ABSTRACT: Genome-wide nuclear run-ons are a powerful way to determine the impact of a perturbation such as transcription factor degradation on transcriptional patterns. But often investigators are interested in monitoring transcriptional effects at specific sets of genes, rather than the entire genome. Here we describe an approach that couples genome engineering to tag endogenous proteins for degradation with a streamlined nuclear run-on assay to yield gene-specific information on primary transcriptional changes elicited by factor depletion. For complete details on the use and execution of this protocol, please refer to Guarnaccia et al. (2021).

SUBMITTER: Guarnaccia AD

PROVIDER: S-EPMC8669106 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Gene-specific quantification of nascent transcription following targeted degradation of endogenous proteins in cultured cells.

Guarnaccia Alissa D AD Weissmiller April M AM Tansey William P WP

STAR protocols 20211208 4

Genome-wide nuclear run-ons are a powerful way to determine the impact of a perturbation such as transcription factor degradation on transcriptional patterns. But often investigators are interested in monitoring transcriptional effects at specific sets of genes, rather than the entire genome. Here we describe an approach that couples genome engineering to tag endogenous proteins for degradation with a streamlined nuclear run-on assay to yield gene-specific information on primary transcriptional ...[more]

PMID: 34917979

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