Abstract
ObjectivesTranscription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is highly regulated at initiation, elongation and termination. Transcription is also coordinated with co-transcriptional processing of the emerging pre-mRNA by capping, splicing, and cleavage and polyadenylation. Polyadenylation (poly(A)) site recognition, which defines the end of the mRNA, relies on the cleavage and polyadenylation (CPA) complex. It was previously observed that knocking-down proteins of the CPA complex affects not only recognition of the poly(A) site but also results in increased pausing of pol II at the beginning of genes. This finding suggests that the CPA complex plays a role in regulating pol II turnover after transcription initiation.Data descriptionTo explore this possibility, we knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq in absence or presence of a transcription elongation inhibitor. In addition, we performed pol II ChIP-qPCR on a subset of protein coding genes after knocking down CFIm68.
Highlights
Data description: To explore this possibility, we knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the cleavage and polyadenylation (CPA) complex and involved in alternative polyadenylation, and performed pol RNA polymerase II (II) chromatin immunoprecipitation (ChIP)-seq in absence or presence of a transcription elongation inhibitor
The end of a protein-coding gene is defined by one or more poly(A) sites and recognition of a poly(A) site is essential for the cleavage and polyadenylation of the mRNA [1, 2]
To determine whether depletion of CFIm affects polymerase II (pol II) pausing and transcription, we used a CRISPR/Cas9 approach to reduce the expression of two subunits of CFIm, CFIm25 and CFIm68 [8, 13], and performed pol II ChIP-seq in the CFIm68KD cell line in absence or presence of an inhibitor of cyclin-dependent kinase (CDK)9, whose activity regulates pol II pause release and entry into productive elongation [14]
Summary
Data description: To explore this possibility, we knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq in absence or presence of a transcription elongation inhibitor. We performed pol II ChIP-qPCR on a subset of protein coding genes after knocking down CFIm68. The end of a protein-coding gene is defined by one or more poly(A) sites and recognition of a poly(A) site is essential for the cleavage and polyadenylation of the mRNA [1, 2].
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