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Defining pervasive transcription units using chromatin RNA-sequencing data.

ABSTRACT: Pervasive transcripts (PTs) are difficult to detect by steady-state RNA-seq, because they are degraded immediately by the nuclear exosome complex. Here, we describe a protocol illustrating a bioinformatic pipeline for genome-wide PTs de novo annotation via chromatin-associated RNA-seq data upon DIS3 depletion. Compared to defining PTs by nascent RNA-seq such as TT-seq and PRO-seq, this protocol is more convenient and cost efficient. In addition, this protocol defines 3'-end of PTs more precisely, while reads from PRO-seq have a skew at the 5'-end. For complete details on the use and execution of this protocol, please refer to Liu et al. (2022).

SUBMITTER: Guo Z

PROVIDER: S-EPMC9184797 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Defining pervasive transcription units using chromatin RNA-sequencing data.

Guo Ziwei Z Liu Xinhong X Chen Mo M

STAR protocols 20220607 2

Pervasive transcripts (PTs) are difficult to detect by steady-state RNA-seq, because they are degraded immediately by the nuclear exosome complex. Here, we describe a protocol illustrating a bioinformatic pipeline for genome-wide PTs <i>de novo</i> annotation via chromatin-associated RNA-seq data upon DIS3 depletion. Compared to defining PTs by nascent RNA-seq such as TT-seq and PRO-seq, this protocol is more convenient and cost efficient. In addition, this protocol defines 3'-end of PTs more pr ...[more]

PMID: 35693207

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