Defining pervasive transcription units using chromatin RNA-sequencing data.

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Pervasive transcripts (PTs) are transient RNA molecules rapidly degraded by the nuclear exosome complex.
• Detecting PTs using standard steady-state RNA sequencing is challenging due to their short half-life.

Purpose of the Study:

• To develop a convenient and cost-efficient bioinformatic pipeline for the *de novo* genome-wide annotation of pervasive transcripts (PTs).
• To improve the precision of PT 3'-end definition compared to existing nascent RNA sequencing methods.

Main Methods:

• Utilized chromatin-associated RNA sequencing data from cells with depleted DIS3 (a key component of the nuclear exosome).
• Developed a bioinformatic pipeline for *de novo* annotation of PTs from the generated RNA-seq data.
• Compared the protocol's performance against nascent RNA-seq methods like TT-seq and PRO-seq.

Main Results:

• The developed protocol enables genome-wide PT annotation.
• This method is more convenient and cost-efficient than TT-seq and PRO-seq.
• The protocol provides more precise 3'-end definition for PTs compared to PRO-seq, which exhibits 5'-end read skew.

Conclusions:

• The described bioinformatic pipeline offers a practical and precise approach for pervasive transcript discovery.
• This method enhances the study of transient RNA species and their regulation by the nuclear exosome.