Persistence of backtracking by human RNA polymerase II

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• RNA polymerase II (RNA Pol II) backtracking exposes nascent RNA.
• Previous methods could only approximate quickly resolved backtracking events.
• The genome-wide distribution and extent of persistent backtracking remained unknown.

Purpose of the Study:

• To develop a method for directly sequencing backtracked 3' RNA.
• To investigate the extent and genome-wide distribution of persistent RNA Pol II backtracking.
• To understand the impact of persistent backtracking on gene expression.

Main Methods:

• Developed a novel method to directly sequence extruded, backtracked 3' RNA.
• Applied the method to analyze RNA Pol II behavior in human cells.
• Investigated the genomic locations and affected gene types associated with persistent backtracking.

Main Results:

• RNA Pol II can backtrack over 20 nucleotides in human cells and persist in this state.
• Persistent backtracking frequently occurs near promoters and intron-exon junctions.
• Genes involved in translation, replication, and development show enrichment for persistent backtracking, leading to decreased expression if unresolved.
• Histone genes are particularly prone to persistent backtracking, crucial for timely expression during cell division.

Conclusions:

• Persistent RNA polymerase II backtracking is a significant biological phenomenon in human cells.
• This backtracking can impede gene expression, particularly in critical cellular processes.
• Understanding persistent backtracking is essential for comprehending gene regulation and its impact on cellular functions.