Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Most RNA processing events, such as splicing and editing, occur concurrently with transcription.
• The structure of nascent RNA (ribonucleic acid) molecules plays a crucial role in these processing events.
• Understanding the relationship between RNA structure and processing is key to deciphering gene regulation.

Purpose of the Study:

• To investigate the structure of nascent RNA transcripts (the "nascent RNA structureome").
• To determine how this structure relates to key RNA processing events: splicing, adenosine-to-inosine (A-I) editing, and transcription speed.
• To explore the impact of altered transcription speed on RNA folding and subsequent processing.

Main Methods:

• Chemical and enzymatic probing of nascent RNA polymerase II (pol II) transcripts.
• Analysis of RNA folding patterns in relation to splicing efficiency and A-I editing.
• Utilizing a slow pol II mutant and UV treatment to modulate transcription speed and observe structural changes.

Main Results:

• Intronic RNA folding and structural transitions at splice sites correlate with efficient co-transcriptional splicing.
• Slower transcription leads to more folded RNA conformations, increased A-I editing, and altered splicing of Alu elements, promoting cryptic splicing and intron retention.
• Changes in RNA folding due to slow transcription can predict alternative splicing outcomes (exon skipping or inclusion), even for post-transcriptional events.

Conclusions:

• The structure of nascent RNA is a critical determinant of co-transcriptional RNA processing.
• Transcription speed dynamically remodels RNA folding, influencing both co-transcriptional and post-transcriptional RNA processing.
• The plasticity of nascent RNA structure has broad implications for gene expression regulation.