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Divergent transcription from active promoters
Amy C Seila1, J Mauro Calabrese, Stuart S Levine
1Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Science (New York, N.Y.)
|December 6, 2008
Summary
Most genes initiate transcription unidirectionally. This study reveals widespread divergent transcription at protein-encoding gene promoters, with short RNAs flanking active promoter regions, suggesting a poised state for regulation.
Area of Science:
- Molecular Biology
- Genetics
- Epigenetics
Background:
- Transcription initiation by RNA polymerase II (RNAPII) is traditionally considered unidirectional.
- The precise mechanisms governing promoter activity and gene regulation are still under investigation.
Purpose of the Study:
- To investigate the phenomenon of divergent transcription at protein-encoding gene promoters.
- To characterize the nature and genomic location of transcription start site-associated RNAs (TSSa-RNAs).
Main Methods:
- Northern blot analysis to detect and characterize TSSa-RNAs.
- Chromatin immunoprecipitation (ChIP) to assess histone modifications (H3K4me3, H3K79me2) and RNAPII occupancy at promoter regions.
Main Results:
- Evidence of widespread divergent transcription, producing both sense and antisense short RNAs, flanking active promoters.
- TSSa-RNAs, ranging from 20-90 nucleotides, exhibit distinct positional biases: antisense peaks upstream and sense peaks downstream of transcription start sites (TSSs).
- Hallmarks of transcription initiation (RNAPII, H3K4me3) colocalize with TSSa-RNA positions, while marks of elongation (H3K79me2) are found downstream of TSSs.
Conclusions:
- Short-distance divergent transcription is a common feature of active protein-encoding gene promoters.
- This divergent transcription may contribute to maintaining promoter regions in a poised state for subsequent gene regulation.
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