To regulate transcription, chromatin factors must impact the activities of promoters and enhancers, for example through altering their accessibility. Enhancers are classically bound by sequence-specific transcription factors that either activate or repress transcription from nearby core promoters. These interactions are poorly understood.
To begin to investigate these questions, we determined the genome-wide landscape of RNA Polymerase II transcription initiation and elongation in C. elegans embryos through sequencing short and long capped nuclear RNAs (Chen et al, 2013). We identified over 70,000 distinct clusters of transcription initiation and assigned promoters to ~8,000 protein coding genes, the vast majority previously unknown because of trans-splicing. Unexpectedly, we found that most transcription initiation events occurred at enhancers, generating long nuclear specific transcripts. Transcription has been also been observed at mammalian enhancer regions, but it is not well-characterized and its function is unclear. We also identified other types of non-coding RNAs, including hundreds of transcripts antisense to protein coding genes and the promoters that drive them. Enhancer and antisense ncRNAs could have regulatory roles, or the process of transcription could act to generate regions of open chromatin in order to enhance accessibility.
This project aims to functionally analyse enhancer and antisense transcription and to investigate the relationship between enhancers and promoters by altering elements in vivo using the newly developed Cas9-CRISPR technology for targeted mutagenesis and transgenes. The factors involved in the regulation will also be investigated using RNAi screens and mutant inactivations of chromatin factors. Further investigations will involve genome-wide mapping of key proteins using chromatin immunoprecipitation followed by high-throughput sequencing and computational analysis.
- Chen, R. A-J., Down, T.A., Stempor, P., Chen, Q.B., Egelhofer, T.A., Hillier, L.W., Jeffers, T.E. and Ahringer, J. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals enhancer and promoter architectures, Genome Research, 8, 1339-47.
- Smallwood A, Ren B. (2013) Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol.25(3):387-94.
- Natoli G, Andrau JC. (2012) Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet. 46:1-19.