4.3 Article

RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants

Journal

G3-GENES GENOMES GENETICS
Volume 11, Issue 11, Pages -

Publisher

OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab273

Keywords

PRO-seq; GRO-seq; promoter; enhancer; regulatory elements; pausing

Funding

  1. project Next Generation Cassava Breeding Project through Bill and Melinda Gates Foundation
  2. Department for International Development of the United Kingdom
  3. USDA-ARS
  4. NIH [GM25232, HG009393]

Ask authors/readers for more resources

New mechanisms of gene expression regulation that play important roles in plants have been identified, which have the potential to aid in crop improvement.
Control of gene expression is fundamental at every level of cell function. Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have only been studied in a handful of research experiments in plants. PRO-Seq analysis in cassava (Manihot esculents) identified peaks of transcriptionally engaged RNA polymerase at both the 5' and 3' end of genes, consistent with paused or slowly moving Polymerase. In addition, we identified divergent transcription at intergenic sites. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many intergenic regulatory element (IRE) candidates. These sites showed distinct patterns of methylation and nucleotide conservation based on genomic evolutionary rate profiling (GERP). SNPs within these IRE candidates explained significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, strongly suggesting a functional importance of these sites. Maize GRO-Seq data showed RNA polymerase occupancy at IREs consistent with patterns in cassava. Furthermore, these IREs in maize significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation, and were enriched for reported eQTL. Our results suggest that bidirectional transcription can identify intergenic genomic regions in plants that play an important role in transcription regulation and whose identification has the potential to aid crop improvement.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.3
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available