Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis
Our integrative analysis reveals multiple distinct classes of regulatory elements in the rice genome, with overlapping but non-identical targets and signatures. Many candidate elements share features consistent with transcriptional enhancement, though the specific criteria for defining active enhancers in plants require further characterization. These findings underscore the importance of using complementary genomic signals to discover and characterize functionally diverse regulatory elements in plant genomes.
Authors
- Patrick P. Edger (ORCID: https://orcid.org/0000-0001-6836-3041)
- Adrian E. Platts (ORCID: https://orcid.org/0000-0001-9238-9647)
- Michael D. Purugganan (ORCID: https://orcid.org/0000-0002-9197-4112)
- Zoé Joly‐Lopez (ORCID: https://orcid.org/0000-0002-7926-322X)
- Aurore Johary
- Jae Young Choi (ORCID: https://orcid.org/0000-0002-0238-8980)
- Marina Goliasse
- Fabian Ortner-Krause
Institutions
- New York University Abu Dhabi (AE)
- University of Kansas (US)
- Université du Québec à Montréal (CA)
- New York University (US)
- Michigan State University (US)
Publication Details
- Journal
- Genome biology
- Published
- 2025-08-18
- DOI
- https://doi.org/10.1186/s13059-025-03715-2
- Citations
- 3
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- National Science Foundation
- U.S. Department of Energy
- Oxford Nanopore Technologies
- New York University Abu Dhabi
- Zegar Family Foundation
- York University
- Canada Research Chairs
- Alliance de recherche numérique du Canada
- National Institutes of Health
- Natural Sciences and Engineering Research Council of Canada
- National Institute of General Medical Sciences