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Cis-regulatory units of grass genomes identified by their DNA methylation
- Source :
- Proc Natl Acad Sci U S A
- Publication Year :
- 2020
-
Abstract
- The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
- Subjects :
- 0106 biological sciences
DNA, Plant
Computational biology
Regulatory Sequences, Nucleic Acid
Biology
Poaceae
Zea mays
01 natural sciences
Genome
03 medical and health sciences
Gene Expression Regulation, Plant
Commentaries
ORFS
Enhancer
Gene
030304 developmental biology
0303 health sciences
Multidisciplinary
Promoter
DNA
DNA Methylation
Biological Sciences
Chromatin
Plant Leaves
Regulatory sequence
DNA methylation
CpG Islands
Genome, Plant
010606 plant biology & botany
Subjects
Details
- ISSN :
- 10916490
- Volume :
- 117
- Issue :
- 41
- Database :
- OpenAIRE
- Journal :
- Proceedings of the National Academy of Sciences of the United States of America
- Accession number :
- edsair.doi.dedup.....4f899533fcb52638e912faead65d024f