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Global Quantitative Mapping of Enhancers in Rice by STARR-seq
- Source :
- Genomics, Proteomics & Bioinformatics, Vol 17, Iss 2, Pp 140-153 (2019)
- Publication Year :
- 2019
- Publisher :
- Elsevier, 2019.
-
Abstract
- Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5′ untranslated regions (5′UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts. Keywords: Plant, Enhancer, Functional analysis, Epigenetic modification, Gene expression
- Subjects :
- Untranslated region
Transposable element
Transcription, Genetic
Computational biology
Biology
Genes, Plant
Biochemistry
Genome
Epigenesis, Genetic
Histones
03 medical and health sciences
0302 clinical medicine
STARR-seq
Genetics
Deoxyribonuclease I
Epigenetics
Promoter Regions, Genetic
Enhancer
Molecular Biology
Gene
lcsh:QH301-705.5
Original Research
Repetitive Sequences, Nucleic Acid
030304 developmental biology
0303 health sciences
Base Sequence
Models, Genetic
Acetylation
Oryza
Genomics
Sequence Analysis, DNA
Histone Code
Computational Mathematics
Enhancer Elements, Genetic
lcsh:Biology (General)
H3K4me3
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 16720229
- Volume :
- 17
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Genomics, Proteomics & Bioinformatics
- Accession number :
- edsair.doi.dedup.....6a552d28382a69bffe1f6b7421e9d4ab