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 ...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 car-ried 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.展开更多
基金the financial support from the National Natural Science Foundation of China (Grant Nos.31571347 to CH and 31771430 to LL)Guangdong Science and Technology Department, China (Grant No. 2016A030313642 to CH)+2 种基金Shenzhen Science and Technology Innovation Commission, China (Grant No. JCYJ20150529152146478 to CH)Huazhong Agricultural University Scientific & Technological Self-innovation Foundation, China to LLthe Thousand Youth Talents Plan of China to CH
文摘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 car-ried 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.
