| Accession |
PRJCA003346 |
| Title |
Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity Mapping in Arabidopsis thaliana |
| Relevance |
Model organism |
| Data types |
Raw sequence reads
Genome sequencing
|
| Organisms |
Arabidopsis thaliana
|
| Description |
Enhancer activity can be quantitatively measured by STARR-seq, which assesses millions fragments in parallel. Here we show that STARR-seq is critically flawed with a systematic error in the cells of Arabidopsis thaliana (A. thaliana). Considerable portion of self-transcripts (STs) can be lost during reverse transcription if a polyadenylation signal (pAS) existed in a test DNA fragment and was used. We solve this problem by using specially designed primer to recover all self-transcribed sequences. In A. thaliana, we identified both active enhancers and enhancers quiescent in the endogenous chromatin. Different from enhancers predicted by DNase I hypersensitive sites (DHSs), majority functionally identified enhancers are mapped in sequences proximal to genes upstream and downstream, and gene expression correlates with enhancer epigenetic states. Our solution applies to methods based on self-transcript measurement, including STARR-seq. In addition, our results provide an invaluable functional enhancer map and insights into the functional complexity of enhancers in A. thaliana. |
| Sample scope |
Multiisolate |
| Release date |
2020-10-14 |
| Grants |
| Agency |
program |
Grant ID |
Grant title |
| National Key R&D Program of China
|
|
2018YFC1004500
|
|
| National Natural Science Foundation of China (NSFC)
|
|
31571347
|
|
| National Natural Science Foundation of China (NSFC)
|
|
31771430
|
|
| Southern University of Science and Technology
|
|
No.G02226301
|
|
| Southern University of Science and Technology
|
|
Y01501821
|
|
|
|
| Submitter |
Jing
Wan (1130014467@qq.com)
|
| Organization |
Huazhong Agricultural University |
| Submission date |
2020-08-27 |
