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Series GSE193494 Query DataSets for GSE193494
Status Public on Jan 06, 2023
Title MAE-seq refines regulatory elements across the genome
Organisms Homo sapiens; Mus musculus; blank sample
Experiment type Other
Summary Proper cell fate determination relies on precise spatial and temporal genome-wide cooperativities among regulatory elements (REs) and their targeted genes. However, the lengths of REs defined by different methods are varied, which indicates sequence redundancy contained and the context of the genome will be unintelligible. To figure this out, we developed a method termed as MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, more than 626,879 active enhancers are identified in mouse embryonic stem cells. Comparative analysis indicates most of histone modification datasets could be annotated by MAE-Seq loci. Additionally, 35.03% (219,623) are identified as de novo ones without any epigenetic modification. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements. Additionally, we examined the functions of some novel elements that can up-regulate gene activities. By integrating with Hi-C data, over 55.64% novel elements may have distal association with different targeted genes. As an example, we find Cdh1 gene is interacting with one novel and two known REs in mESCs. And their biological effects are investigated via CRISPR-Cas9. It indicates these distal associations can coordinate Cdh1 gene expression and mESCs proliferation. Therefore, our study provides an experimental approach to refine the REs at 25-bp resolution and it will be a great improvement to unscramble the underlying genome context.
 
Overall design Established MAE-seq technology and screened 25bp length functional enhancers in mESCs and HEK293T cells.
 
Contributor(s) Zhang Y, Zhu X
Citation(s) 38038259
Submission date Jan 11, 2022
Last update date Feb 08, 2024
Contact name JING LUO
E-mail(s) luoj17@lzu.edu.cn, luojing9520@163.com
Organization name Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences
Street address No 7,Pengfei Road,Dapeng District
City Shenzhen
ZIP/Postal code 518120
Country China
 
Platforms (3)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL29487 Illumina NovaSeq 6000 (blank sample)
Samples (8)
GSM5808469 input
GSM5808470 outputA
GSM5808471 outputB
Relations
BioProject PRJNA796352

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193494_RAW.tar 77.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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