Back

Mechanism of HS5-1 eRNA Regulation of Protocadherin α Cluster via R-loop Formation

Zhou, Y.; Xu, S.; Wu, Q.

2021-08-31 molecular biology
10.1101/2021.08.31.458448 bioRxiv
Show abstract

Enhancers generate bidirectional noncoding enhancer RNAs that may regulate gene expression. At present, mechanisms of eRNA functions are not fully understood. Here, we report an antisense eRNA PEARL that is transcribed from the protocadherin HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA-fragment editing, CRISPRi, and CRISPRa strategies, in conjunction with ChIRP, MeDIP, and DRIP experiments, we find that PEARL regulates Pcdh expression by forming local R-loop in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancer and target promoters. These findings have important implications regarding mechanisms by which the HS5-1 enhancer regulates stochastic Pcdh promoter choice in single cells in the brain.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
eLife
● 5828 papers in training set
Top 3%
18.3%
Similar papers in this journal
2
Molecular Cell
○ 350 papers in training set
Top 0.2%
16.8%
Similar papers in this journal
3
Genome Research
● 468 papers in training set
Top 0.3%
12.3%
Similar papers in this journal
4
Nature Communications
○ 5641 papers in training set
Top 22%
7.2%
Similar papers in this journal
50% of probability mass above
5
The EMBO Journal
○ 309 papers in training set
Top 0.3%
7.2%
Similar papers in this journal
6
Genes & Development
● 90 papers in training set
Top 0.1%
6.6%
7
Cell Reports
○ 1498 papers in training set
Top 6%
5.5%
8
Nucleic Acids Research
◐ 1281 papers in training set
Top 4%
4.4%
9
Science Advances
● 1243 papers in training set
Top 15%
2.4%
10
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 24%
2.1%
11
EMBO Reports
○ 263 papers in training set
Top 5%
1.1%
12
Communications Biology
○ 993 papers in training set
Top 22%
1.1%
13
Journal of Cell Biology
● 392 papers in training set
Top 3%
1.1%
14
Life Science Alliance
● 285 papers in training set
Top 7%
1.0%
15
Genome Biology
○ 637 papers in training set
Top 9%
0.8%
16
Cell Discovery
○ 57 papers in training set
Top 1%
0.6%
17
iScience
○ 1154 papers in training set
Top 42%
0.6%
18
Developmental Cell
○ 196 papers in training set
Top 5%
0.6%
19
Nature Genetics
○ 286 papers in training set
Top 6%
0.6%
20
Protein & Cell
◐ 25 papers in training set
Top 0.6%
0.6%
21
Nature Cell Biology
○ 118 papers in training set
Top 4%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.