Faculty Opinions recommendation of Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness.

Author(s):  
Salvatore Spicuglia
2021 ◽  
Author(s):  
Tomas Pachano ◽  
Víctor Sánchez-Gaya ◽  
Thais Ealo ◽  
Maria Mariner-Faulí ◽  
Tore Bleckwehl ◽  
...  

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Jianan Bai ◽  
Junchi Yu ◽  
Jintian Wang ◽  
Bingyan Xue ◽  
Na He ◽  
...  

Aberrant microRNA (miRNA) expressions contribute to the development and progression of various diseases, including Crohn’s disease (CD). However, the accurate mechanisms of miRNAs in CD are definitely unclear. We employed colonic tissue samples from normal volunteers and CD patients, an acute mice colitis model induced by 2,4,6-trinitro-benzene-sulfonic acid (TNBS), and a cellular oxidative stress model induced by H2O2 in HT-29 cells to determine the effects of oxidative stress on expressions of miR-122, selenium-binding protein 1 (SELENBP1, SBP1), p65 nuclear factor κB (p65NF-κB) signaling, and DNA methylation. We found that SBP1 was mainly located on epithelial cells and was significantly increased in patients with active CD. SBP1 was the target gene of miR-122. miR-122 expression was downregulated while SBP1 expression was upregulated under TNBS-induced colitis or oxidative stress. Pre-miR-122 or siRNA SBP1 (si-SBP1) treatment ameliorated acute TNBS-induced colitis and H2O2-induced oxidative stress. Cotreatment of pre-miR-122 and si-SBP1 enhanced these effects. Besides, pre-miR-122 and si-SBP1 obviously activated the p65NF-κB signaling by phosphorylation of IκBα. Bisulfite sequencing of the CpG islands in the promoter region of miR-122 showed that CpG methylation was significantly increased under oxidative stress. Treating cells with 5′-AZA which was well known as a DNA-demethylating agent significantly increased miR-122 expression. Our results suggest that oxidative stress-induced DNA methylation of miR-122 aggravates colitis targeting SELENBP1 partially by p65NF-κB signaling and may promote the progression of CD.


Author(s):  
Tomás Pachano ◽  
Víctor Sánchez-Gaya ◽  
María Mariner-Faulí ◽  
Thais Ealo ◽  
Helena G. Asenjo ◽  
...  

ARTICLECpG islands (CGIs) represent a distinctive and widespread genetic feature of vertebrate genomes, being associated with ∼70% of all annotated gene promoters1. CGIs have been proposed to control transcription initiation by conferring nearby promoters with unique chromatin properties2–4. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance and mechanism of action are barely known5–7. Here we show that oCGIs are an essential component of poised enhancers (PEs)8, 9 that boost their long-range regulatory activity and dictate the responsiveness of their target genes. Using a CRISPR/Cas9 knock-in strategy in mESC, we introduced PEs with or without oCGIs within topological associating domains (TADs) harbouring genes with different types of promoters. By evaluating the chromatin, topological and regulatory properties of the engineered PEs, we uncover that, rather than increasing their local activation, oCGIs boost the physical and functional communication between PEs and distally located developmental genes. Furthermore, we demonstrate that developmental genes with CpG rich promoters are particularly responsive to PEs and that such responsiveness depends on the presence of oCGIs. Therefore, our work unveils a novel role for CGIs as genetic determinants of the compatibility between genes and enhancers, thus providing major insights into how developmental gene expression programs are deployed under both physiological and pathological conditions10–12.


2020 ◽  
Author(s):  
K Weigert ◽  
O Alejo-Valle ◽  
M Labuhn ◽  
V Amstislavskiy ◽  
S Emmrich ◽  
...  
Keyword(s):  

2016 ◽  
Author(s):  
Bushra Shammout ◽  
Adewonuola Alase ◽  
Miriam Wittmann ◽  
Paul Stewart ◽  
Ana Tiganescu

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 2049-P
Author(s):  
REBECCA K. DAVIDSON ◽  
NOLAN CASEY ◽  
JASON SPAETH

Sign in / Sign up

Export Citation Format

Share Document