scholarly journals BRG1 and BRM Chromatin-Remodeling Complexes Regulate the Hypoxia Response by Acting as Coactivators for a Subset of Hypoxia-Inducible Transcription Factor Target Genes

2013 ◽  
Vol 33 (19) ◽  
pp. 3849-3863 ◽  
Author(s):  
J. A. Sena ◽  
L. Wang ◽  
C.-J. Hu
Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 75-82 ◽  
Author(s):  
Mirana Ramialison ◽  
Ashley J. Waardenberg ◽  
Nicole Schonrock ◽  
Tram Doan ◽  
Danielle de Jong ◽  
...  

2014 ◽  
Vol 31 (6) ◽  
pp. 761-773 ◽  
Author(s):  
Emily Clough ◽  
Erin Jimenez ◽  
Yoo-Ah Kim ◽  
Cale Whitworth ◽  
Megan C. Neville ◽  
...  

2021 ◽  
Author(s):  
Anindita Dutta ◽  
Apurba Das ◽  
Deep Bisht ◽  
Vijendra Arya ◽  
Rohini Muthuswami

Cells respond to oxidative stress by elevating the levels of antioxidants, signaling, and transcriptional regulation often implemented by chromatin remodeling proteins.  The study presented in this paper shows that the expression of PICH, an ATP-dependent chromatin remodeler, is upregulated during oxidative stress in HeLa cells. We also show that PICH regulates the expression of Nrf2, a transcription factor regulating antioxidant response, both in the absence and presence of oxidative stress. In turn, Nrf2 regulates the expression of PICH in the presence of oxidative stress. Both PICH and Nrf2 together regulate the expression of antioxidant genes and this transcriptional regulation is dependent on the ATPase activity of PICH. In addition, H3K27ac modification also plays a role in activating transcription in the presence of oxidative stress. Co-immunoprecipitation experiments show that PICH and Nrf2 interact with H3K27ac in the presence of oxidative stress. Mechanistically, PICH recognizes ARE sequences present on its target genes and introduces a conformational change to the DNA sequences leading us to hypothesize that PICH regulates transcription by remodeling DNA. PICH ablation leads to reduced expression of Nrf2 and impaired antioxidant response leading to increased ROS content, thus, showing PICH is essential for the cell to respond to oxidative stress.


2009 ◽  
Vol 284 (47) ◽  
pp. 32472-32482 ◽  
Author(s):  
Hiroyuki Oya ◽  
Atsushi Yokoyama ◽  
Ikuko Yamaoka ◽  
Ryoji Fujiki ◽  
Masayoshi Yonezawa ◽  
...  

2001 ◽  
Vol 21 (19) ◽  
pp. 6450-6460 ◽  
Author(s):  
Thomas G. Fazzio ◽  
Charles Kooperberg ◽  
Jesse P. Goldmark ◽  
Cassandra Neal ◽  
Ryan Basom ◽  
...  

ABSTRACT The yeast Isw2 chromatin remodeling complex functions in parallel with the Sin3-Rpd3 histone deacetylase complex to repress early meiotic genes upon recruitment by Ume6p. For many of these genes, the effect of an isw2 mutation is partially masked by a functional Sin3-Rpd3 complex. To identify the full range of genes repressed or activated by these factors and uncover hidden targets of Isw2-dependent regulation, we performed full genome expression analyses using cDNA microarrays. We find that the Isw2 complex functions mainly in repression of transcription in a parallel pathway with the Sin3-Rpd3 complex. In addition to Ume6 target genes, we find that many Ume6-independent genes are derepressed in mutants lacking functional Isw2 and Sin3-Rpd3 complexes. Conversely, we find thatume6 mutants, but not isw2 sin3 or isw2 rpd3 double mutants, have reduced fidelity of mitotic chromosome segregation, suggesting that one or more functions of Ume6p are independent of Sin3-Rpd3 and Isw2 complexes. Chromatin structure analyses of two nonmeiotic genes reveals increased DNase I sensitivity within their regulatory regions in an isw2 mutant, as seen previously for one meiotic locus. These data suggest that the Isw2 complex functions at Ume6-dependent and -independent loci to create DNase I-inaccessible chromatin structure by regulating the positioning or placement of nucleosomes.


FEBS Journal ◽  
2008 ◽  
Vol 275 (12) ◽  
pp. 3178-3192 ◽  
Author(s):  
Ralf Mrowka ◽  
Nils Blüthgen ◽  
Michael Fähling

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2823
Author(s):  
Ian M. Overton ◽  
Andrew H. Sims ◽  
Jeremy A. Owen ◽  
Bret S. E. Heale ◽  
Matthew J. Ford ◽  
...  

Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted “neutral” (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington’s epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.


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