scholarly journals Heterogeneous SWI/SNF chromatin remodeling complexes promote expression of microphthalmia-associated transcription factor target genes in melanoma

Oncogene ◽  
2009 ◽  
Vol 29 (1) ◽  
pp. 81-92 ◽  
Author(s):  
B Keenen ◽  
H Qi ◽  
S V Saladi ◽  
M Yeung ◽  
I L de la Serna
Keyword(s):  
Transcription Factor ◽  
Chromatin Remodeling ◽  
Target Genes ◽  
Transcription Factor Target ◽  
Chromatin Remodeling Complexes

Analysis of steric effects in DamID profiling of transcription factor target genes

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 75-82 ◽  
Author(s):  
Mirana Ramialison ◽  
Ashley J. Waardenberg ◽  
Nicole Schonrock ◽  
Tram Doan ◽  
Danielle de Jong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Steric Effects ◽  
Transcription Factor Target

scholarly journals Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

2014 ◽  
Vol 31 (6) ◽  
pp. 761-773 ◽  
Author(s):  
Emily Clough ◽  
Erin Jimenez ◽  
Yoo-Ah Kim ◽  
Cale Whitworth ◽  
Megan C. Neville ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Tissue Specific ◽  
Transcription Factor Target

scholarly journals PICH, an ATP-dependent chromatin remodeling protein, transcriptionally co-regulates oxidative stress response.

2021 ◽  
Author(s):  
Anindita Dutta ◽  
Apurba Das ◽  
Deep Bisht ◽  
Vijendra Arya ◽  
Rohini Muthuswami
Keyword(s):  
Oxidative Stress ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Stress Response ◽  
Chromatin Remodeling ◽  
Dna Sequences ◽  
Target Genes ◽  
Antioxidant Response ◽  
Oxidative Stress Response ◽  
Antioxidant Genes

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.

scholarly journals Phosphorylation of Williams Syndrome Transcription Factor by MAPK Induces a Switching between Two Distinct Chromatin Remodeling Complexes

2009 ◽  
Vol 284 (47) ◽  
pp. 32472-32482 ◽  
Author(s):  
Hiroyuki Oya ◽  
Atsushi Yokoyama ◽  
Ikuko Yamaoka ◽  
Ryoji Fujiki ◽  
Masayoshi Yonezawa ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Chromatin Remodeling ◽  
Williams Syndrome ◽  
Chromatin Remodeling Complexes

scholarly journals Widespread Collaboration of Isw2 and Sin3-Rpd3 Chromatin Remodeling Complexes in Transcriptional Repression

2001 ◽  
Vol 21 (19) ◽  
pp. 6450-6460 ◽  
Author(s):  
Thomas G. Fazzio ◽  
Charles Kooperberg ◽  
Jesse P. Goldmark ◽  
Cassandra Neal ◽  
Ryan Basom ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Full Range ◽  
Dnase I ◽  
Genome Expression ◽  
Complex Functions ◽  
Dnase I Sensitivity ◽  
Chromatin Remodeling Complexes

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.

scholarly journals Seed-based systematic discovery of specific transcription factor target genes

FEBS Journal ◽  
2008 ◽  
Vol 275 (12) ◽  
pp. 3178-3192 ◽  
Author(s):  
Ralf Mrowka ◽  
Nils Blüthgen ◽  
Michael Fähling
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Specific Transcription Factor ◽  
Transcription Factor Target

scholarly journals Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

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 ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Networks ◽  
Epithelial To Mesenchymal Transition ◽  
Target Genes ◽  
Cell Model ◽  
Tumour Progression ◽  
Mesenchymal Transition ◽  
Transcription Factor Target ◽  
Network Modules ◽  
Conserved Gene

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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