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

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
Ralf Mrowka ◽  
Nils Blüthgen ◽  
Szymon Kielbasa ◽  
Pontus Börje Persson ◽  
Michael Fähling
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Specific Transcription Factor ◽  
Transcription Factor Target

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

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 Phosphorylation and Maximal Activity of Saccharomyces cerevisiae Meiosis-Specific Transcription Factor Ndt80 Is Dependent on Ime2

2002 ◽  
Vol 22 (20) ◽  
pp. 7024-7040 ◽  
Author(s):  
Richelle Sopko ◽  
Sheetal Raithatha ◽  
David Stuart
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Target Genes ◽  
Meiotic Chromosome ◽  
Maximal Activity ◽  
Direct Role ◽  
Specific Transcription Factor ◽  
Mutant Strains ◽  
Sporulation Genes

ABSTRACT The Saccharomyces cerevisiae meiosis-specific transcription factor Ndt80 is responsible for the induction of a class of genes referred to as middle sporulation genes. Among the members of this family are the B-type cyclins and other genes whose products are required for meiotic chromosome division and spore morphogenesis. Inactivation of NDT80 leads to a failure to induce the middle sporulation genes and a subsequent arrest in pachytene. The expression of NDT80 is itself highly regulated. The initial transcription of NDT80 is dependent upon the protein kinase Ime2; once Ndt80 protein accumulates, it activates its own promoter, thus generating an autoactivation loop. In addition to being transcriptionally regulated, Ndt80 protein is posttranslationally regulated. Phosphorylation of Ndt80 occurs coincident with its activation as a transcription factor. If expressed prematurely in meiosis, Ndt80 accumulates initially in an unmodified form that is subsequently modified by phosphorylation. In contrast, Ndt80 expressed in ime2 mutant strains does not become modified and has a reduced ability to activate transcription of its target genes. Ime2 can also phosphorylate Ndt80 in vitro, further supporting a direct role for Ime2 in the phosphorylation of Ndt80. These data indicate that Ime2 plays a novel and previously unexpected role in promoting chromosome dissemination and progress through meiotic development by activating Ndt80.

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.

Abstract 2042: Cancer-specific transcription factor BORIS has different effects on expression of its target genes via chromatin structure alterations

2011 ◽  
Author(s):  
Daria A. Gaykalova ◽  
Chad A. Glazer ◽  
Rajita Vatapalli ◽  
Sheetal Bhan ◽  
Chunbo Shao ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Chromatin Structure ◽  
Target Genes ◽  
Specific Transcription Factor

Identification of Target Genes of the Lymphoid-Specific Transcription Factor Oct2

Immunobiology ◽  
1997 ◽  
Vol 198 (1-3) ◽  
pp. 217-226 ◽  
Author(s):  
Petra Pfisterer ◽  
Jochen Hess ◽  
Thomas Wirth
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Specific Transcription Factor
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