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

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 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 Tissue-specific transcription factor target identification in the Caenorhabditis elegans epidermis using targeted DamID

2020 ◽  
Author(s):  
Dimitris Katsanos ◽  
Michalis Barkoulas
Keyword(s):  
Transcription Factor ◽  
Cell Differentiation ◽  
Single Molecule ◽  
Regulatory Networks ◽  
Specific Binding ◽  
Wnt Signalling ◽  
Specific Gene ◽  
List Type ◽  
Tissue Specific ◽  
Transcription Factor Target

SummaryTranscription factors are key orchestrators of development in multicellular animals and display complex patterns of expression, as well as tissue-specific binding to targets. However, our ability to map transcription factor-target interactions in specific tissues of intact animals remains limited. We introduce here targeted DamID (TaDa) as a method to identify transcription factor targets with tissue-specific resolution in C. elegans. We focus on the epidermis as a paradigm and demonstrate that TaDa circumvents problems with Dam-associated toxicity and allows reproducible identification of putative targets. Using a combination of TaDa and single-molecule FISH (smFISH), we refine the positions of LIN-22 and NHR-25 within the epidermal gene network. We reveal direct links between these two factors and the cell differentiation programme, as well as the Wnt signalling pathway. Our results illustrate how TaDa and smFISH can be used to dissect the architecture of tissue-specific gene regulatory networks.HighlightsTaDa circumvents Dam-associated toxicity by keeping levels of Dam expression low.TaDa allows the recovery of tissue-specific methylation profiles representing TF binding.Methylation signal is enriched in regulatory regions of the genome.LIN-22 and NHR-25 targets reveal a link to cell differentiation and Wnt signalling.

scholarly journals Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

2020 ◽  
Author(s):  
Maud Fagny ◽  
Marieke Lydia Kuijjer ◽  
Maike Stam ◽  
Johann Joets ◽  
Olivier Turc ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Regulatory Network ◽  
Tissue Specificity ◽  
Target Genes ◽  
Specific Gene ◽  
Tissue Specific ◽  
Genome Wide ◽  
Gene Regulatory

AbstractEnhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.SignificanceEnhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.

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.

scholarly journals Targetfinder.org: a resource for systematic discovery of transcription factor target genes

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W233-W238 ◽  
Author(s):  
S. M. Kielbasa ◽  
N. Bluthgen ◽  
M. Fahling ◽  
R. Mrowka
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Transcription Factor Target
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