scholarly journals Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate

2012 ◽  
Vol 8 (10) ◽  
pp. e1002734 ◽  
Author(s):  
Jasmin Coulombe-Huntington ◽  
Yu Xia
Keyword(s):  
Transcription Factor ◽  
Network Structure ◽  
Regulatory Network ◽  
Evolutionary Rate

scholarly journals Regulatory network structure determines patterns of intermolecular epistasis

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Mato Lagator ◽  
Srdjan Sarikas ◽  
Hande Acar ◽  
Jonathan P Bollback ◽  
Călin C Guet
Keyword(s):  
Transcription Factor ◽  
Adaptive Evolution ◽  
Network Structure ◽  
Phenotypic Variation ◽  
Regulatory Network ◽  
Individual Component ◽  
Regulatory System ◽  
Molecular Systems ◽  
Transcriptional Regulatory ◽  
Dna Binding Site

Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution.

Construction of transcription factor mutual regulatory network based on a new database

2014 ◽  
Author(s):  
Zhenping Yang ◽  
Wei Wang ◽  
Yang Yang ◽  
Hongfei Chen ◽  
Jinke Wang
Keyword(s):  
Transcription Factor ◽  
Regulatory Network

scholarly journals Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Albert T. Young ◽  
Xavier Carette ◽  
Michaela Helmel ◽  
Hanno Steen ◽  
Robert N. Husson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Mycobacterium Tuberculosis ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Protein Interaction Data ◽  
Kinase Inhibition ◽  
Protein Protein Interaction ◽  
Downstream Effects ◽  
Regulate Cell Growth ◽  
Regulatory Effects

AbstractThe ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

scholarly journals Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm

RSC Advances ◽  
2017 ◽  
Vol 7 (37) ◽  
pp. 23222-23233 ◽  
Author(s):  
Wei Liu ◽  
Wen Zhu ◽  
Bo Liao ◽  
Haowen Chen ◽  
Siqi Ren ◽  
...  
Keyword(s):  
Systems Biology ◽  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Network Structure ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Central Problem ◽  
Expression Data ◽  
Redundancy Reduction ◽  
Gene Regulatory

Inferring gene regulatory networks from expression data is a central problem in systems biology.

scholarly journals Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation

Zebrafish ◽  
2018 ◽  
Vol 15 (2) ◽  
pp. 202-205 ◽  
Author(s):  
Justin King ◽  
Justin Foster ◽  
James M. Davison ◽  
John F. Rawls ◽  
Ghislain Breton
Keyword(s):  
Transcription Factor ◽  
Regulatory Network ◽  
Gene Discovery

Deciphering the transcription factor-microRNA-target gene regulatory network associated with graphene oxide cytotoxicity

2018 ◽  
Vol 12 (9) ◽  
pp. 1014-1026 ◽  
Author(s):  
Masoumeh Farahani ◽  
Mostafa Rezaei–Tavirani ◽  
Hakimeh Zali ◽  
Afsaneh Arefi Oskouie ◽  
Meisam Omidi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Graphene Oxide ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Target Gene ◽  
Microrna Target ◽  
Gene Regulatory

scholarly journals Class I TCP transcription factors regulate trichome branching and cuticle development in Arabidopsis

2020 ◽  
Vol 71 (18) ◽  
pp. 5438-5453
Author(s):  
Alejandra Camoirano ◽  
Agustín L Arce ◽  
Federico D Ariel ◽  
Antonela L Alem ◽  
Daniel H Gonzalez ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Class I ◽  
Branch Number ◽  
Plant Organ ◽  
Cuticle Formation ◽  
Cuticle Development ◽  
Different Levels

Abstract Trichomes and the cuticle are two specialized structures of the aerial epidermis that are important for plant organ development and interaction with the environment. In this study, we report that Arabidopsis thaliana plants affected in the function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 show overbranched trichomes in leaves and stems and increased cuticle permeability. We found that TCP15 regulates the expression of MYB106, a MIXTA-like transcription factor involved in epidermal cell and cuticle development, and overexpression of MYB106 in a tcp14 tcp15 mutant reduces trichome branch number. TCP14 and TCP15 are also required for the expression of the cuticle biosynthesis genes CYP86A4, GPAT6, and CUS2, and of SHN1 and SHN2, two AP2/EREBP transcription factors required for cutin and wax biosynthesis. SHN1 and CUS2 are also targets of TCP15, indicating that class I TCPs influence cuticle formation acting at different levels, through the regulation of MIXTA-like and SHN transcription factors and of cuticle biosynthesis genes. Our study indicates that class I TCPs are coordinators of the regulatory network involved in trichome and cuticle development.

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