scholarly journals Organisation of the transcriptional regulation of genes involved in protein transactions in yeast

2017 ◽  
Author(s):  
Duygu Dikicioglu ◽  
Daniel J H Nightingale ◽  
Valerie Wood ◽  
Kathryn S Lilley ◽  
Stephen G Oliver
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Large Scale ◽  
Topological Analysis ◽  
Network Size ◽  
Transcriptional Level ◽  
Transcriptional Regulatory Networks ◽  
Network Function ◽  
Network Analyses ◽  
Transcriptional Regulatory

AbstractThe topological analyses of many large-scale molecular interaction networks often provide only limited insights into network function or evolution. In this paper, we argue that the functional heterogeneity of network components, rather than network size, is the main factor limiting the utility of topological analysis of large cellular networks. We have analysed large epistatic, functional, and transcriptional regulatory networks of genes that were attributed to the following biological process groupings: protein transactions, gene expression, cell cycle, and small molecule metabolism. Control analyses were performed on networks of randomly selected genes. We identified novel biological features emerging from the analysis of functionally homogenous biological networks irrespective of their size. In particular, direct regulation by transcription as an underrepresented feature of protein transactions. The analysis also demonstrated that the regulation of the genes involved in protein transactions at the transcriptional level was orchestrated by only a small number of regulators. Quantitative proteomic analysis of nuclear- and chromatin-enriched sub-cellular fractions of yeast provided supportive evidence for the conclusions generated by network analyses.

scholarly journals Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment

2021 ◽  
Author(s):  
Eric Ching-Pan Chu ◽  
Alexander Morin ◽  
Tak Hou Calvin Chang ◽  
Tue Nguyen ◽  
Yi-Cheng Tsai ◽  
...  
Keyword(s):  
Nervous System ◽  
Experimental Evidence ◽  
Regulatory Networks ◽  
Large Scale ◽  
Target Genes ◽  
High Confidence ◽  
Transcriptional Regulatory Networks ◽  
Regulatory Interactions ◽  
Transcriptional Regulatory ◽  
Significant Enrichment

To facilitate the development of large-scale transcriptional regulatory networks (TRNs) that may enable in-silico analyses of disease mechanisms, a reliable catalogue of experimentally verified direct transcriptional regulatory interactions (DTRIs) is needed for training and validation. There has been a long history of using low-throughput experiments to validate single DTRIs. Therefore, we hypothesize that a reliable set of DTRIs could be produced by curating the published literature for such evidence. In our survey of previous curation efforts, we identified the lack of details about the quantity and the types of experimental evidence to be a major gap, despite the importance of such details for the identification of bona fide DTRIs. We developed a curation protocol to inspect the published literature for support of DTRIs at the experiment level, focusing on genes important to the development of the mammalian nervous system. We sought to record three types of low-throughput experiments: Transcription factor (TF) perturbation, TF-DNA binding, and TF-reporter assays. Using this protocol, we examined a total of 1,310 papers to assemble a collection of 1,499 unique DTRIs, involving 251 TFs and 825 target genes, many of which were not reported in any other DTRI resource. The majority of DTRIs (965, 64%) were supported by two or more types of experimental evidence and 27% were supported by all three. Of the DTRIs with all three types of evidence, 170 had been tested using primary tissues or cells and 44 had been tested directly in the central nervous system. We used our resource to document research biases among reports towards a small number of well-studied TFs. To demonstrate a use case for this resource, we compared our curation to a previously published high-throughput perturbation screen and found significant enrichment of the curated targets among genes differentially expressed in the developing brain in response to Pax6 deletion. This study demonstrates a proof-of-concept for the assembly of a high confidence DTRI resource in order to support the development of large-scale TRNs.

Topology Analysis of a Metabolic Functional Gene Transcriptional Regulatory Network of Escherichia Coli

2013 ◽  
Vol 461 ◽  
pp. 648-653
Author(s):  
Qing Yu Zou ◽  
Fu Liu ◽  
Hou Tao
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Topological Analysis ◽  
Model Organisms ◽  
Transcriptional Regulatory Networks ◽  
Statistical Characterization ◽  
Functional Annotations ◽  
Physiological Processes ◽  
Transcriptional Regulatory

Under the perspectives of network science and systems biology, the characterizations of transcriptional regulatory networks (TRNs) beyond the context of model organisms have been studied extensively. However, little is still known about the structure and functionality of TRNs that control metabolic physiological processes. In this study, we present a newly version of the TRN of E.coli controlling metabolism based on functional annotations from GeneProtEC and Gene Ontology (GO). We also present an exhaustive topological analysis of the metabolic transcriptional regulatory network (MTRN), focusing on the main statistical characterization describing the topological structure and the comparison with TRN. From the results in this paper we infer that TRN and MTRN have very similar characteristic distribution.

Transcriptional Control of Parturition: Insights from Gene Regulation Studies in the Myometrium

2021 ◽  
Author(s):  
Nawrah Khader ◽  
Virlana M Shchuka ◽  
Oksana Shynlova ◽  
Jennifer A Mitchell
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Transcriptional Control ◽  
Progesterone Receptors ◽  
Activator Protein 1 ◽  
Transcriptional Regulatory Networks ◽  
Regulatory Pathways ◽  
Transcriptional Regulatory ◽  
Mechanistic Basis ◽  
Labour Onset

Abstract The onset of labour is a culmination of a series of highly coordinated and preparatory physiological events that take place throughout the gestational period. In order to produce the associated contractions needed for fetal delivery, smooth muscle cells in the muscular layer of the uterus (i.e. myometrium) undergo a transition from quiescent to contractile phenotypes. Here, we present the current understanding of the roles transcription factors play in critical labour-associated gene expression changes as part of the molecular mechanistic basis for this transition. Consideration is given to both transcription factors that have been well-studied in a myometrial context, i.e. activator protein 1 (AP-1), progesterone receptors (PRs), estrogen receptors (ERs), and nuclear factor kappa B (NF-κB), as well as additional transcription factors whose gestational event-driving contributions have been demonstrated more recently. These transcription factors may form pregnancy- and labour- associated transcriptional regulatory networks in the myometrium to modulate the timing of labour onset. A more thorough understanding of the transcription factor-mediated, labour-promoting regulatory pathways holds promise for the development of new therapeutic treatments that can be used for the prevention of preterm labour in at-risk women.

scholarly journals Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum

2021 ◽  
Vol 22 (6) ◽  
pp. 2837
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Potato Virus ◽  
Regulatory Networks ◽  
Potato Virus X ◽  
Early Response ◽  
Pathogen Resistance ◽  
Transcriptional Regulatory Networks ◽  
Unfolded Protein ◽  
Molecular Pattern ◽  
Transcriptional Regulatory ◽  
Protein Response

Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.

scholarly journals The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lei Chen ◽  
Shirley Luo ◽  
Abigail Dupre ◽  
Roshan P. Vasoya ◽  
Aditya Parthasarathy ◽  
...  
Keyword(s):  
Brush Border ◽  
Regulatory Networks ◽  
Critical Role ◽  
Yolk Sac ◽  
Apical Surface ◽  
Transcriptional Regulatory Networks ◽  
Chromatin Looping ◽  
Multiple Organs ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Mechanisms

AbstractThe brush border is comprised of microvilli surface protrusions on the apical surface of epithelia. This specialized structure greatly increases absorptive surface area and plays crucial roles in human health. However, transcriptional regulatory networks controlling brush border genes are not fully understood. Here, we identify that hepatocyte nuclear factor 4 (HNF4) transcription factor is a conserved and important regulator of brush border gene program in multiple organs, such as intestine, kidney and yolk sac. Compromised brush border gene signatures and impaired transport were observed in these tissues upon HNF4 loss. By ChIP-seq, we find HNF4 binds and activates brush border genes in the intestine and kidney. H3K4me3 HiChIP-seq identifies that HNF4 loss results in impaired chromatin looping between enhancers and promoters at gene loci of brush border genes, and instead enhanced chromatin looping at gene loci of stress fiber genes in the intestine. This study provides comprehensive transcriptional regulatory mechanisms and a functional demonstration of a critical role for HNF4 in brush border gene regulation across multiple murine epithelial tissues.

scholarly journals Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks

2009 ◽  
Vol 25 (22) ◽  
pp. 3001-3004 ◽  
Author(s):  
F. Tian ◽  
P. K. Shah ◽  
X. Liu ◽  
N. Negre ◽  
J. Chen ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Networks ◽  
Transcriptional Regulatory ◽  
Genomic Resource
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