Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues.

08:00 EDT 16th May 2019 | BioPortfolio

Summary of "Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues."

Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster, to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT3 and NR2C2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues.


Journal Details

This article was published in the following journal.

Name: PloS one
ISSN: 1932-6203
Pages: e0216475


DeepDyve research library

PubMed Articles [25928 Associated PubMed Articles listed on BioPortfolio]

Identification of novel Gata3 distal enhancers active in mouse embryonic lens.

The tissue-specific transcriptional programs during normal development require tight control by distal cis-regulatory elements, such as enhancers, with specific DNA sequences recognized by transcripti...

Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method.

Correct species identification is necessary for meat product quality assurance. Genetic markers are useful tools to accurately determine the animal source of meat products. To better protect yak meat ...

Identification of Transcription Factor-Binding Sites in the Mouse FOXO1 Promoter.

One critical determinant of levels of gene expression is binding of transcription factors to cognate DNA sequences in promoter and enhancer regions of target genes. Transcription factors are DNA-bindi...

Promoter analysis and prediction in the human genome using sequence-based deep learning models.

Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initi...

The Use of Cre/loxP Inducible Mouse Models to Dissect the Specific Roles of Calcineurin Signaling in Myeloid Cells.

The calcineurin/nuclear factor of activated T-cell (NFAT) signaling pathway is important for the development and function of different leukocyte subsets. Calcineurin is activated through increased int...

Clinical Trials [8461 Associated Clinical Trials listed on BioPortfolio]

Neuroprotectant for Hypertensive Intracerebral Hemorrhage

Cattle encephalon glycoside and ignotin Cattle encephalon glycoside and ignotin (CEGI) injection (drug approval H22025046; Jilin Sihuan Pharmaceutical Co. LTD., Jilin, People's Republic of...

Impact of Anti-Tumor Necrosis Factor (TNF) Antibodies on the T-Lymphocyte and Macrophage Cooperation in Crohn Disease

The aim of this research is to study Crohn disease patients before and after anti-TNF, the cooperation between lamina propria T-lymphocytes and macrophages, through the expression of co-si...

Effects of Physical Activities on the Expression of Nrf2 and Nf-kb Hemodialysis Patients

Oxidative stress and inflammation are cardiovascular risk factors in patients with chronic kidney disease (CKD) undergoing hemodialysis (HD). Nuclear transcription factors play roles in th...

TIFACT Study – Tissue Factor Expression by Adipose Tissue in Extremely Obese Subjects.

Tissue factor is the main activator of coagulation cascades. Excessive tissue factor expression is made responsible of thrombosis in a number of clinical situations including thrombosis in...

Computed Tomography (CT) and Lung Function Data Collection for Computational Fluid Dynamics (CFD) in Chronic Obstructive Pulmonary Disease (COPD) Patients

In this study, 20 COPD patients will undergo a high-resolution/multi slice CT scan and lung function tests to obtain patient specific geometries of the central and peripheral small airways...

Medical and Biotech [MESH] Definitions

An RNA POLYMERASE II specific transcription factor. It may play a role in transcriptional activation of gene expression by interacting with the TATA-BOX BINDING PROTEIN component of TRANSCRIPTION FACTOR TFIID.

A tissue-specific subunit of NF-E2 transcription factor that interacts with small MAF PROTEINS to regulate gene expression. P45 NF-E2 protein is expressed primarily in MEGAKARYOCYTES; ERYTHROID CELLS; and MAST CELLS.

A basic-leucine zipper transcription factor that regulates GLOBIN gene expression and is related to TRANSCRIPTION FACTOR AP-1. NF-E2 consists of a small MAF protein subunit and a tissue-restricted 45 kDa subunit.

Maf transcription factors are a family of basic-leucine zipper transcription factors that are closely related to V-MAF ONCOGENE PROTEIN. The C-MAF PROTO-ONCOGENE PROTEIN was the first mammalian Maf transcription factor identified, and now the family is known to include a variety of other Maf proteins such as MAFB TRANSCRIPTION FACTOR; MAFF TRANSCRIPTION FACTOR; MAFG TRANSCRIPTION FACTOR; and MAFK TRANSCRIPTION FACTOR.

An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.

Quick Search


DeepDyve research library

Relevant Topic

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article