scholarly journals Corrigendum: Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks

2018 ◽  
Vol 9 ◽  
Author(s):  
Yibo Hu ◽  
Yuqi Qin ◽  
Guodong Liu
Keyword(s):  
Neurospora Crassa ◽  
Aspergillus Nidulans ◽  
Regulatory Networks ◽  
Regulatory Interactions ◽  
Transcriptional Regulatory ◽  
Evolutionary Features

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.

Computational approaches to study transcriptional regulation

2008 ◽  
Vol 36 (4) ◽  
pp. 758-765 ◽  
Author(s):  
M. Madan Babu
Keyword(s):  
Transcriptional Regulation ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Model Organisms ◽  
Emerging Pathogens ◽  
Transcriptional Regulatory Networks ◽  
Regulatory Interactions ◽  
Regulatory Circuits ◽  
Transcriptional Regulatory ◽  
The Individual

In recent years, a number of technical and experimental advances have allowed us to obtain an unprecedented amount of information about living systems on a genomic scale. Although the complete genomes of many organisms are available due to the progress made in sequencing technology, the challenge to understand how the individual genes are regulated within the cell remains. Here, I provide an overview of current computational methods to investigate transcriptional regulation. I will first discuss how representing protein–DNA interactions as a network provides us with a conceptual framework to understand the organization of regulatory interactions in an organism. I will then describe methods to predict transcription factors and cis-regulatory elements using information such as sequence, structure and evolutionary conservation. Finally, I will discuss approaches to infer genome-scale transcriptional regulatory networks using experimentally characterized interactions from model organisms and by reverse-engineering regulatory interactions that makes use of gene expression data and genomewide location data. The methods summarized here can be exploited to discover previously uncharacterized transcriptional pathways in organisms whose genome sequence is known. In addition, such a framework and approach can be invaluable to investigate transcriptional regulation in complex microbial communities such as the human gut flora or populations of emerging pathogens. Apart from these medical applications, the concepts and methods discussed can be used to understand the combinatorial logic of transcriptional regulation and can be exploited in biotechnological applications, such as in synthetic biology experiments aimed at engineering regulatory circuits for various purposes.

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 Genetics and Epigenetics of Atrial Fibrillation

2020 ◽  
Vol 21 (16) ◽  
pp. 5717 ◽  
Author(s):  
Estefanía Lozano-Velasco ◽  
Diego Franco ◽  
Amelia Aranega ◽  
Houria Daimi
Keyword(s):  
Atrial Fibrillation ◽  
Regulatory Networks ◽  
Association Studies ◽  
Functional Characterization ◽  
The Elderly ◽  
Supraventricular Arrhythmia ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Mechanisms

Atrial fibrillation (AF) is known to be the most common supraventricular arrhythmia affecting up to 1% of the general population. Its prevalence exponentially increases with age and could reach up to 8% in the elderly population. The management of AF is a complex issue that is addressed by extensive ongoing basic and clinical research. AF centers around different types of disturbances, including ion channel dysfunction, Ca2+-handling abnormalities, and structural remodeling. Genome-wide association studies (GWAS) have uncovered over 100 genetic loci associated with AF. Most of these loci point to ion channels, distinct cardiac-enriched transcription factors, as well as to other regulatory genes. Recently, the discovery of post-transcriptional regulatory mechanisms, involving non-coding RNAs (especially microRNAs), DNA methylation, and histone modification, has allowed to decipher how a normal heart develops and which modifications are involved in reshaping the processes leading to arrhythmias. This review aims to provide a current state of the field regarding the identification and functional characterization of AF-related epigenetic regulatory networks

Sign in / Sign up

Export Citation Format

Share Document