Versatile interactions and bioinformatics analysis of noncoding RNAs

2019 ◽  
Vol 20 (5) ◽  
pp. 1781-1794 ◽  
Author(s):  
Qi Chen ◽  
Xianwen Meng ◽  
Qi Liao ◽  
Ming Chen
Keyword(s):  
Gene Regulatory Networks ◽  
Functional Annotation ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Bioinformatics Analysis ◽  
Noncoding Rnas ◽  
Biological Functions ◽  
Computational Tools ◽  
Sequencing Technologies ◽  
Gene Regulatory

Abstract Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.

scholarly journals The Hypoxia–Long Noncoding RNA Interaction in Solid Cancers

2021 ◽  
Vol 22 (14) ◽  
pp. 7261
Author(s):  
Seung Wan Son ◽  
Ba Da Yun ◽  
Mun Gyu Song ◽  
Jin Kyeong Lee ◽  
Soo Young Choi ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Apoptotic Cell ◽  
Hallmarks Of Cancer ◽  
Dismal Prognosis ◽  
Gene Regulatory ◽  
Cellular Pathways ◽  
Rna Interaction ◽  
The Relationship

Hypoxia is one of the representative microenvironment features in cancer and is considered to be associated with the dismal prognosis of patients. Hypoxia-driven cellular pathways are largely regulated by hypoxia-inducible factors (HIFs) and notably exert influence on the hallmarks of cancer, such as stemness, angiogenesis, invasion, metastasis, and the resistance towards apoptotic cell death and therapeutic resistance; therefore, hypoxia has been considered as a potential hurdle for cancer therapy. Growing evidence has demonstrated that long noncoding RNAs (lncRNAs) are dysregulated in cancer and take part in gene regulatory networks owing to their various modes of action through interacting with proteins and microRNAs. In this review, we focus attention on the relationship between hypoxia/HIFs and lncRNAs, in company with the possibility of lncRNAs as candidate molecules for controlling cancer.

scholarly journals Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida

2018 ◽  
Author(s):  
Sunjoo Joo ◽  
Ming Hsiu Wang ◽  
Gary Lui ◽  
Jenny Lee ◽  
Andrew Barnas ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Bioinformatics Analysis ◽  
Land Plants ◽  
Protein Protein Interaction ◽  
Functional Conservation ◽  
Developmental Mechanisms ◽  
Gene Regulatory ◽  
Homeobox Transcription Factors

AbstractHomeobox transcription factors (TFs) in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, representing remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. To delineate the ancestry of TALE-TALE heterodimerization, we analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization. These results indicate that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution, a likely function being to accurately execute the haploid-to-diploid transitions during sexual development.Author summaryComplex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Highly conserved TALE-superclass homeobox TF networks in major eukaryotic lineages suggest deep ancestry of developmental mechanisms. Our results support the hypothesis that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes, a system that then diversified in the several lineages that engage in complex multicellular organization.

scholarly journals Non-Coding RNAs and their Integrated Networks

2019 ◽  
Vol 16 (3) ◽  
Author(s):  
Peijing Zhang ◽  
Wenyi Wu ◽  
Qi Chen ◽  
Ming Chen
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Protein Coding ◽  
Integrated Networks ◽  
Cellular Processes ◽  
Sequencing Technologies ◽  
Different Types ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Eukaryotic Genomes

AbstractEukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs’ essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

A Model for a Heterogeneous Genetic Network

2010 ◽  
pp. 523-545 ◽  
Author(s):  
Ângela T.F. Gonçalves ◽  
Ernesto J.F. Costa
Keyword(s):  
Directed Graph ◽  
Gene Regulatory Networks ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Genetic Network ◽  
New Model ◽  
Biological Meaning ◽  
Gene Regulatory

In this chapter, we propose a new model for gene regulatory networks (GRN). The model incorporates more biological detail than other approaches, and is based on an artificial genome from which several products like genes, mRNA, miRNA, noncoding RNA, and proteins are extracted and connected, giving rise to a heterogeneous directed graph. We study the dynamics of the networks thus obtained, along with their topology (using degree distributions). Some considerations are made about the biological meaning of the outcome of the simulations.

scholarly journals Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 337
Author(s):  
Vidya Manian ◽  
Jairo Orozco ◽  
Harshini Gangapuram ◽  
Heeralal Janwa ◽  
Carlos Agrinsoni
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Wall ◽  
Network Analysis ◽  
Root Growth ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Hub Genes ◽  
Computational Tools ◽  
Gene Regulatory ◽  
The Impact

The transcriptomic datasets of the plant model organism Arabidopsis thaliana grown in the International Space Station provided by GeneLab have been mined to isolate the impact of spaceflight microgravity on gene expressions related to root growth. A set of computational tools is used to identify the hub genes that respond differently in spaceflight with controlled lighting compared to on the ground. These computational tools based on graph-theoretic approaches are used to infer gene regulatory networks from the transcriptomic datasets. The three main algorithms used for network analyses are Least Absolute Shrinkage and Selection Operator (LASSO), Pearson correlation, and the Hyperlink-Induced Topic Search (HITS) algorithm. Graph-based spectral analyses reveal distinct properties of the spaceflight microgravity networks for the Wassilewskija (WS), Columbia (Col)-0, and mutant phytochromeD (phyD) ecotypes. The set of hub genes that are significantly altered in spaceflight microgravity are mainly involved in cell wall synthesis, protein transport, response to auxin, stress responses, and catabolic processes. Network analysis highlights five important root growth-regulating hub genes that have the highest outdegree distribution in spaceflight microgravity networks. These concerned genes coding for proteins are identified from the Gene Regulatory Networks (GRNs) corresponding to spaceflight total light environment. Furthermore, network analysis uncovers genes that encode nucleotide-diphospho-sugar interconversion enzymes that have higher transcriptional regulation in spaceflight microgravity and are involved in cell wall biosynthesis.

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