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 How Criticality of Gene Regulatory Networks Affects the Resulting Morphogenesis under Genetic Perturbations

2018 ◽  
Vol 24 (2) ◽  
pp. 85-105 ◽  
Author(s):  
Hyobin Kim ◽  
Hiroki Sayama
Keyword(s):  
Single Cell ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Single Cell Level ◽  
Cell Level ◽  
Genetic Perturbations ◽  
Gene Regulatory ◽  
Seed Cell ◽  
Complex Features ◽  
The Relationship

Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single-cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher level has not been fully explored. Here we aim at revealing a potential role of criticality of GRNs in morphogenesis, which is hard to uncover through the single-cell-level studies, especially from an evolutionary viewpoint. Our model simulated the growth of a cell population from a single seed cell. All the cells were assumed to have identical intracellular GRNs. We induced genetic perturbations to the GRN of the seed cell by adding, deleting, or switching a regulatory link between a pair of genes. From numerical simulations, we found that the criticality of GRNs facilitated the formation of nontrivial morphologies when the GRNs were critical in the presence of the evolutionary perturbations. Moreover, the criticality of GRNs produced topologically homogeneous cell clusters by adjusting the spatial arrangements of cells, which led to the formation of nontrivial morphogenetic patterns. Our findings correspond to an epigenetic viewpoint that heterogeneous and complex features emerge from homogeneous and less complex components through the interactions among them. Thus, our results imply that highly structured tissues or organs in morphogenesis of multicellular organisms might stem from the criticality of GRNs.

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.

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 Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer

PLoS Genetics ◽  
2015 ◽  
Vol 11 (7) ◽  
pp. e1005325 ◽  
Author(s):  
Kim Clarke ◽  
Thomas Daubon ◽  
Nil Turan ◽  
Fabienne Soulet ◽  
Maihafizah Mohd Zahari ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
High Grade Glioma ◽  
High Grade ◽  
Hallmarks Of Cancer ◽  
Gene Regulatory
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