A brief review of circRNA biogenesis, detection and function

2021 ◽  
Vol 22 ◽  
Author(s):  
Ying Liang ◽  
Niannian Liu ◽  
Le Yang ◽  
Jianjun Tang ◽  
Yinglong Wang ◽  
...  
Keyword(s):  
Transcriptional Regulator ◽  
Circular Rna ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Sequence Feature ◽  
Potential Biomarker ◽  
And Function ◽  
The Brain ◽  
Generation Sequencing

: Circular RNA (circRNA) is a non-coding molecule produced through alternative splicing of one or more exons of a gene in the presence of RNA-induced silencing complex (RISC). Its formation depends on complementary intron sequences on both sides of the circularized sequence. CircRNA functions as a sponge for miRNA, playing the role of transcriptional regulator or potential biomarker. It has an impact on fetal growth and on synaptic facilitation in the brain. In this review, we illustrate biogenesis mechanisms, characteristics and functions of cirRNAs. We also summarize methods using sequence feature and RNA next-generation sequencing data for circRNA prediction. Finally, we discuss the state of the research on circRNA in diseases, which will bring new contributions to future disease treatments.

Role of reverse phenotyping in interpretation of next generation sequencing data and a review of INPP5E related disorders

2016 ◽  
Vol 20 (2) ◽  
pp. 286-295 ◽  
Author(s):  
Christian de Goede ◽  
Wyatt W. Yue ◽  
Guanhua Yan ◽  
Shyamala Ariyaratnam ◽  
Kate E. Chandler ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals Circular RNA CREBBP Suppresses Hepatic Fibrosis Via Targeting the hsa-miR-1291/LEFTY2 Axis

2021 ◽  
Vol 12 ◽  
Author(s):  
Ya-Ru Yang ◽  
Shuang Hu ◽  
Fang-Tian Bu ◽  
Hao Li ◽  
Cheng Huang ◽  
...  
Keyword(s):  
Hepatic Fibrosis ◽  
Circular Rna ◽  
Vehicle Group ◽  
Potential Biomarker ◽  
Function Loss ◽  
And Function ◽  
Pro Inflammatory Cytokines

CircRNAs (circRNAs) are commonly dysregulated in a variety of human diseases and are involved in the development and progression of cancer. However, the role of circRNAs in hepatic fibrosis (HF) is still unclear. Our previous high throughput screen revealed changes in many circRNAs in mice with carbon tetrachloride (CCl4)-induced HF. For example, circCREBBP was significantly down-regulated in primary hepatic stellate cells (HSCs) and liver tissue of HF mice induced by CCl4 compared to those in the vehicle group. Overexpression of circCREBBP with AAV8-circCREBBP in vivo prevented CCl4-induced HF worsening by reducing serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) contents, liver hydroxyproline levels, collagen deposition, and levels of pro-fibrosis genes and pro-inflammatory cytokines. Furthermore, in vitro function loss and function gain analysis showed that circCREBBP inhibited HSCs activation and proliferation. Mechanically, circCREBBP acts as a sponge for hsa-miR-1291 and subsequently promotes LEFTY2 expression. In conclusion, our current results reveal a novel mechanism by which circCREBBP alleviates liver fibrosis by targeting the hsa-miR-1291/LEFTY2 axis, and also suggest that circCREBBP may be a potential biomarker for heart failure.

scholarly journals NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

2021 ◽  
Author(s):  
Anne Krogh Nøhr ◽  
Kristian Hanghøj ◽  
Genis Garcia Erill ◽  
Zilong Li ◽  
Ida Moltke ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Software Tool ◽  
Estimation Methods ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C ++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

The role of GABAA receptor biogenesis, structure and function in epilepsy

2006 ◽  
Vol 34 (5) ◽  
pp. 863-867 ◽  
Author(s):  
S. Mizielinska ◽  
S. Greenwood ◽  
C.N. Connolly
Keyword(s):  
Gabaa Receptor ◽  
Structure And Function ◽  
Inhibitory Synapses ◽  
Normal Brain ◽  
Synaptic Targeting ◽  
Acid Type ◽  
Normal Brain Function ◽  
And Function ◽  
The Brain

Maintaining the correct balance in neuronal activation is of paramount importance to normal brain function. Imbalances due to changes in excitation or inhibition can lead to a variety of disorders ranging from the clinically extreme (e.g. epilepsy) to the more subtle (e.g. anxiety). In the brain, the most common inhibitory synapses are regulated by GABAA (γ-aminobutyric acid type A) receptors, a role commensurate with their importance as therapeutic targets. Remarkably, we still know relatively little about GABAA receptor biogenesis. Receptors are constructed as pentameric ion channels, with α and β subunits being the minimal requirement, and the incorporation of a γ subunit being necessary for benzodiazepine modulation and synaptic targeting. Insights have been provided by the discovery of several specific assembly signals within different GABAA receptor subunits. Moreover, a number of recent studies on GABAA receptor mutations associated with epilepsy have further enhanced our understanding of GABAA receptor biogenesis, structure and function.

scholarly journals recoup: flexible and versatile signal visualization from next generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Panagiotis Moulos
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Special Focus ◽  
Next Generation ◽  
Sequencing Data ◽  
User Friendliness ◽  
Computational Environment ◽  
Level Data ◽  
Data Signal ◽  
Generation Sequencing

Abstract Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.

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