scholarly journals Identifying microRNAs and Their Editing Sites in Macaca mulatta

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 682 ◽  
Author(s):  
Qingyi Wang ◽  
Zhigang Zhao ◽  
Xiaotuo Zhang ◽  
Chenyu Lu ◽  
Shuchao Ren ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Macaca Mulatta ◽  
Small Rna ◽  
Homo Sapiens ◽  
Comprehensive Analysis ◽  
Different Types ◽  
Non Coding Rnas ◽  
Species Specific ◽  
Post Transcriptional Regulation ◽  
Mirna Editing

MicroRNAs (miRNAs) are small non-coding RNAs that are critical in post-transcriptional regulation. Macaca mulatta is an important nonhuman primate that is often used in basic and translational researches. However, the annotation of miRNAs in Macaca mulatta is far from complete, and there are no reports of miRNA editing events in Macaca mulatta, although editing may affect the biogenesis or functions of the miRNAs. To improve miRNA annotation and to reveal editing events of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from eight tissues and performed comprehensive analysis of these profiles. We identified 479 conserved pre-miRNAs that have not been reported in Macaca mulatta and 17 species specific miRNAs. Furthermore, we identified 3386 editing sites with significant editing levels from 471 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from 17 different types of organs or tissues. In addition to 16 conserved A-to-I editing sites, we identified five conserved C-to-U editing sites in miRNAs of Macaca mulatta and Homo sapiens. We also identified 11 SNPs in the miRNAs of Macaca mulatta. The analysis of the potential targets of 69 miRNAs with editing or mutation events in their seed regions suggest that these editing or mutation events severely changed their targets and their potential functions. These results significantly increase our understanding of miRNAs and their mutation/editing events in Macaca mulatta.

scholarly journals Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

RNA Biology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Diego Rivera Gelsinger ◽  
Rahul Reddy ◽  
Kathleen Whittington ◽  
Sara Debic ◽  
Jocelyne DiRuggiero
Keyword(s):  
Transcriptional Regulation ◽  
Small Rna ◽  
Redox Homeostasis ◽  
Post Transcriptional Regulation

scholarly journals Role of N6-Methyladenosine RNA Modification in Cardiovascular Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Dandan Song ◽  
Jianhua Hou ◽  
Junduo Wu ◽  
Junnan Wang
Keyword(s):  
Risk Factors ◽  
Cardiovascular Disease ◽  
Transcriptional Regulation ◽  
Recent Progress ◽  
Rna Modification ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Despite treatments being improved and many risk factors being identified, cardiovascular disease (CVD) is still a leading cause of mortality and disability worldwide. N6-methyladenosine (m6A) is the most common, abundant, and conserved internal modification in RNAs and plays an important role in the development of CVD. Many studies have shown that aabnormal m6A modifications of coding RNAs are involved in the development of CVD. In addition, non-coding RNAs (ncRNAs) exert post-transcriptional regulation in many diseases including CVD. Although ncRNAs have also been found to be modified by m6A, the studies on m6A modifications of ncRNAs in CVD are currently lacking. In this review, we summarized the recent progress in understanding m6A modifications in the context of coding RNAs and ncRNAs, as well as their regulatory roles in CVD.

scholarly journals Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli

2009 ◽  
Vol 10 (Suppl 4) ◽  
pp. S6 ◽  
Author(s):  
Rui-Sheng Wang ◽  
Guangxu Jin ◽  
Xiang-Sun Zhang ◽  
Luonan Chen
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Regulation ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

scholarly journals Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

RNA Biology ◽  
2014 ◽  
Vol 11 (11) ◽  
pp. 1375-1385 ◽  
Author(s):  
Jing Gong ◽  
Yuliang Wu ◽  
Xiantong Zhang ◽  
Yifang Liao ◽  
Vusumuzi Leroy Sibanda ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Expression Profiles ◽  
Comprehensive Analysis ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Mirna Editing

scholarly journals Small RNA Regulation of Virulence in Pathogenic Escherichia coli

2021 ◽  
Vol 10 ◽  
Author(s):  
Brandon M. Sy ◽  
Jai J. Tree
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Regulation ◽  
Virulence Factors ◽  
Small Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Human Pathogens ◽  
Rna Regulation ◽  
Wide Range ◽  
Post Transcriptional Regulation

Enteric and extraintestinal pathotypes of Escherichia coli utilize a wide range of virulence factors to colonize niches within the human body. During infection, virulence factors such as adhesins, secretions systems, or toxins require precise regulation and coordination to ensure appropriate expression. Additionally, the bacteria navigate rapidly changing environments with fluctuations in pH, temperature, and nutrient levels. Enteric pathogens utilize sophisticated, interleaved systems of transcriptional and post-transcriptional regulation to sense and respond to these changes and modulate virulence gene expression. Regulatory small RNAs and RNA-binding proteins play critical roles in the post-transcriptional regulation of virulence. In this review we discuss how the mosaic genomes of Escherichia coli pathotypes utilize small RNA regulation to adapt to their niche and become successful human pathogens.

scholarly journals Comprehensive analysis of mRNA poly(A) tail reveals complex and conserved regulation

2021 ◽  
Author(s):  
Yusheng Liu ◽  
Hu Nie ◽  
Yiwei Zhang ◽  
Falong Lu ◽  
Jiaqiang Wang
Keyword(s):  
Transcriptional Regulation ◽  
Mammalian Cells ◽  
Tail Length ◽  
Comprehensive Analysis ◽  
Full Length ◽  
New Method ◽  
Full Length Cdna ◽  
Simultaneous Evaluation ◽  
Eukaryotic Species ◽  
Post Transcriptional Regulation

Non-templated poly(A) tails are added to the 3′-end of most mRNAs, which have important roles in post-transcriptional regulation. Recent studies have revealed that poly(A) tails are not composed purely of A residues, but also contain U, C and G residues internally and at their 3′-ends, revealing new levels of complexity. However, no method is able to analyze these internal and terminal non-A residues simultaneously. Here, we developed a new method called PAIso-seq2 which captures RNA 3′-ends by direct 3′ adaptor ligation and rRNA removal by CRISPR/Cas9. This method allows simultaneous evaluation of the poly(A) tail length and 5′-end, internal, and 3′-end non-A residues together with the full-length cDNA for a transcript. Applying this method, we achieved the first complete transcriptome-wide 3′ tail map of mRNA within the nuclear and cytoplasmic compartments of mammalian cells, uncovering differences in poly(A) tail length and non-A residues between these two mRNA populations. A survey of diverse eukaryotic species revealed the conservation of a subset of poly(A) tails containing consecutive U residues in the internal positions, whereas those with consecutive C or G residues were of much lower abundance. Together, we established the first method to be able to comprehensively analyze poly(A) tail 5′-end, internal and 3′-end non-A residues in addition to the length simultaneously, and reveal the first complete mRNA 3′ tail map, providing rich insights into the regulatory roles of poly(A) tails.

scholarly journals Role of Non-Coding RNAs in Post-Transcriptional Regulation of Lung Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Dharmendra Kumar Soni ◽  
Roopa Biswas
Keyword(s):  
Transcriptional Regulation ◽  
Lung Diseases ◽  
Fine Tuning ◽  
Chronic Obstructive ◽  
Biological Processes ◽  
Obstructive Pulmonary Disease ◽  
Non Coding Rnas ◽  
Specific Tissue ◽  
Post Transcriptional Regulation

Non-coding RNAs (ncRNAs), notably microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), have recently gained increasing consideration because of their versatile role as key regulators of gene expression. They adopt diverse mechanisms to regulate transcription and translation, and thereby, the function of the protein, which is associated with several major biological processes. For example, proliferation, differentiation, apoptosis, and metabolic pathways demand fine-tuning for the precise development of a specific tissue or organ. The deregulation of ncRNA expression is concomitant with multiple diseases, including lung diseases. This review highlights recent advances in the post-transcriptional regulation of miRNAs and lncRNAs in lung diseases such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. Further, we also discuss the emerging role of ncRNAs as biomarkers as well as therapeutic targets for lung diseases. However, more investigations are required to explore miRNAs and lncRNAs interaction, and their function in the regulation of mRNA expression. Understanding these mechanisms might lead to early diagnosis and the development of novel therapeutics for lung diseases.

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