The bioinformatics toolbox for circRNA discovery and analysis DOI Creative Commons
Liang Chen, Changliang Wang,

Huiyan Sun

et al.

Briefings in Bioinformatics, Journal Year: 2020, Volume and Issue: 22(2), P. 1706 - 1728

Published: Jan. 2, 2020

Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which produced by covalent linkage via back-splicing linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field types biological functions circRNAs. In parallel with technological developments, practical applications circRNAs arisen including their utilization as biomarkers human disease. Currently, circRNA-associated can support projects circRNA annotation, identification network analysis competing endogenous (ceRNA). this review, we collected about 100 summarized current attributes capabilities. We also performed text mining on tool publications order reveal trends ongoing development.

Language: Английский

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1 DOI Creative Commons

Daniel J. Klionsky,

Amal Kamal Abdel‐Aziz, Sara Abdelfatah

et al.

Autophagy, Journal Year: 2021, Volume and Issue: 17(1), P. 1 - 382

Published: Jan. 2, 2021

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered field. Our knowledge base relevant new technologies also been expanding. Thus, it is important to formulate on a regular basis updated monitoring autophagy different organisms. Despite numerous reviews, there continues be confusion regarding acceptable methods evaluate autophagy, especially multicellular eukaryotes. Here, present investigators select interpret examine related processes, reviewers provide realistic reasonable critiques reports that are focused these processes. These not meant dogmatic rules, because appropriateness any assay largely depends question being asked system used. Moreover, no individual perfect every situation, calling use multiple techniques properly monitor each experimental setting. Finally, several core components machinery implicated distinct autophagic processes (canonical noncanonical autophagy), implying genetic approaches block should rely targeting two or more autophagy-related genes ideally participate steps pathway. Along similar lines, proteins involved regulate other cellular pathways including apoptosis, all them can used as specific marker bona fide responses. critically discuss current assessing information they can, cannot, provide. ultimate goal encourage intellectual technical innovation

Language: Английский

Citations

1992
Noncoding RNA therapeutics — challenges and potential solutions DOI Open Access
Melanie Winkle, Sherien M. El‐Daly, Muller Fabbri

et al.

Nature Reviews Drug Discovery, Journal Year: 2021, Volume and Issue: 20(8), P. 629 - 651

Published: June 18, 2021

Language: Английский

Citations

1142
Exosomes: key players in cancer and potential therapeutic strategy DOI Creative Commons

Jie Dai,

Yangzhou Su,

Suye Zhong

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2020, Volume and Issue: 5(1)

Published: Aug. 5, 2020

Exosomes are extracellular vesicles secreted by most eukaryotic cells and participate in intercellular communication. The components of exosomes, including proteins, DNA, mRNA, microRNA, long noncoding RNA, circular etc., which play a crucial role regulating tumor growth, metastasis, angiogenesis the process cancer development, can be used as prognostic marker and/or grading basis for patients. Hereby, we mainly summarized followed: exosome contents cancer, focusing on proteins RNA; interaction between exosomes microenvironment; mechanisms that epithelial-mesenchymal transition, invasion migration affected exosomes; suppression strategies based exosomes. Finally, application potential clinical diagnosis therapy is prospected, providing theoretical supports using to serve precise treatment clinic.

Language: Английский

Citations

913
Circular RNA: metabolism, functions and interactions with proteins DOI Creative Commons

Wei‐Yi Zhou,

Zerong Cai, Jia Liu

et al.

Molecular Cancer, Journal Year: 2020, Volume and Issue: 19(1)

Published: Dec. 1, 2020

Circular RNAs (CircRNAs) are single-stranded, covalently closed RNA molecules that ubiquitous across species ranging from viruses to mammals. Important advances have been made in the biogenesis, regulation, localization, degradation and modification of circRNAs. CircRNAs exert biological functions by acting as transcriptional regulators, microRNA (miR) sponges protein templates. Moreover, emerging evidence has revealed a group circRNAs can serve decoys, scaffolds recruiters. However, existing research on circRNA-protein interactions is quite limited. Hence, this review, we briefly summarize recent progress metabolism elaborately discuss patterns interactions, including altering between proteins, tethering or sequestering recruiting proteins chromatin, forming circRNA-protein-mRNA ternary complexes translocating redistributing proteins. Many discoveries unique expression signatures play crucial roles variety diseases, enabling them potentially act diagnostic biomarkers therapeutic targets. This review systematically evaluates mechanisms circRNAs, with hope advancing translational medicine involving

Language: Английский

Citations

886
The emerging roles of circRNAs in cancer and oncology DOI
Lasse S. Kristensen, Theresa Jakobsen, Henrik Hager

et al.

Nature Reviews Clinical Oncology, Journal Year: 2021, Volume and Issue: 19(3), P. 188 - 206

Published: Dec. 15, 2021

Language: Английский

Citations

812
The potential role of RNA N6-methyladenosine in Cancer progression DOI Creative Commons
Tianyi Wang,

Shan Kong,

Mei Tao

et al.

Molecular Cancer, Journal Year: 2020, Volume and Issue: 19(1)

Published: May 12, 2020

Abstract N6-methyladenosine (m6A) is considered the most common, abundant, and conserved internal transcript modification, especially in eukaryotic messenger RNA (mRNA). m6A installed by methyltransferases (METTL3/14, WTAP, RBM15/15B, VIRMA ZC3H13, termed “writers”), removed demethylases (FTO, ALKBH5, ALKBH3, “erasers”), recognized m6A-binding proteins (YTHDC1/2, YTHDF1/2/3, IGF2BP1/2/3, HNRNP, eIF3, “readers”). Accumulating evidence suggests that methylation greatly impacts metabolism involved pathogenesis of many kinds diseases, including cancers. In this review, we focus on physiological functions modification its related regulators, as well potential biological roles these elements human tumors.

Language: Английский

Citations

798
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution DOI Creative Commons
Jernej Ule, Benjamin J. Blencowe

Molecular Cell, Journal Year: 2019, Volume and Issue: 76(2), P. 329 - 345

Published: Oct. 1, 2019

Language: Английский

Citations

615
MicroRNAs and complex diseases: from experimental results to computational models DOI
Xing Chen,

Di Xie,

Qi Zhao

et al.

Briefings in Bioinformatics, Journal Year: 2017, Volume and Issue: 20(2), P. 515 - 539

Published: Sept. 15, 2017

Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one the most important components cell, miRNAs play growing role various essential biological processes. For recent few decades, amounts experimental methods computational models have been designed implemented to identify novel miRNA-disease associations. In this review, functions miRNAs, miRNA-target interactions, associations some publicly available miRNA-related databases discussed detail. Specially, considering fact that an increasing number experimentally confirmed, we selected five human diseases crucial disease-related provided corresponding introductions. Identifying has become goal biomedical research, which will accelerate understanding disease pathogenesis molecular level tools design for diagnosis, treatment prevention. Computational means association identification, could select promising pairs validation significantly reduce time cost experiments. Here, reviewed 20 state-of-the-art predicting from different perspectives. Finally, summarized four factors difficulties potential framework constructing powerful predict including feasible research schemas, future directions further development models.

Language: Английский

Citations

587
Circular RNAs in Cancer: Biogenesis, Function, and Clinical Significance DOI
Jiao Li, Dan Sun, Wenchen Pu

et al.

Trends in cancer, Journal Year: 2020, Volume and Issue: 6(4), P. 319 - 336

Published: Feb. 19, 2020

Language: Английский

Citations

554
The interplay between m6A RNA methylation and noncoding RNA in cancer DOI Creative Commons
Shuai Ma, Chen Chen, Xiang Ji

et al.

Journal of Hematology & Oncology, Journal Year: 2019, Volume and Issue: 12(1)

Published: Nov. 22, 2019

Abstract N6-methyladenosine (m6A) methylation, one of the most common RNA modifications, has been reported to execute important functions that affect normal life activities and diseases. Most studies have suggested m6A modification can complexity cancer progression by regulating biological related cancer. M6A noncoding RNAs regulates cleavage, transport, stability, degradation themselves. It also cell proliferation metastasis, stem differentiation, homeostasis in affecting function cells. Interestingly, play significant roles these modifications. Additionally, it is becoming increasingly clear potentially contribute clinical application treatment. In this review, we summarize effect interactions between modifications on involved progression. particular, discuss role as possible potential biomarkers therapeutic targets treatment cancers.

Language: Английский

Citations

519