ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides

Liu, Haizhou; Xu, Zhou; Yuan, Mengqin; Zhou, Shunheng; Huang, Yue; Hou, Fei; Song, Xiaofeng; Wang, Lihong; Jiang, Wei

doi:10.1016/j.jmb.2020.02.022

Cited by 42 publications

(27 citation statements)

References 16 publications

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“…The functions of circRNA have also been unveiled (Kristensen et al, 2019; Xiao, Ai, & Wilusz, 2020). Existing research have showed that circRNA can be used as a microRNA sponge (Chen et al, 2020; Hansen et al, 2013; Memczak et al, 2013; Panda, 2018; Piwecka et al, 2017; Zheng et al, 2016), RNA‐binding proteins (RBPs) sponge (Ashwal‐Fluss et al, 2014; Xia et al, 2018), or translated and encoded into a polypeptide to participate in functions (Legnini et al, 2017; Liu et al, 2020; Pamudurti et al, 2017). In addition, a class of circRNA (called exon‐intron circRNAs or EIciRNAs) that “retain” introns between exons can enhance the transcription of their parental genes through specific RNA–RNA interactions with U1snRNP (Li et al, 2015).…”

Section: Extended Knowledge On Alternative Splicingmentioning

confidence: 99%

RNA structures in alternative splicing and back‐splicing

Meng

Jin

2020

WIREs RNA

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Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back-and trans-splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and backsplicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and backsplicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases.

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Section: Extended Knowledge On Alternative Splicingmentioning

confidence: 99%

RNA structures in alternative splicing and back‐splicing

Meng

Jin

2020

WIREs RNA

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“…The information about circRNA-encoded proteins is scattered in many published papers, which is not conducive to further exploration on circRNA translation. Liu et al 91 presented an ncEP database, which recorded all published articles containing proteins or peptides encoded by ncRNAs. These discoveries imply that the coding potential of circRNAs has been largely disregarded, which may help to deepen our understanding of circRNAs.…”

Section: Circrnamentioning

confidence: 99%

The Role of N⁶-Methyladenosine Modified Circular RNA in Pathophysiological Processes

Tang

2021

Int. J. Biol. Sci.

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Circular RNA (circRNA) is a type of covalently closed and endogenous non-coding RNA (ncRNA) with tissue- and cell-specific expression patterns generated by a non-canonical splicing event. Previous reports have indicated that circRNAs exert their functions in different ways, thereby participating in various pathophysiological processes. N 6 -methyladenosine (m 6 A) methylation occurs in the N 6 -position, which is the most abundant and conserved internal transcriptional modification in eukaryotes, including mRNA and ncRNAs. Accumulating evidences confirm that m 6 A modification also exists in the circRNA and greatly affects the biological functions of circRNA. Their dysregulated expression can be a cause of various pathophysiological processes, such as spermatogenesis, myoblast differentiation, cancer, cardiovascular disease, mental illness and so on. Understanding the role of m 6 A-modified circRNAs in pathophysiological processes may contribute to better understanding the physiological mechanisms and develop new biomarkers. This review summarizes the regulatory mechanism of m 6 A modification on circRNA metabolism and the role of m 6 A-modified circRNAs in pathophysiological processes. This article may pave the way for a better understanding of the role of epigenetically modified circRNAs in pathophysiological process.

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“…Ribosome profiling sequencing provides a feasible method to explore the coding potential of putative ncRNAs such as long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and pri-miRNA, although this cue is not sufficient to classify transcripts as coding or non-coding (Ingolia et al, 2012;Guttman et al, 2013). Recently, ncEP, a manually curated database for collecting validated ncRNA-encoded proteins or peptides, is constructed and enriches the repository of coding RNAs (Liu et al, 2020). LncRNAs are usually defined as transcripts that are longer than 200 nt in length and do not encode a discernable protein (Chekanova, 2015).…”

Section: Coding Of Short Open Reading Frames In Putative Non-coding Rnasmentioning

confidence: 99%

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

et al. 2021

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Peptides composed of a short chain of amino acids can play significant roles in plant growth, development, and stress responses. Most of these functional peptides are derived by either processing precursor proteins or direct translation of small open reading frames present in the genome and sometimes located in the untranslated region sequence of a messenger RNA. Generally, canonical peptides serve as local signal molecules mediating short- or long-distance intercellular communication. Also, they are commonly used as ligands perceived by an associated receptor, triggering cellular signaling transduction. In recent years, increasing pieces of evidence from studies in both plants and animals have revealed that peptides are also encoded by RNAs currently defined as non-coding RNAs (ncRNAs), including long ncRNAs, circular RNAs, and primary microRNAs. Primary microRNAs (miRNAs) have been reported to encode regulatory peptides in Arabidopsis, grapevine, soybean, and Medicago, called miRNA-encoded peptides (miPEPs). Remarkably, overexpression or exogenous applications of miPEPs specifically increase the expression level of their corresponding miRNAs by enhancing the transcription of the MIRNA (MIR) genes. Here, we first outline the current knowledge regarding the coding of putative ncRNAs. Notably, we review in detail the limited studies available regarding the translation of miPEPs and their relevant regulatory mechanisms. Furthermore, we discuss the potential cellular and molecular mechanisms in which miPEPs might be involved in plants and raise problems that needed to be solved.

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ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides

Cited by 42 publications

References 16 publications

RNA structures in alternative splicing and back‐splicing

RNA structures in alternative splicing and back‐splicing

The Role of N⁶-Methyladenosine Modified Circular RNA in Pathophysiological Processes

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

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ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides

Cited by 42 publications

References 16 publications

RNA structures in alternative splicing and back‐splicing

RNA structures in alternative splicing and back‐splicing

The Role of N6-Methyladenosine Modified Circular RNA in Pathophysiological Processes

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

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The Role of N⁶-Methyladenosine Modified Circular RNA in Pathophysiological Processes