scholarly journals MiREDiBase: a manually curated database of validated and putative editing events in microRNAs

2020 ◽  
Author(s):  
Gioacchino P. Marceca ◽  
Rosario Distefano ◽  
Luisa Tomasello ◽  
Alessandro Lagana ◽  
Francesco Russo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cell Biology ◽  
Enrichment Analysis ◽  
Minimum Free Energy ◽  
Binding Ability ◽  
Cellular Processes ◽  
Non Coding Rnas ◽  
Target Binding ◽  
And Function ◽  
Mirna Editing

AbstractMicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

scholarly journals MiREDiBase, a manually curated database of validated and putative editing events in microRNAs

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Gioacchino P. Marceca ◽  
Rosario Distefano ◽  
Luisa Tomasello ◽  
Alessandro Lagana ◽  
Francesco Russo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cell Biology ◽  
Enrichment Analysis ◽  
Minimum Free Energy ◽  
Binding Ability ◽  
Cellular Processes ◽  
Non Coding Rnas ◽  
Target Binding ◽  
And Function ◽  
Mirna Editing

AbstractMicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

scholarly journals Long non-coding RNAs: novel regulators of cellular physiology and function

2021 ◽  
Author(s):  
James A. Oo ◽  
Ralf P. Brandes ◽  
Matthias S. Leisegang
Keyword(s):  
Damage Control ◽  
Regulation Of Gene Expression ◽  
Cellular Processes ◽  
Current Thinking ◽  
Physiological Relevance ◽  
Non Coding Rnas ◽  
And Migration ◽  
And Function ◽  
Rna And Dna ◽  
Proliferation And Migration

AbstractLong non-coding RNAs were once considered as “junk” RNA produced by aberrant DNA transcription. They are now understood to play central roles in diverse cellular processes from proliferation and migration to differentiation, senescence and DNA damage control. LncRNAs are classed as transcripts longer than 200 nucleotides that do not encode a peptide. They are relevant to many physiological and pathophysiological processes through their control of fundamental molecular functions. This review summarises the recent progress in lncRNA research and highlights the far-reaching physiological relevance of lncRNAs. The main areas of lncRNA research encompassing their characterisation, classification and mechanisms of action will be discussed. In particular, the regulation of gene expression and chromatin landscape through lncRNA control of proteins, DNA and other RNAs will be introduced. This will be exemplified with a selected number of lncRNAs that have been described in numerous physiological contexts and that should be largely representative of the tens-of-thousands of mammalian lncRNAs. To some extent, these lncRNAs have inspired the current thinking on the central dogmas of epigenetics, RNA and DNA mechanisms.

Identification and analysis of RNA editing events in ovarian serous cystadenoma using RNA-seq Data

2021 ◽  
Vol 21 ◽  
Author(s):  
Yulan Wang ◽  
Xiaofeng Song ◽  
Tianyi Xu
Keyword(s):  
Ovarian Cancer ◽  
Rna Editing ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Serous Cystadenoma ◽  
Pathway Enrichment Analysis ◽  
Normal Tissues ◽  
Coding Regions ◽  
Target Binding

Background: Recent studies have revealed thousands of A-to-I RNA editing events in primates. These events are closely related to the occurrence and development of multiple cancers, but the origination and general functions of these events in ovarian cancer remain incompletely understood. Objective: To further the determination of molecular mechanisms of ovarian cancer from the perspective of RNA editing. Methods : Here, we used the SNP-free RNA editing Identification Toolkit (SPRINT) to detect RNA editing sites. These editing sites were then annotated and related functional analysis was performed. Results: In this study, about 1.7 million RES were detected in each sample, and 98% of these sites were due to A-to-G editing and were mainly distributed in non-coding regions. More than 1,000 A-to-G RES were detected in CDS regions, and nearly 700 could lead to amino acid changes. Our results also showed that editing in the 3′UTR regions can influence miRNA-target binding. We predicted the network of changed miRNA-mRNA interaction caused by the A-to-I RNA editing sites. We also screened the differential RNA editing sites between ovarian cancer and adjacent normal tissues, and then performed GO and KEGG pathway enrichment analysis on the genes that contain these differential RNA editing sites. Finally, we identified the potential dysregulated RNA editing events in ovarian cancer samples. Conclusion: This study systematically identified and analyzed RNA editing events in ovarian cancer and laid a foundation to explore the regulatory mechanism of RNA editing and its function in ovarian cancer.

scholarly journals The Structure-To-Function Relationships of Gammaherpesvirus-Encoded Long Non-Coding RNAs and Their Contributions to Viral Pathogenesis

2018 ◽  
Vol 4 (4) ◽  
pp. 24 ◽  
Author(s):  
Gabriela Chavez-Calvillo ◽  
Sarah Martin ◽  
Chad Hamm ◽  
Joanna Sztuba-Solinska
Keyword(s):  
Viral Gene Expression ◽  
Viral Pathogenesis ◽  
Viral Gene ◽  
Cellular Processes ◽  
Messenger Molecules ◽  
Non Coding Rnas ◽  
Function Relationship ◽  
Structure And Function Relationship ◽  
And Function ◽  
Pleiotropic Functions

Advances in next-generation sequencing have facilitated the discovery of a multitude of long non-coding RNAs (lncRNAs) with pleiotropic functions in cellular processes, disease, and viral pathogenesis. It came as no surprise when viruses were also revealed to transcribe their own lncRNAs. Among them, gammaherpesviruses, one of the three subfamilies of the Herpesviridae, code their largest number. These structurally and functionally intricate non-coding (nc) transcripts modulate cellular and viral gene expression to maintain viral latency or prompt lytic reactivation. These lncRNAs allow for the virus to escape cytosolic surveillance, sequester, and re-localize essential cellular factors and modulate the cell cycle and proliferation. Some viral lncRNAs act as “messenger molecules”, transferring information about viral infection to neighboring cells. This broad range of lncRNA functions is achieved through lncRNA structure-mediated interactions with effector molecules of viral and host origin, including other RNAs, proteins and DNAs. In this review, we discuss examples of gammaherpesvirus-encoded lncRNAs, emphasize their unique structural attributes, and link them to viral life cycle, pathogenesis, and disease progression. We will address their potential as novel targets for drug discovery and propose future directions to explore lncRNA structure and function relationship.

scholarly journals Proximity interactome of LC3B in normal growth conditions

2021 ◽  
Author(s):  
Marie Nollet ◽  
Alexander Agrotis ◽  
Fanourios Michailidis ◽  
Arran David Dokal ◽  
Vinothini Rajeeve ◽  
...  
Keyword(s):  
Cell Biology ◽  
Normal Growth ◽  
Growth Conditions ◽  
Biological Functions ◽  
Normal Medium ◽  
Outer Membranes ◽  
Cellular Processes ◽  
Proteomic Approach ◽  
And Function

LC3 (Light Chain 3) is a key player of autophagy, a major stress-responsive proteolysis pathway promoting cellular homeostasis. It coordinates the formation and maturation of autophagosomes and recruits cargo to be further degraded upon autophagosome-lysosome fusion. To orchestrate its functions, LC3 binds to multiple proteins from the autophagosomes inner and outer membranes, but the full extent of these interactions is not known. Moreover, LC3 has been increasingly reported in other cellular locations than the autophagosome, with cellular outcome not fully understood and not all related to autophagy. Furthermore, novel functions of LC3 as well as autophagy can occur in cells growing in a normal medium thus in non-stressed conditions. A better knowledge of the molecule in proximity to LC3 in normal growth conditions will improve the understanding of LC3 function in autophagy and in other cell biology function. Using an APEX2 based proteomic approach, we have detected 407 proteins in proximity to the well-characterised LC3B isoform in non-stress conditions. These include known and novel LC3B proximity proteins, associated with various cell localisation and biological functions. Sixty-nine of these proteins contain a putative LIR (LC3 Interacting Region) including 41 not reported associated to autophagy. Several APEX2 hits were validated by co-immunoprecipitation and co-immunofluorescence. This study uncovers the LC3B global interactome and reveals novel LC3B interactors, irrespective of LC3B localisation and function. This knowledge could be exploited to better understand the role of LC3B in autophagy and non-autophagy cellular processes.

scholarly journals Detecting and Characterizing A-to-I MicroRNA Editing in Cancer

2021 ◽  
Author(s):  
Gioacchino P. Marceca ◽  
Luisa Tomasello ◽  
Rosario Distefano ◽  
Mario Acunzo ◽  
Carlo Croce ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Splicing ◽  
Cancer Biology ◽  
Human Cancer ◽  
Detection Methods ◽  
Rna Modification ◽  
Messenger Rnas ◽  
Validation Methods ◽  
Non Coding Rnas ◽  
Mirna Editing

RNA editing involves the insertion, deletion or substitution of single nucleotides within a RNA molecule, without altering the DNA sequence. Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. Initially, the A-to-I RNA editing phenomenon was discovered and studied in messenger RNAs (mRNAs), where it can influence RNA splicing and cause the recoding of codon sequences. The employment of more powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.

scholarly journals Long Non-Coding RNAs as Key Modulators of Pancreatic β-Cell Mass and Function

2021 ◽  
Vol 11 ◽  
Author(s):  
Livia López–Noriega ◽  
Guy A. Rutter
Keyword(s):  
Cell Biology ◽  
Cell Mass ◽  
Cell Loss ◽  
Β Cell ◽  
Coding Regions ◽  
Response To Stress ◽  
Non Coding Rnas ◽  
Stress Signals ◽  
Β Function ◽  
And Function

Numerous studies have sought to decipher the genetic and other mechanisms contributing to β-cell loss and dysfunction in diabetes mellitus. However, we have yet to fully understand the etiology of the disease or to develop satisfactory treatments. Since the majority of diabetes susceptibility loci are mapped to non-coding regions within the genome, understanding the functions of non-coding RNAs in β-cell biology might provide crucial insights into the pathogenesis of type 1 (T1D) and type 2 (T2D) diabetes. During the past decade, numerous studies have indicated that long non-coding RNAs play important roles in the maintenance of β-cell mass and function. Indeed, lncRNAs have been shown to be involved in controlling β-cell proliferation during development and/or β-cell compensation in response to hyperglycaemia. LncRNAs such as TUG-1 and MEG3 play a role in both β-cell apoptosis and function, while others sensitize β-cells to apoptosis in response to stress signals. In addition, several long non-coding RNAs have been shown to regulate the expression of β-cell-enriched transcription factors in cis or in trans. In this review, we provide an overview of the roles of lncRNAs in maintaining β-function and mass, and discuss their relevance in the development of diabetes.

scholarly journals Cdc48: A Swiss Army Knife of Cell Biology

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Guem Hee Baek ◽  
Haili Cheng ◽  
Vitnary Choe ◽  
Xin Bao ◽  
Jia Shao ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Atpase Activity ◽  
Cell Biology ◽  
Protein Complexes ◽  
Biological Functions ◽  
Cellular Processes ◽  
Broad Array ◽  
And Function ◽  
Regulatory Functions ◽  
Lateral Sclerosis

Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.

Research progress in protein posttranslational modification site prediction

2018 ◽  
Vol 18 (4) ◽  
pp. 220-229 ◽  
Author(s):  
Wenying He ◽  
Leyi Wei ◽  
Quan Zou
Keyword(s):  
Posttranslational Modifications ◽  
Cell Biology ◽  
Research Progress ◽  
Future Research ◽  
Cellular Processes ◽  
Machine Learning Methods ◽  
Bioinformatics Tools ◽  
Glycosylation Sites ◽  
Almost All ◽  
And Function

AbstractPosttranslational modifications (PTMs) play an important role in regulating protein folding, activity and function and are involved in almost all cellular processes. Identification of PTMs of proteins is the basis for elucidating the mechanisms of cell biology and disease treatments. Compared with the laboriousness of equivalent experimental work, PTM prediction using various machine-learning methods can provide accurate, simple and rapid research solutions and generate valuable information for further laboratory studies. In this review, we manually curate most of the bioinformatics tools published since 2008. We also summarize the approaches for predicting ubiquitination sites and glycosylation sites. Moreover, we discuss the challenges of current PTM bioinformatics tools and look forward to future research possibilities.

scholarly journals The Structure-to-Function Relationships of Gammaherpesvirus-Encoded Long Non-Coding RNAs and their Contributions to Viral Pathogenesis

2018 ◽  
Author(s):  
Gabriela Chavez Calvillo ◽  
Sarah Martin ◽  
Chad Hamm ◽  
Joanna Sztuba-Solinska
Keyword(s):  
Viral Gene Expression ◽  
Viral Pathogenesis ◽  
Viral Gene ◽  
Cellular Processes ◽  
Messenger Molecules ◽  
Non Coding Rnas ◽  
Function Relationship ◽  
Structure And Function Relationship ◽  
And Function ◽  
Pleiotropic Functions

Advances in next-generation sequencing have facilitated the discovery of a multitude of long non-coding RNAs (lncRNAs) with pleiotropic functions in cellular processes, disease and viral pathogenesis. It came as no surprise when viruses were also revealed to transcribe their own lncRNAs. Among them, gammaherpesviruses, one of the three subfamilies of the Herpesviridae, code their largest number. These structurally and functionally intricate non-coding (nc) transcripts modulate cellular and viral gene expression to maintain viral latency or prompt lytic reactivation. The lncRNAs allow the virus to escape cytosolic surveillance, sequester and re-localize essential cellular factors and modulate the cell cycle and proliferation. Some viral lncRNAs act as “messenger molecules”, transferring information about viral infection to neighboring cells. This broad range of lncRNA functions is achieved through lncRNA structure-mediated interactions with effector molecules of viral and host origin, including other RNAs, proteins and DNAs. In this review, we discuss examples of gammaherpesvirus-encoded lncRNAs, emphasize their unique structural attributes, and link them to viral life cycle, pathogenesis and disease progression. We will address their potential as novel targets for drug discovery and propose future directions to explore lncRNA structure and function relationship.

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