scholarly journals m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome

2020 ◽  
Vol 49 (D1) ◽  
pp. D134-D143
Author(s):  
Yujiao Tang ◽  
Kunqi Chen ◽  
Bowen Song ◽  
Jiongming Ma ◽  
Xiangyu Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Modification ◽  
Virus Species ◽  
Biological Processes ◽  
Sequence Motifs ◽  
Biological Functions ◽  
Rna Modifications ◽  
User Friendly ◽  
Friendly Graphical User Interface ◽  
Query Visualization

Abstract N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the m6A epitranscriptome. Compared to existing databases, m6A-Atlas features a high-confidence collection of 442 162 reliable m6A sites identified from seven base-resolution technologies and the quantitative (rather than binary) epitranscriptome profiles estimated from 1363 high-throughput sequencing samples. It also offers novel features, such as; the conservation of m6A sites among seven vertebrate species (including human, mouse and chimp), the m6A epitranscriptomes of 10 virus species (including HIV, KSHV and DENV), the putative biological functions of individual m6A sites predicted from epitranscriptome data, and the potential pathogenesis of m6A sites inferred from disease-associated genetic mutations that can directly destroy m6A directing sequence motifs. A user-friendly graphical user interface was constructed to support the query, visualization and sharing of the m6A epitranscriptomes annotated with sites specifying their interaction with post-transcriptional machinery (RBP-binding, microRNA interaction and splicing sites) and interactively display the landscape of multiple RNA modifications. These resources provide fresh opportunities for unraveling the m6A epitranscriptomes. m6A-Atlas is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/atlas.

scholarly journals RNAWRE: a resource of writers, readers and erasers of RNA modifications

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Fulei Nie ◽  
Pengmian Feng ◽  
Xiaoming Song ◽  
Meng Wu ◽  
Qiang Tang ◽  
...  
Keyword(s):  
Regulatory Mechanisms ◽  
Rna Modification ◽  
Biological Processes ◽  
Biological Functions ◽  
Rna Modifications ◽  
Current Version ◽  
Blast Search

Abstract RNA modifications are involved in various kinds of cellular biological processes. Accumulated evidences have demonstrated that the functions of RNA modifications are determined by the effectors that can catalyze, recognize and remove RNA modifications. They are called ‘writers’, ‘readers’ and ‘erasers’. The identification of RNA modification effectors will be helpful for understanding the regulatory mechanisms and biological functions of RNA modifications. In this work, we developed a database called RNAWRE that specially deposits RNA modification effectors. The current version of RNAWRE stored 2045 manually curated writers, readers and erasers for the six major kinds of RNA modifications, namely Cap, m1A, m6A, m5C, ψ and Poly A. The main modules of RNAWRE not only allow browsing and downloading the RNA modification effectors but also support the BLAST search of the potential RNA modification effectors in other species. We hope that RNAWRE will be helpful for the researches on RNA modifications. Database URL: http://rnawre.bio2db.com

RNA modifications in hematopoietic malignancies: A new research frontier

Blood ◽  
2021 ◽  
Author(s):  
Ying Qing ◽  
Rui Su ◽  
Jianjun Chen
Keyword(s):  
Myeloid Leukemia ◽  
Therapeutic Potential ◽  
Rna Modification ◽  
Biological Functions ◽  
Rna Modifications ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Hematopoietic Malignancies ◽  
Underlying Mechanisms ◽  
New Research

Both protein-coding and noncoding RNAs can be decorated with a wealth of chemical modifications and such modifications coordinately orchestrate gene expression during normal hematopoietic differentiation and development. However, aberrant expression and/or dysfunction of the relevant RNA modification modulators/regulators ("writers", "erasers", and "readers") drive the initiation and progression of hematopoietic malignancies, and targeting these dysregulated modulators holds potent therapeutic potential for the treatment of hematopoietic malignancies. In this review, we summarize current progress in the understanding of the biological functions and underlying mechanisms of RNA modifications in normal and malignant hematopoiesis, with a focus on the N6-methyladenosine (m6A) modification, and discuss the therapeutic potential of targeting RNA modifications for the treatment of hematopoietic malignancies, especially acute myeloid leukemia (AML).

scholarly journals RNA methylation in mammalian development and cancer

2021 ◽  
Author(s):  
Peizhe Song ◽  
Subiding Tayier ◽  
Zhihe Cai ◽  
Guifang Jia
Keyword(s):  
Cell Fate ◽  
Cancer Progression ◽  
Rna Modification ◽  
Biological Processes ◽  
Cell Fate Determination ◽  
Mammalian Development ◽  
Rna Modifications ◽  
Temporal And Spatial ◽  
Underlying Mechanisms ◽  
Cellular Components

AbstractSimilar to epigenetic DNA and histone modifications, epitranscriptomic modifications (RNA modifications) have emerged as crucial regulators in temporal and spatial gene expression during eukaryotic development. To date, over 170 diverse types of chemical modifications have been identified upon RNA nucleobases. Some of these post-synthesized modifications can be reversibly installed, removed, and decoded by their specific cellular components and play critical roles in different biological processes. Accordingly, dysregulation of RNA modification effectors is tightly orchestrated with developmental processes. Here, we particularly focus on three well-studied RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N1-methyladenosine (m1A), and summarize recent knowledge of underlying mechanisms and critical roles of these RNA modifications in stem cell fate determination, embryonic development, and cancer progression, providing a better understanding of the whole association between epitranscriptomic regulation and mammalian development.

scholarly journals ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data

2021 ◽  
Author(s):  
Leszek P Pryszcz ◽  
Eva Maria Novoa
Keyword(s):  
Rna Modification ◽  
Nanopore Sequencing ◽  
Computationally Efficient ◽  
Rna Modifications ◽  
Efficient Manner ◽  
Dna And Rna ◽  
File Formats ◽  
User Friendly ◽  
And Storage

DNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. Here we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license.

scholarly journals Critical Roles of N6-Methyladenosine (m6A) in Cancer and Virus Infection

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1071 ◽  
Author(s):  
Ken Asada ◽  
Amina Bolatkan ◽  
Ken Takasawa ◽  
Masaaki Komatsu ◽  
Syuzo Kaneko ◽  
...  
Keyword(s):  
Virus Infection ◽  
Cancer Biology ◽  
Viral Infections ◽  
Regulation Of Gene Expression ◽  
Rna Modification ◽  
Integrated Analysis ◽  
Biological Functions ◽  
Rna Modifications ◽  
Long Time ◽  
Epigenetic Analysis

Studies have shown that epigenetic abnormalities are involved in various diseases, including cancer. In particular, in order to realize precision medicine, the integrated analysis of genetics and epigenetics is considered to be important; detailed epigenetic analysis in the medical field has been becoming increasingly important. In the epigenetics analysis, DNA methylation and histone modification analyses have been actively studied for a long time, and many important findings were accumulated. On the other hand, recently, attention has also been focused on RNA modification in the field of epigenetics; now it is known that RNA modification is associated with various biological functions, such as regulation of gene expression. Among RNA modifications, functional analysis of N6-methyladenosine (m6A), the most abundant RNA modification found from humans to plants is actively progressing, and it has also been known that m6A abnormality is involved in cancer and other diseases. Importantly, recent studies have shown that m6A is related to viral infections. Considering the current world situation under threat of viral infections, it is important to deepen knowledge of RNA modification from the viewpoint of viral diseases. Hence, in this review, we have summarized the recent findings regarding the roles of RNA modifications in biological functions, cancer biology, and virus infection, particularly focusing on m6A in mRNA.

scholarly journals The biological function of m6A reader YTHDF2 and its role in human disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jin-yan Wang ◽  
Ai-qing Lu
Keyword(s):  
Ribosomal Rna ◽  
Biological Function ◽  
Prognostic Biomarker ◽  
Great Part ◽  
Rna Modification ◽  
Biological Processes ◽  
Rrna Processing ◽  
Biological Functions ◽  
Domain Family ◽  
Human Cancers

AbstractN6-methyladenosine (m6A) modification is a dynamic and reversible post-transcriptional modification and the most prevalent internal RNA modification in eukaryotic cells. YT521-B homology domain family 2 (YTHDF2) is a member of m6A “readers” and its role in human diseases remains unclear. Accumulating evidence suggests that YTHDF2 is greatly implicated in many aspects of human cancers and non-cancers through various mechanisms. YTHDF2 takes a great part in multiple biological processes, such as migration, invasion, metastasis, proliferation, apoptosis, cell cycle, cell viability, cell adhesion, differentiation and inflammation, in both human cancers and non-cancers. Additionally, YTHDF2 influences various aspects of RNA metabolism, including mRNA decay and pre-ribosomal RNA (pre-rRNA) processing. Moreover, emerging researches indicate that YTHDF2 predicts the prognosis of different cancers. Herein, we focus on concluding YTHDF2-associated mechanisms and potential biological functions in kinds of cancers and non-cancers, and its prospects as a prognostic biomarker.

scholarly journals BML: a versatile web server for bipartite motif discovery

2021 ◽  
Author(s):  
Mohammad Vahed ◽  
Majid Vahed ◽  
Lana Garmire
Keyword(s):  
Motif Discovery ◽  
High Throughput Sequencing ◽  
Web Server ◽  
Weight Matrix ◽  
Motif Finding ◽  
Sequence Motifs ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Effective Use ◽  
User Friendly

Motif discovery and characterization are important for gene regulation analysis. The lack of intuitive and integrative web servers impedes effective use of motifs. Here we describe Bipartite Motifs Learning (BML), a web server that provides a user-friendly portal for online discovery and analysis of sequence motifs, using high-throughput sequencing data as the input. BML utilizes both position weight matrix (PWM) and dinucleotide weight matrix (DWM), the latter of which enables the expression of the interdependencies of neighboring bases. With input parameters concerning the motifs are given, the BML achieves significantly higher accuracy than other available tools for motif finding. When no parameters are given by non-expert users, unlike other tools BML employs a learning method to identify motifs automatically and achieve accuracy comparable to the scenario where the parameters are set. The BML web server is freely available at http://motif.t-ridership.com/.

scholarly journals Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Kunqi Chen ◽  
Zhen Wei ◽  
Hui Liu ◽  
João Pedro de Magalhães ◽  
Rong Rong ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Gene Expression Regulation ◽  
Functional Characterization ◽  
Biological Significance ◽  
Global Perspective ◽  
Biological Functions ◽  
Rna Modifications ◽  
Rna Molecules ◽  
Weighting Strategy

To date, with well over 100 different types of RNA modifications associated with various molecular functions identified on diverse types of RNA molecules, the epitranscriptome has emerged to be an important layer for gene expression regulation. It is of crucial importance and increasing interest to understand how the epitranscriptome is regulated to facilitate different biological functions from a global perspective, which may be carried forward by finding biologically meaningful epitranscriptome modules that respond to upstream epitranscriptome regulators and lead to downstream biological functions; however, due to the intrinsic properties of RNA molecules, RNA modifications, and relevant sequencing technique, the epitranscriptome profiled from high-throughput sequencing approaches often suffers from various artifacts, jeopardizing the effectiveness of epitranscriptome modules identification when using conventional approaches. To solve this problem, we developed a convenient measurement weighting strategy, which can largely tolerate the artifacts of high-throughput sequencing data. We demonstrated on real data that the proposed measurement weighting strategy indeed brings improved performance in epitranscriptome module discovery in terms of both module accuracy and biological significance. Although the new approach is integrated with Euclidean distance measurement in a hierarchical clustering scenario, it has great potential to be extended to other distance measurements and algorithms as well for addressing various tasks in epitranscriptome analysis. Additionally, we show for the first time with rigorous statistical analysis that the epitranscriptome modules are biologically meaningful with different GO functions enriched, which established the functional basis of epitranscriptome modules, fulfilled a key prerequisite for functional characterization, and deciphered the epitranscriptome and its regulation.

scholarly journals Recent advances in dynamic m 6 A RNA modification

Open Biology ◽  
2016 ◽  
Vol 6 (4) ◽  
pp. 160003 ◽  
Author(s):  
Guangchao Cao ◽  
Hua-Bing Li ◽  
Zhinan Yin ◽  
Richard A. Flavell
Keyword(s):  
Rna Splicing ◽  
High Throughput Sequencing ◽  
Epigenetic Modification ◽  
Rna Modification ◽  
Sequencing Analysis ◽  
Biological Functions ◽  
Dynamic Regulation ◽  
The Past ◽  
Recent Advances

The identification of m 6 A demethylases and high-throughput sequencing analysis of methylated transcriptome corroborated m 6 A RNA epigenetic modification as a dynamic regulation process, and reignited its investigation in the past few years. Many basic concepts of cytogenetics have been revolutionized by the growing understanding of the fundamental role of m 6 A in RNA splicing, degradation and translation. In this review, we summarize typical features of methylated transcriptome in mammals, and highlight the ‘writers’, ‘erasers’ and ‘readers’ of m 6 A RNA modification. Moreover, we emphasize recent advances of biological functions of m 6 A and conceive the possible roles of m 6 A in the regulation of immune response and related diseases.

Comparison and Analysis of Computational Methods for Identifying N6 - methyladenosine Sites in Saccharomyces Cerevisiae

2020 ◽  
Vol 26 ◽  
Author(s):  
Pengmian Feng ◽  
Lijing Feng ◽  
Chaohui Tang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
Computational Analysis ◽  
Computational Prediction ◽  
Experimental Methods ◽  
Biological Processes ◽  
Biological Functions ◽  
Precise Location ◽  
Future Directions ◽  
The Past

Background and Purpose: N 6 -methyladenosine (m6A) plays critical roles in a broad set of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As good complements to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. Methods: In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to give a comprehensive review and comparison on existing methods. Results: Since researches on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progresses on computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites were presented. Conclusion: Taken together, we anticipate that this review will provide important guides for computational analysis of m 6A modifications.

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