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Literature DB >> 33835459

MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database.

Abstract

MODOMICS is an established database of RNA modifications that provides comprehensive information concerning chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. This chapter covers the resources available on MODOMICS web server and the basic steps that can be undertaken by the user to explore them. MODOMICS is available at http://www.genesilico.pl/modomics .

Entities: Chemical

Keywords: Database; Enzymes; Epitranscriptomics; Metabolic pathways; RNA; Ribonucleoside modification; Systems biology

Year: 2021 PMID： 33835459 DOI： 10.1007/978-1-0716-1307-8_26

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

22 in total

Review 1. Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers.

Authors: Hailing Shi; Jiangbo Wei; Chuan He
Journal: Mol Cell Date: 2019-05-16 Impact factor: 17.970

Review 2. The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin?

Authors: Namit Ranjan; Sebastian A Leidel
Journal: FEBS Lett Date: 2019-06-27 Impact factor: 4.124

Review 3. Biosynthesis and function of posttranscriptional modifications of transfer RNAs.

Authors: Basma El Yacoubi; Marc Bailly; Valérie de Crécy-Lagard
Journal: Annu Rev Genet Date: 2012-08-16 Impact factor: 16.830

Review 4. The pivotal regulatory landscape of RNA modifications.

Authors: Sheng Li; Christopher E Mason
Journal: Annu Rev Genomics Hum Genet Date: 2014-06-02 Impact factor: 8.929

Review 5. The emerging biology of RNA post-transcriptional modifications.

Authors: Sigrid Nachtergaele; Chuan He
Journal: RNA Biol Date: 2016-12-12 Impact factor: 4.652

Review 6. Post-transcriptional nucleotide modification and alternative folding of RNA.

Authors: Mark Helm
Journal: Nucleic Acids Res Date: 2006-02-01 Impact factor: 16.971

Review 7. The RNA modification landscape in human disease.

Authors: Nicky Jonkhout; Julia Tran; Martin A Smith; Nicole Schonrock; John S Mattick; Eva Maria Novoa
Journal: RNA Date: 2017-08-30 Impact factor: 4.942

Review 8. The role of m⁶A RNA methylation in human cancer.

Authors: Xiao-Yu Chen; Jing Zhang; Jin-Shui Zhu
Journal: Mol Cancer Date: 2019-05-29 Impact factor: 27.401

9. Matching tRNA modifications in humans to their known and predicted enzymes.

Authors: Valérie de Crécy-Lagard; Pietro Boccaletto; Carl G Mangleburg; Puneet Sharma; Todd M Lowe; Sebastian A Leidel; Janusz M Bujnicki
Journal: Nucleic Acids Res Date: 2019-03-18 Impact factor: 16.971

10. MODOMICS: a database of RNA modification pathways. 2017 update.

Authors: Pietro Boccaletto; Magdalena A Machnicka; Elzbieta Purta; Pawel Piatkowski; Blazej Baginski; Tomasz K Wirecki; Valérie de Crécy-Lagard; Robert Ross; Patrick A Limbach; Annika Kotter; Mark Helm; Janusz M Bujnicki
Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971

10 in total

1. Chronic Hexavalent Chromium Exposure Upregulates the RNA Methyltransferase METTL3 Expression to Promote Cell Transformation, Cancer Stem Cell-Like Property, and Tumorigenesis.

Authors: Zhishan Wang; Mohammad Burhan Uddin; Jie Xie; Hua Tao; Patti C Zeidler-Erdely; Kazuya Kondo; Chengfeng Yang
Journal: Toxicol Sci Date: 2022-04-26 Impact factor: 4.109

2. Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells.

Authors: Mariana Estevez; Rui Li; Biplab Paul; Kaveh Daneshvar; Alan C Mullen; Fabio Romerio; Balasubrahmanyam Addepalli
Journal: RNA Date: 2022-02-15 Impact factor: 5.636

Review 3. Computational methods for RNA modification detection from nanopore direct RNA sequencing data.

Authors: Mattia Furlan; Anna Delgado-Tejedor; Logan Mulroney; Mattia Pelizzola; Eva Maria Novoa; Tommaso Leonardi
Journal: RNA Biol Date: 2021-09-24 Impact factor: 4.652

4. m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Cell-Infiltration Characterization in Head and Neck Cancer.

Authors: Qinghui Yang; Feng Xu; Aiwen Jian; Hongmei Yu; Tao Ye; Weiqi Hu
Journal: Front Cell Dev Biol Date: 2022-02-07

5. N6-Methyladenosine-Related Gene Signature Associated With Monocyte Infiltration Is Clinically Significant in Gestational Diabetes Mellitus.

Authors: Runyu Du; Ling Li; Yanjun Wang
Journal: Front Endocrinol (Lausanne) Date: 2022-03-18 Impact factor: 5.555

Review 6. m⁶A: An Emerging Role in Programmed Cell Death.

Authors: Fajuan Tang; Lin Chen; Hu Gao; Dongqiong Xiao; Xihong Li
Journal: Front Cell Dev Biol Date: 2022-01-24

7. ADAR2 Protein Is Associated with Overall Survival in GBM Patients and Its Decrease Triggers the Anchorage-Independent Cell Growth Signature.

Authors: Valeriana Cesarini; Domenico Alessandro Silvestris; Federica Galeano; Valentina Tassinari; Maurizio Martini; Franco Locatelli; Angela Gallo
Journal: Biomolecules Date: 2022-08-19

Review 8. The Epitranscriptomic Mechanism of Metal Toxicity and Carcinogenesis.

Authors: Chengfeng Yang; Zhishan Wang
Journal: Int J Mol Sci Date: 2022-10-05 Impact factor: 6.208

Review 9. RNA methyltransferase METTL16: Targets and function.

Authors: Emily R Satterwhite; Kyle D Mansfield
Journal: Wiley Interdiscip Rev RNA Date: 2021-07-06 Impact factor: 9.349

10. Human Mitochondrial Ribosomal RNA Modification-Based Classification Contributes to Discriminate the Prognosis and Immunotherapy Response of Glioma Patients.

Authors: Peng Wang; Jingying Li; Miaojing Wu; Minghua Ye; Kai Huang; Xingen Zhu
Journal: Front Immunol Date: 2021-09-09 Impact factor: 7.561