Knowledge in the Investigation of A-to-I RNA Editing Signals

Frontiers in Bioengineering and Biotechnology
Giovanni NigitaAlfredo Pulvirenti

Abstract

RNA editing is a post-transcriptional alteration of RNA sequences that is able to affect protein structure as well as RNA and protein expression. Adenosine-to-inosine (A-to-I) RNA editing is the most frequent and common post-transcriptional modification in human, where adenosine (A) deamination produces its conversion into inosine (I), which in turn is interpreted by the translation and splicing machineries as guanosine (G). The disruption of the editing machinery has been associated to various human diseases such as cancer or neurodegenerative diseases. This biological phenomenon is catalyzed by members of the adenosine deaminase acting on RNA (ADAR) family of enzymes and occurs on dsRNA structures. Despite the enormous efforts made in the last decade, the real biological function underlying such a phenomenon, as well as ADAR's substrate features still remain unknown. In this work, we summarize the major computational aspects of predicting and understanding RNA editing events. We also investigate the detection of short motif sequences potentially characterizing RNA editing signals and the use of a logistic regression technique to model a predictor of RNA editing events. The latter, named AIRlINER, an algorithmic approach to as...Continue Reading

References

Apr 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·R W WagnerK Nishikura
Nov 22, 1994·Proceedings of the National Academy of Sciences of the United States of America·U KimK Nishikura
Apr 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·J H YangT Maniatis
May 20, 1999·Nature·S M RueterR B Emeson
Jun 26, 2001·RNA·S K WongD W Lazinski
Jun 5, 2002·Annual Review of Biochemistry·Brenda L Bass
Aug 9, 2003·Science·Barry HoopengardnerRobert Reenan
May 8, 2004·Science·Gill BejeranoDavid Haussler
Jul 20, 2004·Nature Biotechnology·Erez Y LevanonMichael F Jantsch
Sep 3, 2004·Genome Research·Dennis D Y KimAbram Gabriel
Nov 10, 2004·PLoS Biology·Alekos AthanasiadisStefan Maas
Dec 2, 2006·Nature Reviews. Molecular Cell Biology·Kazuko Nishikura
Dec 19, 2007·Biochimica Et Biophysica Acta·James E C Jepson, Robert A Reenan
Apr 24, 2008·RNA·Eva M RiedmannMichael F Jantsch
Aug 8, 2008·Nucleic Acids Research·Yukio KawaharaKazuko Nishikura
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Sep 25, 2009·Human Molecular Genetics·Glen M BorchertBeverly L Davidson
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Jun 16, 2010·Bioinformatics·Anmol Kiran, Pavel V Baranov
Sep 14, 2010·Nature Chemical Biology·Masayuki SakuraiTsutomu Suzuki
May 19, 2011·Nature Communications·Julie M EggingtonBrenda L Bass
Sep 21, 2011·Seminars in Cell & Developmental Biology·Federica GaleanoAngela Gallo
Oct 7, 2011·Wiley Interdisciplinary Reviews. RNA·Helene Wahlstedt, Marie Ohman
Oct 26, 2011·Biochemistry. Biokhimii︠a︡·A A H Su, L Randau
Oct 27, 2011·PLoS Genetics·Shai CarmiErez Y Levanon
Mar 1, 2012·Frontiers in Genetics·Sheetal A MitraTimothy J Triche
Mar 17, 2012·Science·Claudia L Kleinman, Jacek Majewski
Mar 17, 2012·Science·Joseph K PickrellJonathan K Pritchard
Apr 10, 2012·Nature Methods·Gokul RamaswamiJin Billy Li
Oct 18, 2012·Nucleic Acids Research·Anmol M KiranPavel V Baranov
Jan 8, 2013·Nature Methods·Gokul RamaswamiJin Billy Li
Oct 29, 2013·Nucleic Acids Research·Gokul Ramaswami, Jin Billy Li

❮ Previous
Next ❯

Citations

Jun 15, 2016·Nucleic Acids Research·Giovanni NigitaCarlo M Croce
Oct 4, 2016·Briefings in Bioinformatics·David JohnShizuka Uchida
Oct 13, 2018·Briefings in Functional Genomics·Yan GuoYing-Yong Zhao
Sep 17, 2021·Functional & Integrative Genomics·Huseyin Avni TacUgur Sezerman

❮ Previous
Next ❯

Methods Mentioned

BETA
deamination
RNAseq
ICE
RNA-seq

Software Mentioned

ADAR
AIRlINER
RADAR
MEME
InosinePredict
DARNED

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Mini Reviews in Medicinal Chemistry
Barry Hoopengardner
Carcinogenesis
Dan DominissiniGideon Rechavi
Current Topics in Microbiology and Immunology
Carl R WalkleyJochen C Hartner
© 2022 Meta ULC. All rights reserved