Identifying RNA editing sites using RNA sequencing data alone
Gokul Ramaswami,Rui Zhang,Robert Piskol,Liam Keegan,Patricia Deng,Mary A O'Connell,Jin Billy Li +6 more
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TLDR
It is shown that RNA editing sites can be called with high confidence using RNA sequencing data from multiple samples across either individuals or species, without the need for matched genomic DNA sequence.Abstract:
We show that RNA editing sites can be called with high confidence using RNA sequencing data from multiple samples across either individuals or species, without the need for matched genomic DNA sequence. We identified many previously unidentified editing sites in both humans and Drosophila; our results nearly double the known number of human protein recoding events. We also found that human genes harboring conserved editing sites within Alu repeats are enriched for neuronal functions.read more
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
A-to-I editing of coding and non-coding RNAs by ADARs
TL;DR: Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA, leading to reduced expression or altered function of mature miRNAs and certain microRNA precursors.
Journal ArticleDOI
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.
Lily Bazak,Ami Haviv,Michal Barak,Jasmine Jacob-Hirsch,Jasmine Jacob-Hirsch,Patricia Deng,Rui Zhang,Farren J. Isaacs,Gideon Rechavi,Gideon Rechavi,Jin Billy Li,Eli Eisenberg,Erez Y. Levanon +12 more
TL;DR: It is found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels, doubling the number of edited sites in the human genome.
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RADAR: a rigorously annotated database of A-to-I RNA editing
Gokul Ramaswami,Jin Billy Li +1 more
TL;DR: RADAR includes a comprehensive collection of A-to-I RNA editing sites identified in humans (Homo sapiens), mice and flies (Mus musculus) and flies, together with extensive manually curated annotations for each editing site.
Journal ArticleDOI
Dynamic landscape and regulation of RNA editing in mammals
Meng How Tan,Qin Li,Raghuvaran Shanmugam,Robert Piskol,Jennefer N. Kohler,Amy N. Young,Kaiwen Ivy Liu,Rui Zhang,Gokul Ramaswami,Kentaro Ariyoshi,Ankita Gupte,Liam Keegan,Cyril X. George,Avinash Ramu,Ni Huang,Elizabeth A. Pollina,Dena S. Leeman,Alessandra Rustighi,Y. P. Sharon Goh,Ajay Chawla,Giannino Del Sal,Gary Peltz,Anne Brunet,Donald F. Conrad,Charles E. Samuel,Mary A. O’Connell,Mary A. O’Connell,Carl R. Walkley,Carl R. Walkley,Kazuko Nishikura,Jin Billy Li +30 more
TL;DR: This work curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation.
References
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
Functions and Regulation of RNA Editing by ADAR Deaminases
TL;DR: Recent findings that indicate new functions for A-->I editing in the regulation of noncoding RNAs and for interactions between RNA editing and RNA interference mechanisms are reviewed.