Literature DB >> 31367845

Programmable RNA manipulation in living cells.

Yu Pei1, Mingxing Lu2.   

Abstract

RNAs are responsible for mediating genetic information flow within the cell. RNA splicing, modification, trafficking, translation, and stability are all controlled at the transcript level. However, biological tools to study and manipulate them in a programmable fashion are currently limited. In this review, we summarize recent advances regarding available RNA-targeting systems discovered so far, including CRISPR-based technologies-Cas9 and Cas13, and programmable RNA-binding proteins-PUF and PPR. These tools allow transcript-specific manipulation in gene expression.

Entities:  

Keywords:  APEX2; CRISPR; Cas13; Cas9; PPR; PUF; RNA-binding proteins; bioID

Year:  2019        PMID: 31367845     DOI: 10.1007/s00018-019-03252-9

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  72 in total

1.  Modular recognition of RNA by a human pumilio-homology domain.

Authors:  Xiaoqiang Wang; Juanita McLachlan; Phillip D Zamore; Traci M Tanaka Hall
Journal:  Cell       Date:  2002-08-23       Impact factor: 41.582

2.  The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.

Authors:  Mathias Munschauer; Celina T Nguyen; Klara Sirokman; Christina R Hartigan; Larson Hogstrom; Jesse M Engreitz; Jacob C Ulirsch; Charles P Fulco; Vidya Subramanian; Jenny Chen; Monica Schenone; Mitchell Guttman; Steven A Carr; Eric S Lander
Journal:  Nature       Date:  2018-08-27       Impact factor: 49.962

3.  CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9.

Authors:  Gaurav Dugar; Ryan T Leenay; Sara K Eisenbart; Thorsten Bischler; Belinda U Aul; Chase L Beisel; Cynthia M Sharma
Journal:  Mol Cell       Date:  2018-03-01       Impact factor: 17.970

4.  Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus.

Authors:  Gintautas Tamulaitis; Migle Kazlauskiene; Elena Manakova; Česlovas Venclovas; Alison O Nwokeoji; Mark J Dickman; Philippe Horvath; Virginijus Siksnys
Journal:  Mol Cell       Date:  2014-11-06       Impact factor: 17.970

5.  The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.

Authors:  Jesse M Engreitz; Amy Pandya-Jones; Patrick McDonel; Alexander Shishkin; Klara Sirokman; Christine Surka; Sabah Kadri; Jeffrey Xing; Alon Goren; Eric S Lander; Kathrin Plath; Mitchell Guttman
Journal:  Science       Date:  2013-07-04       Impact factor: 47.728

6.  Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d.

Authors:  Cheng Zhang; Silvana Konermann; Nicholas J Brideau; Peter Lotfy; Xuebing Wu; Scott J Novick; Timothy Strutzenberg; Patrick R Griffin; Patrick D Hsu; Dmitry Lyumkis
Journal:  Cell       Date:  2018-09-20       Impact factor: 41.582

7.  Targeted m6A Reader Proteins To Study Epitranscriptomic Regulation of Single RNAs.

Authors:  Simone Rauch; Chuan He; Bryan C Dickinson
Journal:  J Am Chem Soc       Date:  2018-09-18       Impact factor: 15.419

8.  RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes.

Authors:  Alexandra East-Seletsky; Mitchell R O'Connell; David Burstein; Gavin J Knott; Jennifer A Doudna
Journal:  Mol Cell       Date:  2017-05-04       Impact factor: 17.970

9.  RNA-dependent RNA targeting by CRISPR-Cas9.

Authors:  Steven C Strutt; Rachel M Torrez; Emine Kaya; Oscar A Negrete; Jennifer A Doudna
Journal:  Elife       Date:  2018-01-05       Impact factor: 8.140

10.  Efficient genome editing in zebrafish using a CRISPR-Cas system.

Authors:  Woong Y Hwang; Yanfang Fu; Deepak Reyon; Morgan L Maeder; Shengdar Q Tsai; Jeffry D Sander; Randall T Peterson; J-R Joanna Yeh; J Keith Joung
Journal:  Nat Biotechnol       Date:  2013-01-29       Impact factor: 54.908

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  4 in total

1.  Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13.

Authors:  Brandon Joseph Davis Burris; Adrian Moises Molina Vargas; Brandon J Park; Mitchell R O'Connell
Journal:  Methods       Date:  2022-08-17       Impact factor: 4.647

Review 2.  Cas13d: A New Molecular Scissor for Transcriptome Engineering.

Authors:  Rahul Gupta; Arijit Ghosh; Rudra Chakravarti; Rajveer Singh; Velayutham Ravichandiran; Snehasikta Swarnakar; Dipanjan Ghosh
Journal:  Front Cell Dev Biol       Date:  2022-03-31

3.  CRISPR-Guided Proximity Labeling of RNA-Protein Interactions.

Authors:  Mingxing Lu; Zuowei Wang; Yixiu Wang; Bingbing Ren
Journal:  Genes (Basel)       Date:  2022-08-27       Impact factor: 4.141

4.  Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes.

Authors:  Aditi Kulkarni; Wanqin Yu; Alex S Moon; Ashmita Pandey; Kathryn A Hanley; Jiannong Xu
Journal:  J Genomics       Date:  2020-03-01
  4 in total

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