Literature DB >> 35796972

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.

Chao Zeng1,2, Atsushi Takeda3, Kotaro Sekine3, Naoki Osato3, Tsukasa Fukunaga4, Michiaki Hamada5,6.   

Abstract

With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bioinformatics; Functional element; Non-coding RNA; Repetitive element; Transposable element; ncRNA

Mesh：

Substances：

Year:  2022        PMID： 35796972     DOI： 10.1007/978-1-0716-2380-0_19

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


  155 in total

1.  New twists on long noncoding RNAs: from mobile elements to motile cancer cells.

Authors:  Tuan M Nguyen; Sumayya Alchalabi; Adewunmi Oluwatoyosi; Ali S Ropri; Jason I Herschkowitz; Jeffrey M Rosen
Journal:  RNA Biol       Date:  2020-06-10       Impact factor: 4.652

Review 2.  Long non-coding RNAs: insights into functions.

Authors:  Tim R Mercer; Marcel E Dinger; John S Mattick
Journal:  Nat Rev Genet       Date:  2009-03       Impact factor: 53.242

3.  An atlas of human long non-coding RNAs with accurate 5' ends.

Authors:  Chung-Chau Hon; Jordan A Ramilowski; Jayson Harshbarger; Nicolas Bertin; Owen J L Rackham; Julian Gough; Elena Denisenko; Sebastian Schmeier; Thomas M Poulsen; Jessica Severin; Marina Lizio; Hideya Kawaji; Takeya Kasukawa; Masayoshi Itoh; A Maxwell Burroughs; Shohei Noma; Sarah Djebali; Tanvir Alam; Yulia A Medvedeva; Alison C Testa; Leonard Lipovich; Chi-Wai Yip; Imad Abugessaisa; Mickaël Mendez; Akira Hasegawa; Dave Tang; Timo Lassmann; Peter Heutink; Magda Babina; Christine A Wells; Soichi Kojima; Yukio Nakamura; Harukazu Suzuki; Carsten O Daub; Michiel J L de Hoon; Erik Arner; Yoshihide Hayashizaki; Piero Carninci; Alistair R R Forrest
Journal:  Nature       Date:  2017-03-01       Impact factor: 49.962

4.  LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases.

Authors:  Zhenyu Bao; Zhen Yang; Zhou Huang; Yiran Zhou; Qinghua Cui; Dong Dong
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

5.  The landscape of long noncoding RNAs in the human transcriptome.

Authors:  Matthew K Iyer; Yashar S Niknafs; Rohit Malik; Udit Singhal; Anirban Sahu; Yasuyuki Hosono; Terrence R Barrette; John R Prensner; Joseph R Evans; Shuang Zhao; Anton Poliakov; Xuhong Cao; Saravana M Dhanasekaran; Yi-Mi Wu; Dan R Robinson; David G Beer; Felix Y Feng; Hariharan K Iyer; Arul M Chinnaiyan
Journal:  Nat Genet       Date:  2015-01-19       Impact factor: 38.330

6.  Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs.

Authors:  Joana Carlevaro-Fita; Taisia Polidori; Monalisa Das; Carmen Navarro; Tatjana I Zoller; Rory Johnson
Journal:  Genome Res       Date:  2018-12-26       Impact factor: 9.043

7.  Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

Authors:  Aurélie Kapusta; Zev Kronenberg; Vincent J Lynch; Xiaoyu Zhuo; LeeAnn Ramsay; Guillaume Bourque; Mark Yandell; Cédric Feschotte
Journal:  PLoS Genet       Date:  2013-04-25       Impact factor: 5.917

8.  Transposable elements reveal a stem cell-specific class of long noncoding RNAs.

Authors:  David Kelley; John Rinn
Journal:  Genome Biol       Date:  2012-11-26       Impact factor: 13.583

9.  GENCODE reference annotation for the human and mouse genomes.

Authors:  Adam Frankish; Mark Diekhans; Anne-Maud Ferreira; Rory Johnson; Irwin Jungreis; Jane Loveland; Jonathan M Mudge; Cristina Sisu; James Wright; Joel Armstrong; If Barnes; Andrew Berry; Alexandra Bignell; Silvia Carbonell Sala; Jacqueline Chrast; Fiona Cunningham; Tomás Di Domenico; Sarah Donaldson; Ian T Fiddes; Carlos García Girón; Jose Manuel Gonzalez; Tiago Grego; Matthew Hardy; Thibaut Hourlier; Toby Hunt; Osagie G Izuogu; Julien Lagarde; Fergal J Martin; Laura Martínez; Shamika Mohanan; Paul Muir; Fabio C P Navarro; Anne Parker; Baikang Pei; Fernando Pozo; Magali Ruffier; Bianca M Schmitt; Eloise Stapleton; Marie-Marthe Suner; Irina Sycheva; Barbara Uszczynska-Ratajczak; Jinuri Xu; Andrew Yates; Daniel Zerbino; Yan Zhang; Bronwen Aken; Jyoti S Choudhary; Mark Gerstein; Roderic Guigó; Tim J P Hubbard; Manolis Kellis; Benedict Paten; Alexandre Reymond; Michael L Tress; Paul Flicek
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

10.  NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.

Authors:  Lianhe Zhao; Jiajia Wang; Yanyan Li; Tingrui Song; Yang Wu; Shuangsang Fang; Dechao Bu; Hui Li; Liang Sun; Dong Pei; Yu Zheng; Jianqin Huang; Mingqing Xu; Runsheng Chen; Yi Zhao; Shunmin He
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971
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