Literature DB >> 26828742

Biological Processes Discovered by High-Throughput Sequencing.

Brian J Reon1, Anindya Dutta2.   

Abstract

Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible technology that allows scientists to sequence an entire transcriptome or genome in a timely and cost-effective manner. Application of HTS techniques has led to many key discoveries, including the identification of long noncoding RNAs, microDNAs, a family of small extrachromosomal circular DNA species, and tRNA-derived fragments, which are a group of small non-miRNAs that are derived from tRNAs. Furthermore, public sequencing repositories provide unique opportunities for laboratories to parse large sequencing databases to identify proteins and noncoding RNAs at a scale that was not possible a decade ago. Herein, we review how HTS has led to the discovery of novel nucleic acid species and uncovered new biological processes during the course.
Copyright © 2016 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2016        PMID: 26828742      PMCID: PMC5807928          DOI: 10.1016/j.ajpath.2015.10.033

Source DB:  PubMed          Journal:  Am J Pathol        ISSN: 0002-9440            Impact factor:   4.307


  68 in total

Review 1.  Genome-wide transcription and the implications for genomic organization.

Authors:  Philipp Kapranov; Aarron T Willingham; Thomas R Gingeras
Journal:  Nat Rev Genet       Date:  2007-05-08       Impact factor: 53.242

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Authors:  P MANDEL; P METAIS
Journal:  C R Seances Soc Biol Fil       Date:  1948-02

3.  Overview of circulating nucleic acids in plasma/serum.

Authors:  Asif N Butt; R Swaminathan
Journal:  Ann N Y Acad Sci       Date:  2008-08       Impact factor: 5.691

4.  MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis.

Authors:  Adam C Mueller; Magdalena A Cichewicz; Bijan K Dey; Ryan Layer; Brian J Reon; Jeffrey R Gagan; Anindya Dutta
Journal:  Mol Cell Biol       Date:  2014-11-17       Impact factor: 4.272

Review 5.  Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health.

Authors:  William L Towns; Thomas J Begley
Journal:  DNA Cell Biol       Date:  2011-12-22       Impact factor: 3.311

Review 6.  Somatic mosaicism: implications for disease and transmission genetics.

Authors:  Ian M Campbell; Chad A Shaw; Pawel Stankiewicz; James R Lupski
Journal:  Trends Genet       Date:  2015-04-21       Impact factor: 11.639

7.  An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment.

Authors:  Nianwei Lin; Kung-Yen Chang; Zhonghan Li; Keith Gates; Zacharia A Rana; Jason Dang; Danhua Zhang; Tianxu Han; Chao-Shun Yang; Thomas J Cunningham; Steven R Head; Gregg Duester; P Duc Si Dong; Tariq M Rana
Journal:  Mol Cell       Date:  2014-02-13       Impact factor: 17.970

8.  Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.

Authors:  Aleksandra Helwak; Grzegorz Kudla; Tatiana Dudnakova; David Tollervey
Journal:  Cell       Date:  2013-04-25       Impact factor: 41.582

9.  The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors:  Thomas Derrien; Rory Johnson; Giovanni Bussotti; Andrea Tanzer; Sarah Djebali; Hagen Tilgner; Gregory Guernec; David Martin; Angelika Merkel; David G Knowles; Julien Lagarde; Lavanya Veeravalli; Xiaoan Ruan; Yijun Ruan; Timo Lassmann; Piero Carninci; James B Brown; Leonard Lipovich; Jose M Gonzalez; Mark Thomas; Carrie A Davis; Ramin Shiekhattar; Thomas R Gingeras; Tim J Hubbard; Cedric Notredame; Jennifer Harrow; Roderic Guigó
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

10.  Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.

Authors:  Shivendra Kishore; Andreas R Gruber; Dominik J Jedlinski; Afzal P Syed; Hadi Jorjani; Mihaela Zavolan
Journal:  Genome Biol       Date:  2013-05-26       Impact factor: 13.583

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  7 in total

Review 1.  Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy?

Authors:  Jing Zhu; Siyu Chen; Fan Zhang; Liang Wang
Journal:  Mol Diagn Ther       Date:  2018-10       Impact factor: 4.074

2.  Heat Stress Regulates the Expression of Genes at Transcriptional and Post-Transcriptional Levels, Revealed by RNA-seq in Brachypodium distachyon.

Authors:  Shoukun Chen; Haifeng Li
Journal:  Front Plant Sci       Date:  2017-01-10       Impact factor: 5.753

3.  Expression profiles of long noncoding RNAs and mRNAs in peripheral blood mononuclear cells of patients with acute myocardial infarction.

Authors:  Pingsen Zhao; Heming Wu; Zhixiong Zhong; Qifeng Zhang; Wei Zhong; Bin Li; Cunren Li; Zhidong Liu; Min Yang
Journal:  Medicine (Baltimore)       Date:  2018-10       Impact factor: 1.817

4.  A Novel lncRNA, LINC00460, Affects Cell Proliferation and Apoptosis by Regulating KLF2 and CUL4A Expression in Colorectal Cancer.

Authors:  Yifan Lian; Changsheng Yan; Hongzhi Xu; Jiebin Yang; Yang Yu; Jing Zhou; Yongguo Shi; Jianlin Ren; Guozhong Ji; Keming Wang
Journal:  Mol Ther Nucleic Acids       Date:  2018-07-06       Impact factor: 8.886

Review 5.  Extrachromosomal Circular DNA (eccDNA): From Chaos to Function.

Authors:  Shanru Zuo; Yihu Yi; Chen Wang; Xueguang Li; Mingqing Zhou; Qiyao Peng; Junhua Zhou; Yide Yang; Quanyuan He
Journal:  Front Cell Dev Biol       Date:  2022-01-06

Review 6.  Extrachromosomal Circular DNA: A New Target in Cancer.

Authors:  Pan Wu; Yuhang Liu; Ruijia Zhou; Lingyun Liu; Hongli Zeng; Fang Xiong; Shanshan Zhang; Zhaojian Gong; Wenling Zhang; Can Guo; Fuyan Wang; Ming Zhou; Xuyu Zu; Zhaoyang Zeng; Yong Li; Guiyuan Li; He Huang; Wei Xiong
Journal:  Front Oncol       Date:  2022-04-14       Impact factor: 5.738

7.  Long non-coding RNA expression profiles in peripheral blood mononuclear cells of patients with coronary artery disease.

Authors:  Wei Zhong; Qiaoting Deng; Xunwei Deng; Zhixiong Zhong; Jingyuan Hou
Journal:  J Thorac Dis       Date:  2020-11       Impact factor: 3.005

  7 in total

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