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Literature DB >> 25435401

Mining diverse small RNA species in the deep transcriptome.

Kasey C Vickers¹, Leslie A Roteta², Holli Hucheson-Dilks³, Leng Han⁴, Yan Guo⁵.

Abstract

Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance.

Entities: Disease Gene Species

Keywords: RNA sequencing; data analysis; high-throughput sequencing; long-noncoding RNA; microRNA; small RNA; transcriptome

Mesh：

Substances：

Year: 2014 PMID： 25435401 PMCID： PMC4362530 DOI： 10.1016/j.tibs.2014.10.009

Source DB: PubMed Journal: Trends Biochem Sci ISSN： 0968-0004 Impact factor: 13.807

16 in total

1. Complementary DNA sequencing: expressed sequence tags and human genome project.

Authors: M D Adams; J M Kelley; J D Gocayne; M Dubnick; M H Polymeropoulos; H Xiao; C R Merril; A Wu; B Olde; R F Moreno
Journal: Science Date: 1991-06-21 Impact factor: 47.728

Review 2. Waste not, want not--transcript excess in multicellular eukaryotes.

Authors: Jürgen Brosius
Journal: Trends Genet Date: 2005-05 Impact factor: 11.639

Review 3. Specialization and evolution of endogenous small RNA pathways.

Authors: Elisabeth J Chapman; James C Carrington
Journal: Nat Rev Genet Date: 2007-11 Impact factor: 53.242

4. Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors: Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal: Nat Methods Date: 2008-05-30 Impact factor: 28.547

5. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

Authors: M Schena; D Shalon; R W Davis; P O Brown
Journal: Science Date: 1995-10-20 Impact factor: 47.728

Review 6. Small silencing RNAs: an expanding universe.

Authors: Megha Ghildiyal; Phillip D Zamore
Journal: Nat Rev Genet Date: 2009-02 Impact factor: 53.242

7. Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells.

Authors: Andrew Sobala; Gyorgy Hutvagner
Journal: RNA Biol Date: 2013-04-01 Impact factor: 4.652

8. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction.

Authors: Joseph M Dhahbi; Stephen R Spindler; Hani Atamna; Amy Yamakawa; Dario Boffelli; Patricia Mote; David I K Martin
Journal: BMC Genomics Date: 2013-05-02 Impact factor: 3.969

9. Hidden layers of human small RNAs.

Authors: Hideya Kawaji; Mari Nakamura; Yukari Takahashi; Albin Sandelin; Shintaro Katayama; Shiro Fukuda; Carsten O Daub; Chikatoshi Kai; Jun Kawai; Jun Yasuda; Piero Carninci; Yoshihide Hayashizaki
Journal: BMC Genomics Date: 2008-04-10 Impact factor: 3.969

Review 10. Biases in small RNA deep sequencing data.

Authors: Carsten A Raabe; Thean-Hock Tang; Juergen Brosius; Timofey S Rozhdestvensky
Journal: Nucleic Acids Res Date: 2013-11-05 Impact factor: 16.971

34 in total

1. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data.

Authors: Pan Zhang; David C Samuels; Brian Lehmann; Thomas Stricker; Jennifer Pietenpol; Yu Shyr; Yan Guo
Journal: Brief Bioinform Date: 2015-08-05 Impact factor: 11.622

2. MicroRNAs and tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute myeloid leukemia.

Authors: Yan Guo; Stephen A Strickland; Sanjay Mohan; Shaoying Li; Amma Bosompem; Kasey C Vickers; Shilin Zhao; Quanhu Sheng; Annette S Kim
Journal: Leuk Lymphoma Date: 2017-01-13

Mining diverse small RNA species in the deep transcriptome.

1. Complementary DNA sequencing: expressed sequence tags and human genome project.

Review 2. Waste not, want not--transcript excess in multicellular eukaryotes.

Review 3. Specialization and evolution of endogenous small RNA pathways.

4. Mapping and quantifying mammalian transcriptomes by RNA-Seq.

5. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

Review 6. Small silencing RNAs: an expanding universe.

7. Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells.

8. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction.

9. Hidden layers of human small RNAs.

Review 10. Biases in small RNA deep sequencing data.

1. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data.

2. MicroRNAs and tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute myeloid leukemia.

Review 3. Small non-coding RNAs in human cancer: function, clinical utility, and characterization.

4. Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification.

5. Multi-perspective quality control of Illumina RNA sequencing data analysis.

Review 6. Alternative Applications of Genotyping Array Data Using Multivariant Methods.

7. Target-enrichment sequencing for detailed characterization of small RNAs.

Review 8. Small RNA Modifications: Integral to Function and Disease.

9. A micro-RNA expression signature for human NAFLD progression.

Review 10. HDL and microRNA therapeutics in cardiovascular disease.