Discovery of posttranscriptional regulatory RNAs using next generation sequencing technologies

Methods in Molecular Biology

Volumn 985, Issue , 2013, Pages 269-295

  Gelderman, Grant ^a   Contreras, Lydia M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Deep sequencing; Illumina; Next generation sequencing; Small RNA discovery

Indexed keywords

SMALL UNTRANSLATED RNA;

ARTICLE; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SEQUENCE ANALYSIS;

ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

MLCS; MLOWN;

EID: 84880782457     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-299-5_14     Document Type: Article

References (33)

1. Gorke B, Vogel J (2008) Noncoding RNA control the making and breaking of sugars. Genes Dev 22:2914-2925
2. Gottesman S (2005) Micros for microbes: noncoding regulatory RNAs in bacteria. Trends Genet 21:399-404
3. Romby P, Vandenesch F, Wagner EGH (2006) The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 9:229-236
4. Siegel G et al (2011) Gene expression in Trypansoma brucei: lessons from high throughput RNA sequencing. Trends Parasitol 27: 434-441
5. Clayton CE (2002) Life without transcriptional control? From fly to man and back again. EMBO J 21:1881-1888
6. Haile S, Papadopoulou B (2007) Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr Opin Microbiol 10:569-577
7. Metzker ML (2010) Sequencing technologies- The next generation. Nat Rev Genet 11:31-46
8. Rusk N (2011) Torrents of sequence. Nat Methods 8:44
9. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12): 5463-5467
10. Franca LT, Carrilho E, Kist TB (2002) A review of DNA sequencing techniques. Q Rev Biophys 35(2):169-200
11. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402
12. Margulies E et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380
13. Kuchenbauer M et al (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 18:1787-1797
14. Schweiger MR, Kerick M, Timmermann B et al (2011) The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations. Cancer Metastasis Rev 30:199-2010
15. Tawfik DS, Griffiths AD (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16:652-656
16. Slamon DJ, Leyland-Jones B, Shak S et al (2001) Use of chemotherapy plus monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med 344:783-792
17. Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732
18. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682
19. Wang Z, Gerstein M, Snyder M (2009) RNASeq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
20. Lu C, Meyers BC, Green PJ (2007) Construction of small RNA cDNA libraries for deep sequencing. Methods 43:110-117
21. Noonan H et al (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113-1118
22. Nakamura S, Nakaya T, Iida T (2011) Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing. Exp Biol Med 236:968-971
23. Ren R et al (2000) Genome-wide profiles of STAT1 of DNA binding proteins. Science 290: 2306-2309
24. Niedringhaus M et al (2011) Landscape of next-generation sequencing technologies. Anal Chem 83:4327-4341
25. Lister O'M et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536
26. Cloonan F et al (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613-619
27. Lin Q et al (1999) Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science 285(5433):1558-1562
28. Li H et al (2009) The sequence alignment/ map format and SAMtools. Bioinformatics 25: 2078-2079
29. Linsen SE, de Wit E et al (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 6:474-476
30. Dressman Y et al (2003) Transforming single DNA molecules into fluorescent magnetic particle for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100: 8817-8822
31. Feurco R et al (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34:e22
32. McCormick KP, Willmann MR, Meyers BC (2011) Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence J 2:2
33. Liu L et al (2009) Experimental discovery of sRNAs in Vibrio cholera by direct cloning, 5S/ tRNA depletion and parallel sequencing. Nucleic Acids Res 37:e46