Go Deep! New Tools for Sequencing DNA and RNA

Go Deep!
Reported by
Don Monroe

Posted April 24, 2008

New technology now enables researchers to rapidly sequence megabases of both nuclear DNA and cDNAs generated from small RNA. This "deep sequencing," in turn, has given researchers the power to investigate a new set of biological problems.

Strictly speaking, "deep sequencing" implies highly redundant coverage of the target DNA, but researchers sometimes use "deep" as shorthand for the new, high-throughput equipment. In 2005, 454 Life Sciences, since acquired by Roche, introduced this expensive but powerful technology. In 2007, Illumina introduced an even more capable technology it acquired with Solexa.

At a March 10, 2008, symposium at the Academy, speakers showed results from both the 454 and Solexa systems. Michael Snyder of Yale University described three different uses of high-throughput sequencing of DNA. The other two speakers, Graham Ruby, of the Whitehead Institute for Biomedical Research at MIT and Katsutomo Okamura, of the Memorial Sloan-Kettering Cancer Center, use high-throughput sequencing to classify short RNAs.

Web Sites

454 Life Sciences
454 Life Sciences is the Roche subsidiary that makes one of the high-throughput sequencing machines.

Illumina Sequencing
Illumina sequencing is the high-throughput technology acquired with Solexa.

Applied Biosystems' SOLiD
A high-throughput sequencing system developed by Agencourt.

Helicos Genetic Analysis System
Helicos has developed a single-molecule sequencer.

The Polonator G.007
The Polonator G.007 is an open platform for sequencing developed with the Church lab at Harvard Medical School.

Journal Articles


von Bubnoff A. 2008. Next-generation sequencing: the race is on. Cell 132: 721-723.

Michael Snyder

Korbel JO, Urban AE, Affourtit JP, et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426.

Robertson G, Hirst M, Bainbridge M, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4: 651-657.

Smith MG, Gianoulis TA, Pukatzki S, et al. 2007. New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 21: 601-614. FULL TEXT

Graham Ruby

Ruby JG, Jan CH, Bartel DP. 2007. Intronic microRNA precursors that bypass Drosha processing. Nature 448: 83-86.

Ruby JG, Jan C, Player C, et al. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207. FULL TEXT

Ruby JG, Stark A, Johnston WK et al. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17:1850-1864. FULL TEXT

Katsutomo Okamura

Berezikov E, Chung WJ, Willis J, et al. 2007. Mammalian mirtron genes. Mol. Cell 28: 328-336.

Okamura K, Hagen JW, Duan H, et al. 2007. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130: 89-100.

Okamura K, Phillips MD, Tyler DM, et al. 2008. MicroRNA* species have substantial influence on regulatory networks. Nat. Struct. Mol. Biol. (accepted)

Tyler DM, Okamura K, Chung WJ, et al. 2008. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22: 26-36.


Michael Snyder, PhD

Yale University
e-mail | web site | publications

Michael Snyder is Lewis B. Cullman Professor of Molecular, Cellular, and Developmental Biology at Yale University. He is also a member of the Yale Comprehensive Cancer Center. His work focuses on topics including the control of cell division and cell morphology in yeast, the characterization of proteomes, analysis of regulatory circuits in yeast, characterization of the human genome, and sex-specific gene expression in mammals. After completing his PhD at the California Institute of Technology, he held postdoctoral fellowships at CalTech and Stanford, before joining Yale in 1986.

Graham Ruby

Whitehead Institute for Biomedical Research, MIT
e-mail | web site | publications

Graham Ruby is a graduate student in Dave Bartel's lab at the Massachusetts Institute of Technology.

Katsutomo Okamura, PhD

Memorial Sloan-Kettering Cancer Center
e-mail | web site | publications

Katsutomo Okamura is a research fellow in Eric Lai's lab at Memorial Sloan Kettering Cancer Center.