DNA Sequencing) Time Binding Sites and Other Functional Sites Using Sequencing As a Means of Evaluating Chromatin Immunoprecipitation (Chip) Elaine R
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COMMENTARY for re-sequencing genomes. With next- generation-based applications, we rapidly A brief history of will begin to annotate the human genome with the positions of regulatory protein- (DNA sequencing) time binding sites and other functional sites using sequencing as a means of evaluating chromatin immunoprecipitation (ChIP) Elaine R. Mardis experiments. A variant of ChIP will eluci- date how genome-wide patterns of histone Each spring, I co-teach a course to under- binding and DNA methylation relate to graduates that aims to introduce them to gene-expression regulation in various cell the brief history of genome sequencing states, such as differentiation or disease. and then immerses them in its current The short read-lengths of next-generation practices. Looking out at their eager faces, platforms also are ideal for discovering the I try (perhaps in vain) to capture for them sequences of non-coding RNA genes that in a 1 hour lecture what has been my life’s cannot be elucidated by in silico methods. focus for the past 20 years or so — DNA Bioinformatics-based analysis of genome- sequencing. If forced to summarize this wide DNA copy number, DNA-sequence time period succinctly, I would say, “Never variation and RNA-expression data sets, all a dull moment!” This is largely owing to the produced by next-generation sequencers, technological advances that have catapulted will be integrated to stitch together the genome sequencing from a cottage industry pieces of the biological ‘story’ being told to a high-throughput enterprise, akin to by genomic data. These stories will, in a factory. That said, the constant winds of transition not only allowed automated turn, help us to make sense of our clinical change that swirl around DNA sequencing detection and base calling of sequence observations, and suggest cures to aberrant are about to change the paradigm yet again, reads, but also made sequencing safer and biological states. Present day sequencing owing to next-generation approaches. more readily automated. What about the technology advances have the potential to The history of DNA sequencing is a development of automated picking robots revolutionize the translation of genomic brief one — first described by Fred Sanger that replaced manual harvesting with sterile information into clinical practice. in 1977, merely 30 years ago. In that brief toothpicks? The automated imaging of agar To have been a part of sequencing up time, progress has been staggering, owing plates coupled with actuator-driven steel to now is to have a unique perspective on in large part to interdisciplinary innova- pins for harvesting colonies was key to how far we have come and how our accom- tions that have built on the fundamental high-throughput pipelines, and saved the plishments rest on the shoulders of those and elegant concept of dideoxynucleotide eyesight and careers of many technicians. innovators. I pause to wonder what I will be termination. The milestones that I describe How about the transition from hand-held teaching my students in the years to come, to my students are familiar territory to to robotic multi-pipettors? This provided and quickly realize that presently I might me, and I strive to convey the ingenuity another crucial step in high-throughput not even be able to imagine it. So, at the end and intelligence that were required to automated pipelines, especially at of our hour together, I choose to leave the make each one a reality, and to capture the 384-well plate densities. Or consider, only past behind, and attempt to invigorate my definitive impact of each discovery on our 8 years ago, when slab-gel sequencers were students with the same sense of potential capabilities. Indeed, where would DNA replaced by capillary-array sequencers? for questions yet to be answered that I first sequencing be today without synthetic Eliminating hand loading, image files felt in graduate school and still feel to this oligonucleotides, fluorescence resonance and gel-lane tracking allowed a tremendous day. The context and potential are not that energy transfer dideoxynucleotides, high- acceleration of throughput and capacity different now from then. Certainly, they will fidelity polymerases and cycle sequencing? with a drastic decrease in labour. What have an ever-increasing number of next- Taken alone or together, each of these about the profound impact of finely-tuned generation sequencing instruments, applica- discoveries allowed a quantum leap in bioinformatics tools that allow the assem- tions and bioinformatics tools available to sequencing data quality and throughput. bly, annotation and analysis of a genome them; moreover, the reach of sequencing Can my students ever appreciate the sequence, teasing out its every secret by as an approach to answering genome-scale transition from radioactive to fluorescent clever approaches? Genomics simply would biological questions will be greater than labelling? Although it took sequencing not be possible without bioinformatics. ever. My hope is that they not only will laboratories several years to trust the data It was this delicate integration of respect the brief but illustrious past of DNA quality from fluorescent sequencers, this chemistry, engineering, enzymology, sepa- sequencing, but also will choose to become ration sciences and software that allowed a part of its promising future. us to first describe the human genome … the technological advances Elaine R. Mardis is Associate Professor in Genetics and sequence, and that now has set the stage for Molecular Microbiology, and Co-Director of the have catapulted genome even greater accomplishments at a previ- Genome Sequencing Center at the Washington sequencing from a cottage ously unimagined pace. In fact, with next- University School of Medicine, 4444 Forest Park generation technology, we now have an Boulevard, St. Louis, Missouri 63108, USA. industry to a high-throughput amazingly accurate genome-wide readout e-mail: [email protected] enterprise, akin to a factory. for many types of experiments, not merely doi: 10.1038/mrg2240 natUre milestones | DNA TECHNOLOGIES october 2007 | S21 © 2007 Nature Publishing Group .