Ribosomal footprints on a transcriptome landscape 英文参考文献.docVIP

Minireview Ribosomal footprints on a transcriptome landscape David R Morris Address: Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA. Email: dmorris@ Published: 28 April 2009 Genome Biology 2009, 10:215 (doi:10.1186/gb-2009-10-4-215) The electronic version of this article is the complete one and can be found online at /2009/10/4/215 ? 2009 BioMed Central Ltd Abstract Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome. The introduction of massively parallel DNA sequencing platforms over the past five years - so-called ‘next-generation’ sequencing technology - has created the capacity to generate tens of millions of short sequence reads in a single run. These sequences can be identified by alignment to the known genomes of the all-important model organisms, including Homo sapiens [1]. The information garnered from this technology is providing new insights into important areas of genome, chromatin and transcriptome biology. [6], Wolin and Walter showed that eukaryotic ribosomes carrying out translation protected around 30 nucleotides of mRNA sequence from digestion by RNase [7]. Exploiting this observation, they demonstrated clusters of ribosome protection at discrete sites in the preprolactin transcript. These clusters were interpreted as reflecting rate-limiting steps at translation initiation and termination, as well as ribosome pausing at the site of interaction of the nascent signal peptide with the signal recognition particle. One of the applications of next-generation sequencing - short-read cDNA analysis or ‘RNAseq’ [2,3] - has its conceptual roots in serial analysis of gene expression (SAGE) [4]. Whereas SAGE provides thousands of sequences of short sequence tags th