First Genome-Wide Profiling of Transcription Start Sites in Drosophila melanogaster
In an international effort, scientists at the Illinois Institute of Technology together with industrial partners at DNAFORM in Japan, imaGenes in Germany, FASTERIS in Switzerland, and Precision Biomarker Resources in USA have for the first time prepared a genome-wide map of Transcription Start Sites (TSS) for the fruit fly Drosophila melanogaster. Drosophila is one of the best studied model organisms in biology and has greatly contributed to our understanding of genetics, development, physiology, and behavior.
With the increasing availability of genome sequences, research has shifted to transcriptome analysis for greater understanding of how genomic information is utilized in a regulated manner. Recent data mostly obtained by new Next-Generation Sequencing Methods indicate genome-wide RNA transcription from both DNA strands at unexpectedly high levels with complex overlapping patterns. Of the different approaches to genome and transcriptome analysis, the Cap Analysis Gene Expression (CAGE) Method developed by the RIKEN Omics Center and DNAFORM, in combination with Next-Generation Sequencing is uniquely placed to experimentally identify TSS on a genome-wide level with the high accuracy and the precision required assessing such diverse expression patterns. After major contributions to the RIKEN FANTOM and NIH ENCODE projects, CAGE has now for the first time been applied to Drosophila melanogaster. Identification of TSS in Drosophila is a valuable contribution to what is already arguably the best annotated genome. The availability of genome sequences of 11 additional Drosophila species in combination with CAGE-identified TSS in Drosophila melanogaster promises great insights into evolutionary aspects of gene expression.
We expected most highly expressed CAGE tags to be linked to well annotated gene transcripts in Drosophila. However, initial analysis of our data shows only 25% of the highly expressed CAGE tag clusters map close to annotated TSS. CAGE studies of other organisms showed that about half of all genes have alternate promoters and/or transcripts originating within genes and distances upstream. That 75% of our highly expressed CAGE tag clusters are not tightly linked to known TSS even in the well annotated Drosophila genome suggests that transcription is much more complex than previously thought. Associating CAGE tags with exons and 3' UTRs, and linking transcripts to genes at variable distances away on both DNA strands will promise greater understanding of genome expression in Drosophila. Moreover, less highly expressed CAGE tag clusters point to wider expression of the Drosophila genome than described by the present annotation. Our study has thus potentially indentified new promoter sites for known genes as well as entirely new transcriptional events.
A unique advantage of the Drosophila system is that the worldwide Drosophila research community can rapidly test the implications of our new CAGE results. Molecular, genetic, developmental, and behavioral experiments on genes of particular interest will test the biological importance of newly detected promoter regions and the gene expression they drive. Considerable similarities have been found between flies and human, and results from Drosophila are expected to drive further advances in other species, including human.
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