High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

• DOI: 10.1101/gr.139618.112
• Publication Date: 2012-08-31T04:46:01Z
• Authors: Philippe Batut; Alexander Dobin; Charles Plessy; Piero Carninci; Thomas R. Gingeras
• Keywords: 572; Transcription, Genetic; transposons; Method; Genes, Insect; 03 medical and health sciences; Animals; genetics & nucleic acid processing; Genes, Developmental; RNA structure; genes; Promoter Regions, Genetic; Gene Library; genomics and proteomics; function; modification; Life Cycle Stages; 0303 health sciences; promoter; Gene Expression Regulation, Developmental; DNA; Sequence Analysis, DNA; Drosophila melanogaster; gene expression; DNA Transposable Elements; structure and function; Transcription Initiation Site; Transcriptome; DNA expression

Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating and deciphering their individual regulatory dynamics is critical for gene profiling applications our understanding of complexity. We introduce RAMPAGE, a novel promoter activity approach that combines extremely specific 5'-complete cDNA sequencing an integrated data analysis workflow, to address the limitations current techniques. RAMPAGE features streamlined protocol fast easy generation highly multiplexed libraries, offers very high transcription start site specificity, generates accurate reproducible measurements, yields extensive transcript connectivity information through paired-end sequencing. used in genome-wide study throughout 36 stages life cycle Drosophila melanogaster, describe here comprehensive set represents first available developmental time-course usage. found >40% developmentally expressed have at least two generally implement programs. Transposable elements, long proposed play central role evolution host genomes ability regulate expression, contribute 1300 shaping transcriptome D. melanogaster. Hundreds these drive annotated genes, transposons often impart own specificity upon they regulate. These observations provide support theory may innovation distribution stereotyped cis-regulatory modules genomes.