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MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

ABSTRACT: MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

PROVIDER: PRJNA517665 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8502570_1.fastq.gz	Fastqsanger.gz
	SRR8502570_2.fastq.gz	Fastqsanger.gz
	SRR8502580_1.fastq.gz	Fastqsanger.gz
	SRR8502580_2.fastq.gz	Fastqsanger.gz
	SRR8502571_1.fastq.gz	Fastqsanger.gz

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MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

Project description:Promoter architecture, shape and usage play an important role in the regulation of eukaryotic gene expression. Several promoter profiling techniques have been developed to detect transcription start sites and alternative promoter usage between tissues or during development. However promoter profiling has not been utilized in studies that demand quantification of expression changes between developmental stages, tissues and conditions. In this study, we combine promoter profiling and differential expression analysis in a single setup, using a fast and simple protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with a new software “icetea” (https://bioconductor.org/packages/icetea). The use of random molecular barcodes and spike-ins in MAPCap enables accurate quantification of expression from promoters. We detected sex-specific promoter usage in the brains of Drosophila melanogaster larvae. Comparison of male and female mutant flies of the male-less helicase (MLE), a protein known to be essential for the dosage compensation of the male X-chromosome, indicated that the sensitivity of promoters to dosage compensation depends on their genomic location. Our results expand the scope of promoter profiling methods to differential expression analysis and provide quantitative insights into promoter usage during dosage compensation.

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MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.

Project description:The position, shape and number of transcription start sites (TSS) are critical determinants of gene regulation. Most methods developed to detect TSSs and study promoter usage are, however, of limited use in studies that demand quantification of expression changes between two or more groups. In this study, we combine high-resolution detection of transcription start sites and differential expression analysis using a simplified TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with the software icetea . Applying MAPCap on developing Drosophila melanogaster embryos and larvae, we detected stage and sex-specific promoter and enhancer activity and quantify the effect of mutants of maleless (MLE) helicase at X-chromosomal promoters. We observe that MLE mutation leads to a median 1.9 fold drop in expression of X-chromosome promoters and affects the expression of several TSSs with a sexually dimorphic expression on autosomes. Our results provide quantitative insights into promoter activity during dosage compensation.

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