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

Vivek Bhardwaj, Giuseppe Semplicio, Niyazi Umut Erdogdu, Thomas Manke and Asifa Akhtar ()
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Vivek Bhardwaj: Max Planck Institute for Immunobiology and Epigenetics
Giuseppe Semplicio: Max Planck Institute for Immunobiology and Epigenetics
Niyazi Umut Erdogdu: Max Planck Institute for Immunobiology and Epigenetics
Thomas Manke: Max Planck Institute for Immunobiology and Epigenetics
Asifa Akhtar: Max Planck Institute for Immunobiology and Epigenetics

Nature Communications, 2019, vol. 10, issue 1, 1-15

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-11115-x

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