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

MPS-Authors

Bhardwaj,  Vivek
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Semplicio,  Giuseppe
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Erdogdu,  Niyazi Umut
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Manke,  Thomas
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Akhtar,  Asifa
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Citation

Bhardwaj, V., Semplicio, G., Erdogdu, N. U., Manke, T., & Akhtar, A. (2019). MapCap allows high-resolution detection and differential expression analysis of transcription start sites. Nature Communications, 10, 3219. doi:10.1038/s41467-019-11115-x.


Cite as: http://hdl.handle.net/21.11116/0000-0005-DA3A-5
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.