ArticleNature communications2019
MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Redefining normal breast cell populations using long noncoding RNAs.Nucleic acids research · 2023Article
- A large deletion at the cortex locus eliminates butterfly wing patterning.G3 (Bethesda, Md.) · 2022Article
- Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TSSr: an R package for comprehensive analyses of TSS sequencing data.NAR genomics and bioinformatics · 2021Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Generation and characterization ofJournal of neurogenetics · 2021Article
- Expression of theJournal of neurogenetics · 2021Article
- Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR.NAR genomics and bioinformatics · 2021Article
- Identifying transcript 5' capped ends inPeerJ · 2021Article
- Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.Genome research · 2020Article
- High-Resolution Mapping of Transcription Initiation in the Asexual Stages ofFrontiers in cellular and infection microbiology · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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