ArticleGenome research2020
Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux.FEBS letters · 2026Article
- Genetic dissection of transcription start site selection by RNA polymerase II in Saccharomyces cerevisiae.Genetics · 2026Article
- Important role in transcription start site selection for the RNA polymerase II-TFIIE-TFIIH interface in Saccharomyces cerevisiae.Genetics · 2026Article
- Mapping and quantifying nascent transcript start sites using TT-TSS-seq.Genome research · 2026Article
- Article
- RNA polymerase II-TFIIE-TFIIH interface functions in transcription start site selection inbioRxiv : the preprint server for biology · 2025Article
- Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress.BMC genomics · 2025Article
- Genetic dissection of transcription start site selection by RNA Polymerase II inbioRxiv : the preprint server for biology · 2025Article
- Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning.Genome biology · 2025Article
- TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation.Scientific reports · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning.eLife · 2024Article
- An improved method for the highly specific detection of transcription start sites.Nucleic acids research · 2024Article
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- The molecular grammar of protein disorder guiding genome-binding locations.Nucleic acids research · 2023Article
- Recycling of parental histones preserves the epigenetic landscape during embryonic development.Science advances · 2023Article
- Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi.Journal of fungi (Basel, Switzerland) · 2022Review
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- Article
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4 authors.
Funding
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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