ArticleNature methods2010
A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
106 citing papers in PubMed, 176 citations in OpenAlex.
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- The nascent transcriptome delineates the regulatory landscape in human health and disease.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes.Genome research · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Dissecting thebioRxiv : the preprint server for biology · 2024Article
- Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation.Science advances · 2024Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing.mSystems · 2024Article
- KSHV 3.0: A State-of-the-Art Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing.bioRxiv : the preprint server for biology · 2023Article
- Genome-Wide Mapping of 5' Isoforms with 5'-Seq.Current protocols · 2023Article
- Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi.Journal of fungi (Basel, Switzerland) · 2022Review
- In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing.Viruses · 2022Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Dynamic regulation of NNature communications · 2021Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- A universal framework for detectingGenome research · 2021Article
- Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.Nucleic acids research · 2021Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
Abstract
Recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster in both narrow and broad genomic windows. Here we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs. Furthermore, we identified many 5' capped transcripts originating from coding exons; our analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. We demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.