ArticleGenome research2011
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 143 citations in OpenAlex.
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- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Regulation of R-Loops in DNA Tumor Viruses.Pathogens (Basel, Switzerland) · 2024Review
- 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
- 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
- Transcriptional Regulation of Liver-Type OATP1B3 (Lt-OATP1B3) and Cancer-Type OATP1B3 (Ct-OATP1B3) Studied in Hepatocyte-Derived and Colon Cancer-Derived Cell Lines.Pharmaceutics · 2023Article
- Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines.Japanese journal of clinical oncology · 2023Article
- Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.The Plant journal : for cell and molecular biology · 2022Article
- Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation.Cell systems · 2022Article
- Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Plasticity and heterogeneity of thermogenic adipose tissue.Nature metabolism · 2021Review
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.Scientific reports · 2021Article
- Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice.Genome medicine · 2021Article
- Investigation of the Wilson gene ATP7B transcriptional start site and the effect of core promoter alterations.Scientific reports · 2021Article
- Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.Genome research · 2021Article
- Transcription initiation of distant core promoters in a large-sized genome of an insect.BMC biology · 2021Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We performed a genome-wide analysis of transcriptional start sites (TSSs) in human genes by multifaceted use of a massively parallel sequencer. By analyzing 800 million sequences that were obtained from various types of transcriptome analyses, we characterized 140 million TSS tags in 12 human cell types. Despite the large number of TSS clusters (TSCs), the number of TSCs was observed to decrease sharply with increasing expression levels. Highly expressed TSCs exhibited several characteristic features: Nucleosome-seq analysis revealed highly ordered nucleosome structures, ChIP-seq analysis detected clear RNA polymerase II binding signals in their surrounding regions, evaluations of previously sequenced and newly shotgun-sequenced complete cDNA sequences showed that they encode preferable transcripts for protein translation, and RNA-seq analysis of polysome-incorporated RNAs yielded direct evidence that those transcripts are actually translated into proteins. We also demonstrate that integrative interpretation of transcriptome data is essential for the selection of putative alternative promoter TSCs, two of which also have protein consequences. Furthermore, discriminative chromatin features that separate TSCs at different expression levels were found for both genic TSCs and intergenic TSCs. The collected integrative information should provide a useful basis for future biological characterization of TSCs.
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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.