ArticlePloS one2011
Systematic clustering of transcription start site landscapes.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- VprBP drives prostate tumorigenesis by its kinase activity targeting histone H2A.Cell communication and signaling : CCS · 2026Article
- Pervasive Transcription in the Human Genome Exceeds Background Noise.Genome biology and evolution · 2026Article
- HDAC1 has intrinsic protease activity and regulates transcription through clipping histone H3 N-terminal tail.Cell death and differentiation · 2026Article
- VprBP regulates osteoclast differentiation via an epigenetic mechanism involving histone H2A phosphorylation.Epigenetics & chromatin · 2024Article
- MMP-9-dependent proteolysis of the histone H3 N-terminal tail: a critical epigenetic step in driving oncogenic transcription and colon tumorigenesis.Molecular oncology · 2024Article
- Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats.The New phytologist · 2024Article
- KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing.mSystems · 2024Article
- VprBP/DCAF1 Triggers Melanomagenic Gene Silencing through Histone H2A Phosphorylation.Biomedicines · 2023Article
- Trends in disease burden of hepatitis B infection in Jiangsu Province, China, 1990-2021.Infectious Disease Modelling · 2023Article
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Phosphorylation and stabilization of EZH2 by DCAF1/VprBP trigger aberrant gene silencing in colon cancer.Nature communications · 2023Article
- MMP-9 drives the melanomagenic transcription program through histone H3 tail proteolysis.Oncogene · 2022Article
- VprBP directs epigenetic gene silencing through histone H2A phosphorylation in colon cancer.Molecular oncology · 2021Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Identifying transcript 5' capped ends inPeerJ · 2021Article
- MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.Nature communications · 2019Article
- Article
- Comprehensive comparative analysis of 5'-end RNA-sequencing methods.Nature methods · 2018Article
- Glucotypes reveal new patterns of glucose dysregulation.PLoS biology · 2018Article
- Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.Functional & integrative genomics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide, high-throughput methods for transcription start site (TSS) detection have shown that most promoters have an array of neighboring TSSs where some are used more than others, forming a distribution of initiation propensities. TSS distributions (TSSDs) vary widely between promoters and earlier studies have shown that the TSSDs have biological implications in both regulation and function. However, no systematic study has been made to explore how many types of TSSDs and by extension core promoters exist and to understand which biological features distinguish them. In this study, we developed a new non-parametric dissimilarity measure and clustering approach to explore the similarities and stabilities of clusters of TSSDs. Previous studies have used arbitrary thresholds to arrive at two general classes: broad and sharp. We demonstrated that in addition to the previous broad/sharp dichotomy an additional category of promoters exists. Unlike typical TATA-driven sharp TSSDs where the TSS position can vary a few nucleotides, in this category virtually all TSSs originate from the same genomic position. These promoters lack epigenetic signatures of typical mRNA promoters and a substantial subset of them are mapping upstream of ribosomal protein pseudogenes. We present evidence that these are likely mapping errors, which have confounded earlier analyses, due to the high similarity of ribosomal gene promoters in combination with known G addition bias in the CAGE libraries. Thus, previous two-class separations of promoter based on TSS distributions are motivated, but the ultra-sharp TSS distributions will confound downstream analyses if not removed.
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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.