ArticleGenome research2008
A code for transcription initiation in mammalian genomes.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
166 citing papers in PubMed.
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.bioRxiv : the preprint server for biology · 2026Article
- GPR3 is an immediate-early gene-like GPCR regulating CREB-dependent neuronal differentiation.iScience · 2026Article
- Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.Stem cell reports · 2026Article
- Mapping and quantifying nascent transcript start sites using TT-TSS-seq.Genome research · 2026Article
- Meta-unstable mRNAs in activated CD8Nature communications · 2026Article
- Comparative TSS-seq analysis among natural variations ofNAR genomics and bioinformatics · 2025Article
- CG-Based Stratification of 8-mers Highlights Functional Roles and Phylogenetic Divergence Markers.International journal of molecular sciences · 2025Article
- scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data.Genome biology · 2025Article
- Disruption of TAD hierarchy promotes LTR co-option in cancer.Nature genetics · 2025Article
- p53 reveals principles of chromatin remodeling and enhancer activation.Nucleic acids research · 2025Article
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.Developmental cell · 2025Article
- Alternative promoter usage during organ development.PLoS genetics · 2025Article
- Dissecting thebioRxiv : the preprint server for biology · 2024Article
- Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites.BMC biology · 2024Article
- The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.Nature communications · 2024Article
- High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436.NAR genomics and bioinformatics · 2024Article
- Article
- Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing.NPJ Parkinson's disease · 2024Article
106 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS, but an array of closely located TSSs with different rates of initiation. As a rule, genes have more than one such core promoter; however, defining the boundaries between core promoters is not trivial. These discoveries prompt a re-evaluation of our models for transcription initiation. We describe a new framework for understanding the organization of transcription initiation. We show that initiation events are clustered on the chromosomes at multiple scales-clusters within clusters-indicating multiple regulatory processes. Within the smallest of such clusters, which can be interpreted as core promoters, the local DNA sequence predicts the relative transcription start usage of each nucleotide with a remarkable 91% accuracy, implying the existence of a DNA code that determines TSS selection. Conversely, the total expression strength of such clusters is only partially determined by the local DNA sequence. Thus, the overall control of transcription can be understood as a combination of large- and small-scale effects; the selection of transcription start sites is largely governed by the local DNA sequence, whereas the transcriptional activity of a locus is regulated at a different level; it is affected by distal features or events such as enhancers and chromatin remodeling.
Indexed as
Identifiers
What OpenQuestion holds
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.