ArticleNature genetics2017
Promoter shape varies across populations and affects promoter evolution and expression noise.
Article in Nature genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Machine learning analysis of the human initiator region reveals key features of different types of core promoters.Genes & development · 2026Article
- Decoding promoter activity from DNA sequence using pre-trained language models.Scientific reports · 2026Article
- Transcription Start Site Choice Regulates mGenes · 2026Article
- Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs in three ray-finned fishes.bioRxiv : the preprint server for biology · 2026Article
- Article
- mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain.bioRxiv : the preprint server for biology · 2025Article
- fSuSiE enables fine-mapping of QTLs from genome-scale molecular profiles.bioRxiv : the preprint server for biology · 2025Article
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- A compendium of genetic variations associated with promoter usage across 49 human tissues.Nature communications · 2024Article
- eRNA co-expression network uncovers TF dependency and convergent cooperativity.Scientific reports · 2023Article
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Transcription factor IID parks and drives preinitiation complexes at sharp or broad promoters.Trends in biochemical sciences · 2023Review
- Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.The Journal of biological chemistry · 2023Review
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Dynamic interplay between non-coding enhancer transcription and gene activity in development.Nature communications · 2023Article
- Plant Promoters and Terminators for High-Precision Bioengineering.Biodesign research · 2023Review
- Investigating the sequence landscape in thePeerJ · 2023Article
- Mechanisms of robustness in gene regulatory networks involved in neural development.Frontiers in molecular neuroscience · 2023Review
- Article
- Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.
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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.