ArticleiScience2019
Deciphering the Gene Regulatory Landscape Encoded in DNA Biophysical Features.
Article in iScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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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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.
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Who cites it
6 citing papers in PubMed.
- Identification and evaluation of 41 risk loci for juvenile idiopathic arthritis informs precision medicine: mechanistic implications of DNA topology and an HLA-A*02:01-ERAP2 interaction.medRxiv : the preprint server for health sciences · 2026Article
- Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development.Development (Cambridge, England) · 2022Article
- Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification.NAR genomics and bioinformatics · 2021Article
- Single-molecule micromanipulation studies of methylated DNA.Biophysical journal · 2021Article
- 90 YEARS OF PROGESTERONE: Molecular mechanisms of progesterone receptor action on the breast cancer genome.Journal of molecular endocrinology · 2020Review
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulation in higher organisms involves a sophisticated interplay between genetic and epigenetic mechanisms. Despite advances, the logic in selective usage of certain genomic regions as regulatory elements remains unclear. Here we show that the inherent biophysical properties of the DNA encode epigenetic state and the underlying regulatory potential. We find that the propeller twist (ProT) level is indicative of genomic location of the regulatory elements, their strength, the affinity landscape of transcription factors, and distribution in the nuclear 3D space. We experimentally show that ProT levels confer increased DNA flexibility and surface accessibility, and thus potentially primes usage of high ProT regions as regulatory elements. ProT levels also correlate with occurrence and phenotypic consequences of mutations. Interestingly, cell-fate switches involve a transient usage of low ProT regulatory elements. Altogether, our work provides unprecedented insights into the gene regulatory landscape encoded in the DNA biophysical features.
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Registered trials
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