ArticleBioinformatics and biology insights2012
DNA structural properties in the classification of genomic transcription regulation elements.
Article in Bioinformatics and biology insights, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change.International journal of molecular sciences · 2023Review
- Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes.Nature communications · 2022Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies.Nucleic acids research · 2020Article
- Article
- Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.Nucleic acids research · 2018Article
- DNA structural features of eukaryotic TATA-containing and TATA-less promoters.FEBS open bio · 2017Article
- Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Article
- Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.PLoS computational biology · 2015Article
- The impact of sequence length and number of sequences on promoter prediction performance.BMC bioinformatics · 2015Article
- Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2014Article
- Structural properties of prokaryotic promoter regions correlate with functional features.PloS one · 2014Article
- Distribution of MGEs and their insertion sites in the Macaca mulatta genome.Mobile genetic elements · 2012Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been long known that DNA molecules encode information at various levels. The most basic level comprises the base sequence itself and is primarily important for the encoding of proteins and direct base recognition by DNA-binding proteins. A more elusive level consists of the local structural properties of the DNA molecule wherein the DNA sequence only plays an indirect supportive role. These properties are nevertheless an important factor in a large number of biomolecular processes and can be considered as informative signals for the presence of a variety of genomic features. Several recent studies have unequivocally shown the benefit of relying on such DNA properties for modeling and predicting genomic features as diverse as transcription start sites, transcription factor binding sites, or nucleosome occupancy. This review is meant to provide an overview of the key aspects of these DNA conformational and physicochemical properties. To illustrate their potential added value compared to relying solely on the nucleotide sequence in genomics studies, we discuss their application in research on transcription regulation mechanisms as representative cases.
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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.