ReviewBriefings in functional genomics2015
Evolving insights on how cytosine methylation affects protein-DNA binding.
Review in Briefings in functional genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 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.
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
69 citing papers in PubMed, 126 citations in OpenAlex.
- Miniaturized HOXB13 Mimetics Are Sequence-Specific, Methyl-Sensitive DNA Binders.Journal of the American Chemical Society · 2026Article
- DNA methylation enhances cooperative disentanglement by the Hfq nucleoid-associated protein.European biophysics journal : EBJ · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Fundamentals of DNA methylation in development.Pediatric research · 2025Review
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Origin, fate and function of extraembryonic tissues during mammalian development.Nature reviews. Molecular cell biology · 2025Review
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Mini review: Studying epigenomic alterations can shed light on coping and adaptive abilities during heat stress in monogastric livestock.Frontiers in genetics · 2025Review
- Charting epimutation dynamics in human hematopoietic differentiation.Blood science (Baltimore, Md.) · 2024Article
- Article
- DNA methylation regulates the secondary metabolism of saponins to improve the adaptability of Eleutherococcus senticosus during drought stress.BMC genomics · 2024Article
- The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.Nucleic acids research · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- Fatty Acid Induced Hypermethylation in theInternational journal of molecular sciences · 2023Article
- Article
- The dynamics of chromatin states mediated by epigenetic modifications during somatic cell reprogramming.Frontiers in cell and developmental biology · 2023Review
- Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation.Nature genetics · 2022Article
- DNA methylation levels of RELN promoter region in ultra-high risk, first episode and chronic schizophrenia cohorts of schizophrenia.Schizophrenia (Heidelberg, Germany) · 2022Article
9 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
8 authors at 2 institutions in 1 country.
Funding
Abstract
Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, in general, the underlying mechanisms of this effect are poorly understood. In this review, we summarize what is currently known about how this important, but mysterious, epigenetic mark impacts cellular functions. Cytosine methylation can abrogate or enhance interactions with DNA-binding proteins, or it may have no effect, depending on the context. Despite being only a small chemical change, the addition of a methyl group to cytosine can affect base readout via hydrophobic contacts in the major groove and shape readout via electrostatic contacts in the minor groove. We discuss the recent discovery that CpG methylation increases DNase I cleavage at adjacent positions by an order of magnitude through altering the local 3D DNA shape and the possible implications of this structural insight for understanding the methylation sensitivity of transcription factors (TFs). Additionally, 5-methylcytosines change the stability of nucleosomes and, thus, affect the local chromatin structure and access of TFs to genomic DNA. Given these complexities, it seems unlikely that the influence of DNA methylation on protein-DNA binding can be captured in a small set of general rules. Hence, data-driven approaches may be essential to gain a better understanding of these mechanisms.
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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.