ArticleGene2009
Repetitive DNA elements, nucleosome binding and human gene expression.
Article in Gene, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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Who cites it
19 citing papers in PubMed, 46 citations in OpenAlex.
- Common Chiffchaffs (Phylloscopus collybita) Diverge in a Genomic Region Associated With Migration Differences in Willow Warblers (Phylloscopus trochilus).Molecular ecology · 2026Article
- PlantRep: a database of plant repetitive elements.Plant cell reports · 2022Article
- Article
- An atlas of transposable element-derived alternative splicing in cancer.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence.Turkish journal of biology = Turk biyoloji dergisi · 2020Article
- Distinct DNA Sequence Preference for Histone Occupancy in Primary and Transformed Cells.Cancer informatics · 2019Article
- Article
- Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Article
- Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.Biology · 2016Review
- Article
- Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.International journal of bioinformatics research and applications · 2014Article
- Searching microsatellites in DNA sequences: approaches used and tools developed.Physiology and molecular biology of plants : an international journal of functional plant biology · 2012Article
- Fast computation and applications of genome mappability.PloS one · 2012Article
- Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome.BMC genomics · 2011Article
- The struggle for life of the genome's selfish architects.Biology direct · 2011Review
- Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.Journal of molecular evolution · 2010Article
- The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements.PloS one · 2010Article
- Epigenetic histone modifications of human transposable elements: genome defense versus exaptation.Mobile DNA · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
We evaluated the epigenetic contributions of repetitive DNA elements to human gene regulation. Human proximal promoter sequences show distinct distributions of transposable elements (TEs) and simple sequence repeats (SSRs). TEs are enriched distal from transcriptional start sites (TSSs) and their frequency decreases closer to TSSs, being largely absent from the core promoter region. SSRs, on the other hand, are found at low frequency distal to the TSS and then increase in frequency starting approximately 150 bp upstream of the TSS. The peak of SSR density is centered around the -35 bp position where the basal transcriptional machinery assembles. These trends in repetitive sequence distribution are strongly correlated, positively for TEs and negatively for SSRs, with relative nucleosome binding affinities along the promoters. Nucleosomes bind with highest probability distal from the TSS and the nucleosome binding affinity steadily decreases reaching its nadir just upstream of the TSS at the same point where SSR frequency is at its highest. Promoters that are enriched for TEs are more highly and broadly expressed, on average, than promoters that are devoid of TEs. In addition, promoters that have similar repetitive DNA profiles regulate genes that have more similar expression patterns and encode proteins with more similar functions than promoters that differ with respect to their repetitive DNA. Furthermore, distinct repetitive DNA promoter profiles are correlated with tissue-specific patterns of expression. These observations indicate that repetitive DNA elements mediate chromatin accessibility in proximal promoter regions and the repeat content of promoters is relevant to both gene expression and function.
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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.