ArticleBMC genomics2010
Effects of Alu elements on global nucleosome positioning in the human genome.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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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Who cites it
33 citing papers in PubMed, 55 citations in OpenAlex.
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Repeatome Analysis of Plasma Circulating DNA in Patients with Cardiovascular Disease: Variation with Cell-Free DNA Integrity/Length and Clinical Parameters.International journal of molecular sciences · 2025Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler.Nucleic acids research · 2024Article
- Article
- A study of strong nucleosomes in the human genome.iScience · 2022Article
- The 'Alu-ome' shapes the epigenetic environment of regulatory elements controlling cellular defense.Nucleic acids research · 2022Article
- Review
- Nucleosome-induced homology recognition in chromatin.Journal of the Royal Society, Interface · 2021Article
- ALU non-B-DNA conformations, flipons, binary codes and evolution.Royal Society open science · 2020Review
- Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat.GigaScience · 2020Article
- Transposable elements teach T cells new tricks.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- RNA-guided retargeting of SeLife · 2020Article
- TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation.Molecular cell · 2020Article
- The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes.Nucleic acids research · 2019Article
- RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.Nucleic acids research · 2018Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer.Cell reports · 2016Article
- Retroviral integration: Site matters: Mechanisms and consequences of retroviral integration site selection.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Review
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 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUnderstanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes.
resultsWith Fourier analysis, we found that this is not the case: 84-bp and 167-bp periodicities are prevalent in primates. The 167-bp periodicity is intriguing because it is almost equal to the sum of the lengths of a nucleosomal unit and its linker region. After masking Alu elements, these periodicities were greatly diminished. Next, using two independent large-scale sets of nucleosome mapping data, we analyzed the distribution of nucleosomes in the vicinity of Alu elements and showed that (1) there are one or two fixed slot(s) for nucleosome positioning within the Alu element and (2) the positioning of neighboring nucleosomes seems to be in phase, more or less, with the presence of Alu elements. Furthermore, (3) these effects of Alu elements on nucleosome positioning are consistent with inactivation of promoter activity in Alu elements.
conclusionsOur discoveries suggest that the principle governing nucleosome positioning differs greatly across species and that the Alu family is an important factor in primate genomes.
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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.