ArticleGenome research2010
The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed, 51 citations in OpenAlex.
- Transposable Elements Are Dynamically Regulated in Medium Spiny Neurons and May Contribute to the Molecular and Behavioral Adaptations to Cocaine.Biological psychiatry · 2026Article
- Transposable elements in mammalian chromatin organization.Nature reviews. Genetics · 2023Review
- Article
- Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality.Life (Basel, Switzerland) · 2022Article
- Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.Molecular biology and evolution · 2020Article
- Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.Genome biology · 2019Article
- Evolution and diversity of transposable elements in fish genomes.Scientific reports · 2019Article
- The role of 3D genome organization in disease: From compartments to single nucleotides.Seminars in cell & developmental biology · 2019Review
- Ten things you should know about transposable elements.Genome biology · 2018Review
- Mammalian transposable elements and their impacts on genome evolution.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- A high throughput screen for active human transposable elements.BMC genomics · 2018Article
- Article
- Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals.Genome biology and evolution · 2017Article
- Regulatory activities of transposable elements: from conflicts to benefits.Nature reviews. Genetics · 2017Review
- The transposable element environment of human genes is associated with histone and expression changes in cancer.BMC genomics · 2016Article
- Article
- Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.PLoS computational biology · 2016Article
- Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.Genome biology and evolution · 2015Article
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Genomic landscape of human, bat, and ex vivo DNA transposon integrations.Molecular biology and evolution · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the sex chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1 element density, respectively. Second, we analyze sex chromosome versus autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu and L1 distributions not only persists after accounting for these effects, but even presents differences in patterns, confirming preferential Alu integration in the male germline, yet likely integration of L1s in both male and female germlines or in early embryogenesis. Additionally, our models reveal that local base composition (measured by GC content and density of L1 target sites) and natural selection (inferred via density of most conserved elements) are significant to predicting densities of L1s. Interestingly, measurements of local double-stranded breaks (a 13-mer associated with genome instability) strongly correlate with densities of Alu elements; little evidence was found for the role of recombination-driven deletion in driving TE distributions over evolutionary time. Thus, Alu and L1 densities have been influenced by the combination of distinct local genome landscapes and the unique evolutionary dynamics of sex chromosomes.
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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.