ArticlePLoS computational biology2009
Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content.BMC biology · 2021Pooled it
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- Formation of Circular RNAs.Advances in experimental medicine and biology · 2025Review
- Mouse and human embryonic genome activation initiate at the one-cell stage.Frontiers in cell and developmental biology · 2025Article
- Impact of Gold Nanoparticles and Ionizing Radiation on Whole Chromatin Organization as Detected by Single-Molecule Localization Microscopy.International journal of molecular sciences · 2024Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Epigenetic Gene-Regulatory Loci in Alu Elements Associated with Autism Susceptibility in the Prefrontal Cortex of ASD.International journal of molecular sciences · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.Nature communications · 2022Article
- Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression.Cell reports · 2022Article
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- B1 repetitive sequence methylation enhances wound healing of second-degree burns in rats.Biomedical reports · 2022Article
- Identification and functional characterization of the German cockroach, Blattella germanica, short interspersed nuclear elements.PloS one · 2022Article
- Alu RNA Structural Features Modulate Immune Cell Activation and A-to-I Editing of Alu RNAs Is Diminished in Human Inflammatory Bowel Disease.Frontiers in immunology · 2022Article
- Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome.Cell research · 2021Article
- ADAR1 Stimulation by IFN-α Downregulates the Expression of MAVS via RNA Editing to Regulate the Anti-HBV Response.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae.Molecular biology and evolution · 2020Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Alu and B1 repeats are mobile elements that originated in an initial duplication of the 7SL RNA gene prior to the primate-rodent split about 80 million years ago and currently account for a substantial fraction of the human and mouse genome, respectively. Following the primate-rodent split, Alu and B1 elements spread independently in each of the two genomes in a seemingly random manner, and, according to the prevailing hypothesis, negative selection shaped their final distribution in each genome by forcing the selective loss of certain Alu and B1 copies. In this paper, contrary to the prevailing hypothesis, we present evidence that Alu and B1 elements have been selectively retained in the upstream and intronic regions of genes belonging to specific functional classes. At the same time, we found no evidence for selective loss of these elements in any functional class. A subset of the functional links we discovered corresponds to functions where Alu involvement has actually been experimentally validated, whereas the majority of the functional links we report are novel. Finally, the unexpected finding that Alu and B1 elements show similar biases in their distribution across functional classes, despite having spread independently in their respective genomes, further supports our claim that the extant instances of Alu and B1 elements are the result of positive selection.
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