Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements may guide genomic stability which will give rise to CNVs either by non-allelic homologous recombination (NAHR) or non-homologous end joining (NHEJ). Here, we present a short guide based on previously documented cases of disease-associated CNVs in order to provide a general view on the impact of repeated elements on the stability of the genomic sequence and consequently in the origin of the human pathogenic variome.
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http://dx.doi.org/10.1186/s40246-016-0088-9 | DOI Listing |
Commun Biol
January 2025
Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA.
Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal's genome.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
Background: Classical genome-wide association studies (GWAS) of Alzheimer's disease (AD), which successfully identified over 75 risk loci to date, are limited to the content of the imputation panels that typically do not cover all types of genetic variation, e.g., tandem repeats encompassing >55% of human genome.
View Article and Find Full Text PDFGenome Biol
January 2025
State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China.
We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately labeled chromatin loop anchor interactions and associated gene transcription during myogenic differentiation.
View Article and Find Full Text PDFNat Commun
January 2025
Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
The human genome is composed of distinct genomic regions that are susceptible to various types of somatic mutations. Among these, Short Tandem Repeats (STRs) stand out as the most mutable genetic elements. STRs are short repetitive polymorphic sequences, predominantly situated within noncoding sectors of the genome.
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