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ABSTRACT:
PROVIDER: PRJNA323503 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional fates of human-specific segmental duplications
| PRJNA475610 | ENA
Project description:While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.
2013-08-10 | GSE45741 | GEO
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome.
2010-12-31 | GSE19932 | GEO
Project description:While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition. Agilent arrays were custom designed for probes to be relatively evenly spaced across the reference genomes of chimpanzee, orang-utan, and rhesus macaque. For each species 9 one million probe arrays were used to cover the autosomes and a single 400k probe array was used for the sex chromosomes.
2013-08-10 | E-GEOD-45741 | biostudies-arrayexpress
Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.
2011-08-03 | GSE30559 | GEO
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. aCGH control vs. patient, total of 7 patients Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.
2010-12-31 | E-GEOD-19932 | biostudies-arrayexpress
Project description:This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf. Using computational approaches all segmental duplications were identified in the canFam2 genome of the dog. A custom aCGH chip was then built that densely interrogated these segmental duplications for CNVs in a panel of diverse dog breeds and a single wolf.
2010-05-17 | E-GEOD-13266 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13884: INTER_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor GSE13885: INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor Refer to individual Series
2009-03-05 | E-GEOD-13934 | biostudies-arrayexpress
Project description:Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. We generated approximately 10-fold genomic sequence coverage from a western lowland gorilla and integrated these data into a physical and cytogenetic framework to develop a comprehensive view of structural variation. We discovered and validated over 7,665 structural changes within the gorilla lineage including sequence resolution of inversions, deletions, duplications and retrotranspositions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet parallel patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human. all combinations of human, chimpanzee and gorilla are used in 2 different arrayCGH designs. First, a standard 2.1 was used to detected CNVs, and second, we used a custom designed arrayCGH to validate gorilla specific duplications and deletions
2011-05-01 | E-GEOD-27072 | biostudies-arrayexpress
Project description:Gene duplication and deletion are pivotal processes shaping the structural and functional repertoire of genomes, with implications for disease, adaptation and evolution. We employed an experimental evolution framework partnered with high-throughput genomics to assess the molecular and transcriptional characteristics of novel gene copy-number variants (CNVs) in Caenorhabditis elegans populations subjected to varying intensity of selection. Here, we report a direct spontaneous genome-wide rate of gene duplication of 2.9 × 10-5 /gene/generation in C. elegans, the highest for any species to date. The increase in average transcript abundance of new duplicates arising under minimal selection is significantly greater than two-fold compared to single-copies of the same gene, suggesting that genes in segmental duplications are frequently overactive at inception. The average increase in transcriptional activity of gene duplicates is greater in MA lines that passed through single individual bottlenecks than in MA lines with larger population bottlenecks. Furthermore, there is an inverse relationship between the ancestral transcription levels of newly originating gene duplicates and population size, with duplicate copies of highly expressed genes less likely to accumulate in larger populations. The results demonstrate that there is a fitness cost of superfluous gene expression and purifying selection against new gene duplicates. However, on average, duplications also provide a significant increase in gene expression that can facilitate adaptation to novel environmental challenges.
2018-04-07 | GSE112821 | GEO