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Single-cell strand sequencing of a macaque genome reveals nested inversions and breakpoint reuse during primate evolution

ABSTRACT: Identification of human-rhesus macaque inversions using Strand-seq and characterization of chromatin architecture with Hi-C in lymphoblastoid cell lines.

PROVIDER: PRJEB37908 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4501103_1.fastq.gz	Fastqsanger.gz
	ERR4501103_2.fastq.gz	Fastqsanger.gz
	ERR4501104_1.fastq.gz	Fastqsanger.gz
	ERR4501104_2.fastq.gz	Fastqsanger.gz

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Comparative 3D genomic architectures elucidate the function of the adaptive human-specific inversions in human brain evolution

Project description:Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. Based on a comprehensive SV atlas in rhesus macaque populations, we found that inversions are selectively constrained from the perspective of 3D genome, those inducing dramatic changes in chromosomal conformation tends to be purged by the action of purifying selection, implying the inconspicuous adaptive roles of inversions associated with strong effects. Furthermore, by integrating comparative genomics and multi-omics data across human and rhesus macaque, such as gene structures, regulatory elements and 3D genomic organizations, we highlighted a category of human-specific inversions with strong effects and found that they had undergone rapid fixation and caused significant changes in gene expression in human brain development, which may represent a driving force in human brain evolution. Overall, our findings reveal the great value of comparative 3D Hi-C maps in elucidating the adaptive functions of structural variants.

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Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.

Project description:Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.

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Strand-specific RNA-seq of nine rhesus macaque tissues

Project description:This experiment is contains rhesus macaque organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from three different animals as biological replicates. This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.

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Transcriptome sequencing of two macaques, crab-eating macaque and Indian rhesus macaque

Project description:Deep sequencing of mRNA from two macaques, crab-eating macaque and Indian rhesus macaque

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Project description:The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. Keywords: cross hybridization

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Comparison of proteome alternations during aging in temporal lobe from human and rhesus macaque

Project description:Aging of population is a great challenge of healthcare. In china, the number of the elderly is rapidly growing, and it was estimated that there will be approximately 400 million citizens above 65 years old in 2050.Study on the changes of brain during aging may help elucidate the mechanism of the pathological process, and hence prevent or treat these neurological diseases.Rhesus macaque (Macaca mulatta) and human have a genetic homology of 95%, and their anatomy structures or physiological process are highly similar, which make rhesus macaque one of the most important nonhuman primate models.Thus, the comparison between the change of protein profile during aging in human and rhesus macaque is still necessary, and the characteristics of proteins that are conservative or divergent are of interest.The aim of the(our) study is to identify the conservative changes of pathways during aging, and to reveal the potential difference between human and rhesus macaque so that relevant studies based on primate models can be interpreted more accurately.

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Rhesus macaque rhadinovirus (RRV) gene expression in vivo

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Rhesus macaque aCGH

2011-05-11 | GSE19881 | GEO

Rhesus macaque aCGH

Project description:Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations. a custom designed Agilent array-based comparative genomic hybridization (aCGH) platform, which comprises 950,843 unique 60-mer oligonucleotide probes specific to the rhesus macaque reference genome (rheMac2), to compare the genomic DNAs of 17 unrelated rhesus macaques of Indian origin to the genome of an unrelated sample from the same species.

2011-05-11 | E-GEOD-19881 | biostudies-arrayexpress

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