Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 4 of 4

Similar Datasets

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.

| S-EPMC7605249 | biostudies-literature

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.

2024-05-22 | GSE213693 | GEO

Evolutionary comparison of CTCF and YY1 binding in primate lymphoblastoid cell lines

Project description:We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver.

2013-11-20 | E-MTAB-1511 | biostudies-arrayexpress

Sequence-based detection and breakpoint assembly of polymorphic inversions.

Project description:Inversion polymorphisms have occupied a privileged place in Drosophila genetic research since their discovery in the 1920s. Indeed, inversions seem to be nearly ubiquitous, and the majority of species that have been thoroughly surveyed have been found to be polymorphic for one or more chromosomal inversions. Despite enduring interest, however, inversions remain difficult to study because their effects are often cryptic, and few efficient assays have been developed. Even in Drosophila melanogaster, in which inversions can be reliably detected and have received considerable attention, the breakpoints of only three inversions have been characterized molecularly. Hence, inversion detection and assay design remain important unsolved problems. Here, we present a method for identification and local de novo assembly of inversion breakpoints using next-generation paired-end reads derived from D. melanogaster isofemale lines. PCR and cytological confirmations demonstrate that our method can reliably assemble inversion breakpoints, providing tools for future research on D. melanogaster inversions as well as a framework for detection and assay design of inversions and other chromosome aberrations in diverse taxa.

| S-EPMC3430529 | biostudies-literature

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

Project description:Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. The human-specific loops are significantly enriched in enhancer-enhancer interactions and the regulated genes show human-specific expression changes in the subplate, a transient zone of the developing brain critical for neural circuit formation and plasticity. Notably, many human-specific sequence changes are located in the human-specific TAD boundaries and loop anchors, which may lead to the formation of new transcription factor binding sites and chromatin structures in human. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of brain development and evolution.

2020-12-15 | GSE163177 | GEO

Discovery of chromosomal inversions in the mosquito Aedes aegypti

Project description:Chromosomal inversions play a fundamental role in evolution and have been shown to be responsible for the epidemiologically important traits in malaria mosquitoes. However, they have never been characterized in the major vector of arboviruses Aedes aegypti because of the poor structure of its polytene chromosomes. In this study, we applied a Hi-C proximity ligation approach to identify chromosomal inversions in 23 recently collected strains of Ae. aegypti from its worldwide distribution, two old laboratory colonies, and Ae. mascarensis.

2024-09-06 | GSE243024 | GEO

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.

2012-12-21 | E-MTAB-2799 | biostudies-arrayexpress

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

2011-10-14 | GSE29629 | GEO

macaque

Project description:Methylome compariation of Tibetan macaque (M. thibetana) and Chinese rhesus macaque (M. mulatta lasiota)

| PRJNA357178 | ENA

Transcription profiling by array of four strains of budding yeast with inversions engineered between TY1 elements against matching controls

Project description:Gene expression changes due to genome region inversions was studied. Four strains of Saccharomyces cerevisiae strains with inversions engineered between TY1 elements were compared to matching controls.

2014-11-05 | E-MTAB-2613 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data