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Series GSE167579 Query DataSets for GSE167579
Status Public on Apr 12, 2022
Title Comparative 3D Genome Architecture in Vertebrates (Hi-C)
Organisms Danio rerio; Gallus gallus; Macaca mulatta; Homo sapiens; Canis lupus familiaris; Felis catus; Bos taurus; Ovis aries; Oryctolagus cuniculus; Mus musculus; Rattus norvegicus
Experiment type Other
Summary Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.
Overall design To comprehensively explore the evolutionary principles governing 3D genome architecture and to assess the contributions of genome architecture to transcriptional regulation across species, we performed comparative analyses of high-throughput chromosome conformation capture (Hi-C) in fibroblast cells of 12 vertebrates, including two representative mammalian lineages: euarchontoglires including humans, rhesus macaques, mice, rats, and rabbits; boreoeutheria including dogs, cats, pigs, sheep, and cows; as well as two non-mammals including birds (chickens) and fish (zebrafish). We performed the Hi-C experiments in 25 fibroblasts from 11 vertebrates with 1 to 5 biological replicates (distinct cell lines or primary cells derived from different individuals) for each species, produced a total of ~ 5.75-billion uniquely aligned contacts with an average depth of ~230 million (M) contacts per library (range from ~102 M for zebrafish with a relatively small genome size of ~ 1.23 Gb to ~442 M for mouse with a genome size of ~2.73 Gb). We also combined the resulting datasets with those previously generated by us for four pig fibroblasts (pig_DB-2, pig_DB-3, pig_RC-7, and pig_RC-8) (X Tian et al.,2020) and two mouse fibroblasts (mouse_3T6 and mouse_MEF) (M He et al.,2018) using the same experimental protocol. Among these, ~ 63.03% are intra-chromosomal contacts, of which ~74.40% were occurred within 10 Mb. After KR-normalization and quantile-normalization, we generated 31 intra-chromosomal contact maps at 20-kb resolution for each of 31 libraries. With the bin size at 20-kb, there are about 83.12% of bins have at least 1,000 intra-chromosomal contacts. TAD and compartment A/B were also identified by using the 20-kb matrix.
Contributor(s) Li D, He M, Tang Q, Tian S
Citation(s) 35524220
Submission date Feb 25, 2021
Last update date Jul 18, 2022
Contact name Mengnan He
Phone 15283521733
Organization name Sichuan Agriculture University
Street address Huimin road 211#
City Chengdu
ZIP/Postal code 611130
Country China
Platforms (11)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
GPL23085 HiSeq X Ten (Danio rerio)
Samples (25)
GSM5110924 Hi-C data of Cow replicate 1
GSM5110925 Hi-C data of Cow replicate 2
GSM5110926 Hi-C data of Sheep replicate 1
This SubSeries is part of SuperSeries:
GSE167581 Comparative 3D Genome Architecture in Vertebrates
BioProject PRJNA704984
SRA SRP308268

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE167579.hdf5 4.0 Gb (ftp)(http) HDF5
GSE167579_1.hdf5 3.0 Gb (ftp)(http) HDF5
GSE167579_2.hdf5 5.3 Gb (ftp)(http) HDF5
GSE167579_3.hdf5 5.4 Gb (ftp)(http) HDF5
GSE167579_3T6.ABindex.xls.gz 1.5 Mb (ftp)(http) XLS
GSE167579_4.hdf5 5.1 Gb (ftp)(http) HDF5
GSE167579_5.hdf5 5.1 Gb (ftp)(http) HDF5
GSE167579_DB-2.ABindex.xls.gz 1.4 Mb (ftp)(http) XLS
GSE167579_DB-3.ABindex.xls.gz 1.4 Mb (ftp)(http) XLS
GSE167579_MEF.ABindex.xls.gz 1.5 Mb (ftp)(http) XLS
GSE167579_Mouse.3T6.DI.tad.bed.gz 12.6 Kb (ftp)(http) BED
GSE167579_Mouse.MEF.DI.tad.bed.gz 11.7 Kb (ftp)(http) BED
GSE167579_Pig.DB-2.DI.tad.bed.gz 12.3 Kb (ftp)(http) BED
GSE167579_Pig.DB-3.DI.tad.bed.gz 12.1 Kb (ftp)(http) BED
GSE167579_Pig.RC-7.DI.tad.bed.gz 12.7 Kb (ftp)(http) BED
GSE167579_Pig.RC-8.DI.tad.bed.gz 12.3 Kb (ftp)(http) BED
GSE167579_RAW.tar 89.0 Gb (http)(custom) TAR (of BED, HDF5, XLS)
GSE167579_RC-7.ABindex.xls.gz 1.4 Mb (ftp)(http) XLS
GSE167579_RC-8.ABindex.xls.gz 1.4 Mb (ftp)(http) XLS
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Raw data are available in SRA
Processed data provided as supplementary file

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