ChromOS services online access to the data resources from Chromosome Orchestration System (OS) , a research project supported by MEXT Japan.
Chromosomes play a fundamental role in many biological processes. Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription, replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time. The main goal of this project is to describe the mechanisms that regulate the functional unity of the chromosomes (chromosome OS) by thoroughly examining the structural relationship between, and the hierarchy of, individual chromosomal functions.
|Accession||Cell||Organism||Restriction enzyme||Condition||Run ID|
|OLP-2-620||RPE||human||MboI||ESCO1, 2 KD (siRNA transfection 48 h), No Sync||1809JNHX-0004_si11-19_res|
|OLP-2-614||RPE||human||MboI||RAD21 KD (siRNA transfection 72 h), No Sync||1809JNHX-0003_si621_res|
|OLP-2-628||RPE||human||MboI||PDS5B KD (siRNA transfection 48 h), No Sync||HN00102383_si91_res|
|OLP-2-621||RPE||human||MboI||MAU2 KD (siRNA transfection 72 h), No Sync||1809JNHX-0004_si251_res|
|OLP-2-613||RPE||human||MboI||RAD21 KD (siRNA transfection 72 h), No Sync||1809JNHX-0003_si7-621_res|
|OLP-2-623||RPE||human||MboI||CTCF KD (siRNA transfection 72 h), No Sync||1811KHX-0110_R_626_628_d3_res|
|OLP-2-624||RPE||human||MboI||WAPL KD (siRNA transfection 48 h), No Sync||HN00102380_si31_res|
|OLP-2-625||RPE||human||MboI||PDS5A KD (siRNA transfection 72 h), No Sync||HN00102380_si88_d3_res|
|OLP-2-619||RPE||human||MboI||ESCO1 KD (siRNA transfection 48 h), No Sync||1809JNHX-0004_si11_res|
|OLP-2-626||RPE||human||MboI||JQ1 (BRD Inhibitor), No Sync||HN00102383_JQ1_plus_res|
|OLP-2-615||RPE||human||MboI||Control, No Sync||1807JNHX-0018_Ctrl_res|
|OLP-2-627||RPE||human||MboI||PDS5A,B KD (siRNA transfection 48 h), No Sync||HN00102383_si88_91_res|
|OLP-2-616||RPE||human||MboI||Control, No Sync||1809JNHX-0003_Ctrl_res|
|OLP-2-618||RPE||human||MboI||CTCF KD (siRNA transfection 72 h), No Sync||1811KHX-0109_FT_WT_res|
|OLP-2-617||RPE||human||MboI||CTCF KD (siRNA transfection 72 h), No Sync||1809JNHX-0003_si628_res|
|OLP-2-622||RPE||human||MboI||Control, No Sync||1811KHX-0109_R_Ctrl_res|
|OLP-2-629||LCL||human||MboI||WT, No Sync||1904JNHX-0009_GIA_res|
|OLP-2-630||LCL||human||MboI||HP1beta mutation, No Sync||1904JNHX-0009_RIM_res|
|OLP-2-631||HCT116/Rad21-mAD/TIR1||human||MboI||NIPBL, exon3 frame-shift, No Sync||1903JNHX-0034_B3_res|
|OLP-2-633||HCT116/ESCO1-mAD/TIR1||human||MboI||Dox 12 h -> IAA 3 h (ESCO1 depletion), No Sync||1907JNHX-0026_E1_dox_iaa_res|
|OLP-2-632||HCT116/ESCO1-mAD/TIR1||human||MboI||Dox 16 h -> (control), No Sync||1908JNHX-0025_E1_dox_res|
|OLP-2-634||HCT116||human||MboI||NIPBL, exon 3 single allele mutation, No sync||1807JNHX-0018_HCT_3-3_res|
|OLP-2-635||HCT116||human||MboI||Wild Type, No Sync||1807JNHX-0018_HCT_Wt_res|
|OLP-2-641||fibroblast||human||MboI||WT, female, No Sync||1807JNHX-0018_GM2036_res|
|OLP-2-640||fibroblast||human||MboI||WT, female, No Sync||1904JNHX-0009_2036_res|
|OLP-2-639||fibroblast||human||MboI||CdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync||1807JNHX-0018_CdLS304_res|
|OLP-2-636||fibroblast||human||MboI||CdLS, NIPBL: 1372C>T;Q458X / Nonsense, female, No Sync||1807JNHX-0018_CdLS510_res|
|OLP-2-642||fibroblast||human||MboI||WT, male, No Sync||1807JNHX-0018_GM3348_res|
|OLP-2-638||fibroblast||human||MboI||CdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync||1807JNHX-0018_CdLS087_res|
|OLP-2-637||fibroblast||human||MboI||WT, male, No Sync||1807JNHX-0018_CdLS006_res|
|OLP-2-643||Blood Cell Stem Cell||mouse||MboI||STAG2 conditional KO||1811KHX-0110_KO_561_res|
|OLP-2-646||Blood Cell Stem Cell||mouse||MboI||STAG2 conditional KO||1811KHX-0110_KO_544_res|
|OLP-2-645||Blood Cell Stem Cell||mouse||MboI||WT||1811KHX-0110_WT_546_res|
|OLP-2-644||Blood Cell Stem Cell||mouse||MboI||WT||1811KHX-0110_WT_563_res|
|OLP-2-654||293FT||human||MboI||WT, No Sync||1905JNHX-0006_FT_res|
|OLP-2-648||293FT||human||MboI||lentiviral vector Infection, Control, No Sync||1903JNHX-0034_FT-vi24_res|
|OLP-2-649||293FT||human||MboI||lentiviral vector Infection, Control, No Sync||1903JNHX-0035_FT-Wt_res|
|OLP-2-651||293FT||human||MboI||lentiviral vector Infection, Control, No Sync||1908JNHX-0026_vi24_res|
|OLP-2-652||293FT||human||MboI||Wild AFF4 lentiviral vector Infection, No Sync||1908JNHX-0026_vi27_res|
|OLP-2-647||293FT||human||MboI||Mutant AFF4 lentiviral vector Infection, No Sync||1903JNHX-0035_FT-vi28_res|
|OLP-2-653||293FT||human||MboI||Mutant AFF4 lentiviral vector Infection, No Sync||1908JNHX-0026_vi28_res|
|OLP-2-650||293FT||human||MboI||NIPBL, exon 3 bi-allele mutation, No Sync||1811KHX-0109_FT_ND1_res|
OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays. Simultaneously, OLP provides a platform that supports opening and sharing the data.
Three-dimensional nuclear organization in Arabidopsis thaliana.
Pontvianne F, Grob S (J Plant Res. 2020 Jul;133(4):479-488)
In recent years, the study of plant three-dimensional nuclear architecture received increasing attention. Enabled by technological advances, our knowledge on nuclear architecture has greatly increased and we can now access large data sets describing its manifold aspects. The principles of nuclear organization in plants do not significantly differ from those in animals. Plant nuclear organization comprises various scales, ranging from gene loops to topologically associating domains to nuclear compartmentalization. However, whether plant three-dimensional chromosomal features also exert similar functions as in animals is less clear. This review discusses recent advances in the fields of three-dimensional chromosome folding and nuclear compartmentalization and describes a novel silencing mechanism, which is closely linked to nuclear architecture....
Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome.
Li Y, Gao G, Lin Y, Hu S, Luo Y, Wang G, Jin L, Wang Q, Wang J, Tang Q, Li M (Gigascience. 2020 Oct 24;9(10):)
BACKGROUND: The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing....
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.
Liu L, Hyeon C (Nucleic Acids Res. 2020 Oct 23;:)
The accessibility of target gene, a factor critical for gene regulation, is controlled by epigenetic fine-tuning of chromatin organization. While there are multiple experimental techniques to study change of chromatin architecture with its epigenetic state, measurements from them are not always complementary. A qualitative discrepancy is noted between recent super-resolution imaging studies, particularly on Polycomb-group protein repressed domains in Drosophila cell. One of the studies shows that Polycomb-repressed domains are more compact than inactive domains and are segregated from neighboring active domains, whereas Hi-C and chromatin accessibility assay as well as the other super-resolution imaging studies paint a different picture. To examine this issue in detail, we analyzed Hi-C libraries of Drosophila chromosomes as well as distance constraints from one of the imaging studies, and modeled different epigenetic domains by employing a polymer-based approach. According to our chromosome models, both Polycomb-repressed and inactive domains are featured with a similar degree of intra-domain packaging and significant intermixing with adjacent active domains. The epigenetic domain......
High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome.
Bevan S, Schoenfelder S, Young RJ, Zhang L, Andrews S, Fraser P, O'Callaghan PM (Biotechnol Bioeng. 2020 Oct 23;:)
Chinese hamster ovary (CHO) cell lines are the pillars of a multi-billion dollar biopharmaceutical industry producing recombinant therapeutic proteins. The effects of local chromatin organisation and epigenetic repression within these cell lines result in unpredictable and unstable transgene expression following random integration. Limited knowledge of the CHO genome and its higher-order chromatin organisation has thus far impeded functional genomics approaches required to tackle these issues. Here, we present an integrative three-dimensional (3D) map of genome organisation within the CHOK1SV® 10E9 cell line in conjunction with an improved, less fragmented CHOK1SV® 10E9 genome assembly. Using our high-resolution chromatin conformation datasets, we have assigned ≈ 90% of sequence to a chromosome-scale genome assembly. Our genome-wide 3D map identifies higher-order chromatin structures such as topologically associated domains, incorporates our chromatin accessibility data to enhance the identification of active cis-regulatory elements and importantly links these cis-regulatory elements to target promoters in a 3D promoter interactome. We demonstrate the power of our improved func......
ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures.
Ye T, Ma W (Nucleic Acids Res. 2020 Oct 19;:)
The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin orga......