scholarly journals 3DGV: Immersive Exploration of 3D Genome Structures using Virtual Reality

2019 ◽  
Author(s):  
Éric Zhang ◽  
Chrisostomos Drogaris ◽  
Antoine Gédon ◽  
Aaron Sossin ◽  
Rajae Faraj ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Genome Organization ◽  
Spatial Organization ◽  
Genomic Data ◽  
Regulatory Mechanisms ◽  
3D Genome ◽  
Open Platform ◽  
3D Objects ◽  
Link Type ◽  
Genome Viewer

The analysis of 3D genomic data is expected to revolutionize our understanding of genome organization and regulatory mechanisms. Yet, the complex spatial organization of this information can be difficult to interpret with 2D viewers. Virtual Reality (VR) technologies offer an opportunity to rethink our methods to visualize and navigate 3D objects. In this paper, we introduce the Virtual Reality 3D Genome Viewer (3DGV), an open platform to experiment and develop VR solutions to explore 3D genome structures.Availabilityhttp://3dgv.cs.mcgill.ca/

scholarly journals Targeted mutations on 3D hub loci alter spatial interaction environment

2015 ◽  
Author(s):  
Bo Ding ◽  
Lina Zheng ◽  
David Medovoy ◽  
Wei Wang
Keyword(s):  
Genome Organization ◽  
Spatial Organization ◽  
Spatial Interaction ◽  
Genome Structure ◽  
Chromosomal Structure ◽  
Scale Free ◽  
3D Genome ◽  
Coding Regions ◽  
Gene Coding ◽  
Related Genotype

Many disease-related genotype variations (GVs) reside in non-gene coding regions and the mechanisms of their association with diseases are largely unknown. A possible impact of GVs on disease formation is to alter the spatial organization of chromosome. However, the relationship between GVs and 3D genome structure has not been studied at the chromosome scale. The kilobase resolution of chromosomal structures measured by Hi-C have provided an unprecedented opportunity to tackle this problem. Here we proposed a network-based method to capture global properties of the chromosomal structure. We uncovered that genome organization is scale free and the genomic loci interacting with many other loci in space, termed as hubs, are critical for stabilizing local chromosomal structure. Importantly, we found that cancer-specific GVs target hubs to drastically alter the local chromosomal interactions. These analyses revealed the general principles of 3D genome organization and provided a new direction to pinpoint genotype variations in non-coding regions that are critical for disease formation.

scholarly journals Understanding gene regulatory mechanisms based on gene classification

2021 ◽  
Author(s):  
Hao Tian ◽  
Yueying He ◽  
Yue Xue ◽  
Yi Qin Gao
Keyword(s):  
Gene Regulation ◽  
Density Distribution ◽  
Genome Organization ◽  
Housekeeping Genes ◽  
Structural Features ◽  
Regulatory Mechanisms ◽  
3D Genome ◽  
Human Genes ◽  
Cpg Dinucleotide ◽  
Gene Regulatory

The CpG dinucleotide and its methylation play vital roles in gene regulation as well as 3D genome organization. Previous studies have divided genes into several categories based on the CpG intensity around transcription starting sites (TSS) and found that housekeeping genes tend to possess high CpG density while tissue-specific genes are generally characterized by low CpG density. In this study, we investigated how the CpG density distribution of a gene affects its transcription and regulation pattern. Based on the CpG density distribution around TSS, the human genes are clearly divided into different categories. Not only sequence properties, these different clusters exhibited distinctly different structural features, regulatory mechanisms, and correlation patterns between expression level and CpG/TpG density. These results emphasized that the usage of epigenetic marks in gene regulation is partially rooted in the sequence property of genes, such as their CpG density distribution.

scholarly journals Shaping of the 3D genome by the ATPase machine cohesin

2020 ◽  
Vol 52 (12) ◽  
pp. 1891-1897
Author(s):  
Yoori Kim ◽  
Hongtao Yu
Keyword(s):  
Genome Organization ◽  
Spatial Organization ◽  
Atp Hydrolysis ◽  
Molecular Level ◽  
Genome Structure ◽  
Genome Replication ◽  
Biological Processes ◽  
Direct Visualization ◽  
Interphase Chromatin ◽  
3D Genome

AbstractThe spatial organization of the genome is critical for fundamental biological processes, including transcription, genome replication, and segregation. Chromatin is compacted and organized with defined patterns and proper dynamics during the cell cycle. Aided by direct visualization and indirect genome reconstruction tools, recent discoveries have advanced our understanding of how interphase chromatin is dynamically folded at the molecular level. Here, we review the current understanding of interphase genome organization with a focus on the major regulator of genome structure, the cohesin complex. We further discuss how cohesin harnesses the energy of ATP hydrolysis to shape the genome by extruding chromatin loops.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Erythrocytes 3D genome organization in vertebrates

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anastasia Ryzhkova ◽  
Alena Taskina ◽  
Anna Khabarova ◽  
Veniamin Fishman ◽  
Nariman Battulin
Keyword(s):  
Blood Cells ◽  
Genome Organization ◽  
Large Scale ◽  
Chromatin Condensation ◽  
Erythroid Differentiation ◽  
Interaction Patterns ◽  
3D Interaction ◽  
Interphase Chromosome ◽  
3D Genome ◽  
Contact Maps

AbstractGeneration of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.

Exploring genomes with a game engine

2014 ◽  
Vol 169 ◽  
pp. 443-453 ◽  
Author(s):  
Jeremiah J. Shepherd ◽  
Lingxi Zhou ◽  
William Arndt ◽  
Yan Zhang ◽  
W. Jim Zheng ◽  
...  
Keyword(s):  
Real Time ◽  
Video Game ◽  
Linear Structure ◽  
Structural Data ◽  
Game Engine ◽  
3D Genome ◽  
Genome Viewer ◽  
A Genome ◽  
Visualization Techniques ◽  
Insight Into

More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation–function relationships of a genome.

The 3D Genome Structure of Single Cells

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tianming Zhou ◽  
Ruochi Zhang ◽  
Jian Ma
Keyword(s):  
Single Cell ◽  
Data Science ◽  
Spatial Organization ◽  
Method Development ◽  
Single Cells ◽  
Genome Structure ◽  
Computational Method ◽  
Publication Date ◽  
3D Genome ◽  
Genome Features

The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Mental States of a Personality in a Didactic VR Environment

2021 ◽  
Author(s):  
V.V. Selivanov
Keyword(s):  
Virtual Reality ◽  
Empirical Research ◽  
Well Being ◽  
Mental States ◽  
Fundamental Importance ◽  
Short Term ◽  
Independent Variables ◽  
3D Objects

The work is aimed at examining the influence of modern didactic programs in virtual reality (VR) on mental states in adolescence. The materials of empirical research obtained on a sample of 3—4 year students from Moscow and Smolensk universities are presented. Study 1 (N = 50) involved respondents aged 19 to 26 years. We used the methodology of AS Kulikov L.V., didactic VR programs were used as instructive independent variables. The results obtained indicate that the didactic VR environment of the highest level has a significant effect on mental states, increasing indicators on the scales of activation, excitement, tone, euphoria, and reducing asthenia. Conditions such as well-being, normal mood, calmness remain stable in immersive didactic VR. The effectiveness of VR programs in influencing mental states is determined by the successful modeling of 3D objects, high animation, interactivity, originally incorporated into the content of VR of the highest level. The data on an increase in the experience of the degree of presence in VR when using new helmets, even in short VR programs, are of fundamental importance. This indicates the possibility of the formation of addictions to VR with their repeated, short-term use.

Sign in / Sign up

Export Citation Format

Share Document