scholarly journals HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

2016 ◽  
Author(s):  
Maxwell R. Mumbach ◽  
Adam J. Rubin ◽  
Ryan A. Flynn ◽  
Chao Dai ◽  
Paul A. Khavari ◽  
...  
Keyword(s):  
Biomedical Applications ◽  
Genome Structure ◽  
Genome Architecture ◽  
Gene Control ◽  
Chromatin Conformation ◽  
Sensitive Analysis ◽  
3D Genome ◽  
Multi Scale ◽  
3D Genome Structure

AbstractGenome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers input requirement over 100-fold relative to ChIA-PET. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to background than in situ Hi-C. Thus, HiChIP adds to the toolbox of 3D genome structure and regulation for diverse biomedical applications.

Hi-CO: 3D genome structure analysis with nucleosome resolution

2021 ◽  
Author(s):  
Masae Ohno ◽  
Tadashi Ando ◽  
David G. Priest ◽  
Yuichi Taniguchi
Keyword(s):  
Structure Analysis ◽  
Genome Structure ◽  
3D Genome ◽  
3D Genome Structure

scholarly journals Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

PLoS Genetics ◽  
2018 ◽  
Vol 14 (10) ◽  
pp. e1007467 ◽  
Author(s):  
David J. Winter ◽  
Austen R. D. Ganley ◽  
Carolyn A. Young ◽  
Ivan Liachko ◽  
Christopher L. Schardl ◽  
...  
Keyword(s):  
Filamentous Fungus ◽  
Genome Structure ◽  
Repeat Elements ◽  
3D Genome ◽  
Epichloë Festucae ◽  
3D Genome Structure

scholarly journals TADBD: a sensitive and fast method for detection of typologically associated domain boundaries

BioTechniques ◽  
2020 ◽  
Vol 69 (1) ◽  
pp. 18-25
Author(s):  
Hongqiang Lyu ◽  
Lin Li ◽  
Zhifang Wu ◽  
Tian Wang ◽  
Jiguang Zheng ◽  
...  
Keyword(s):  
R Package ◽  
Computational Method ◽  
Genome Architecture ◽  
Fast Method ◽  
3D Genome ◽  
Multi Scale ◽  
Comparison Results ◽  
Contact Matrix ◽  
Domain Boundaries ◽  
Template Size

A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. This method implements a Haar-based algorithm by considering Haar diagonal template, acceleration via a compact integrogram, multi-scale aggregation at template size and statistical filtering. In most cases, comparison results from simulated and experimental data show that TADBD outperforms the other five methods. In addition, a new R package for TADBD is freely available online.

scholarly journals Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection

Acta Naturae ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 34-46
Author(s):  
S. V. Razin ◽  
A. A. Gavrilov ◽  
O. V. Iarovaia
Keyword(s):  
Viral Infection ◽  
Cell Nucleus ◽  
Genome Structure ◽  
Antiviral Defense ◽  
3D Genome ◽  
Nuclear Compartments ◽  
Defense Systems ◽  
3D Genome Structure ◽  
Cellular Genome

The review addresses the question of how the structural and functional compartmentalization of the cell nucleus and the 3D organization of the cellular genome are modified during the infection of cells with various viruses. Particular attention is paid to the role of the introduced changes in the implementation of the viral strategy to evade the antiviral defense systems and provide conditions for viral replication. The discussion focuses on viruses replicating in the cell nucleus. Cytoplasmic viruses are mentioned in cases when a significant reorganization of the nuclear compartments or the 3D genome structure occurs during an infection with these viruses.

scholarly journals Exploring the Effects of Genetic Variation on Gene Regulation in Cancer in the Context of 3D Genome Structure

2021 ◽  
Author(s):  
Noha Osman ◽  
Abd-El-Monsif Shawky ◽  
Michal Brylinski
Keyword(s):  
High Risk ◽  
Genetic Variants ◽  
Large Scale ◽  
Target Genes ◽  
Genome Structure ◽  
Regulatory Elements ◽  
3D Genome ◽  
Risk Snps ◽  
Prostate Cancers ◽  
3D Genome Structure

Abstract Background: Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging.Results: In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants.Conclusions: Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.

scholarly journals Constricted migration is associated with stable 3D genome structure differences in melanoma cells

2019 ◽  
Author(s):  
Rosela Golloshi ◽  
Trevor F. Freeman ◽  
Priyojit Das ◽  
Thomas Isaac Raines ◽  
Rebeca San Martin ◽  
...  
Keyword(s):  
Chromosome Structure ◽  
Metastatic Cancer ◽  
Genome Structure ◽  
Collagen Matrix ◽  
Phenotypic Differences ◽  
3D Genome ◽  
Expression Of Genes ◽  
Structure Changes ◽  
3D Genome Structure ◽  
Nuclear Deformations

AbstractTo spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation and DNA repair, here we investigate how confined migration affects or is affected by 3D genome structure. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Using Hi-C, we observe differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. These sequentially constricted cells also show more nuclear deformations and altered behavior in a 3D collagen matrix. Our observations reveal a relationship between chromosome structure changes, metastatic gene signatures, and the altered nuclear appearance of aggressive melanoma.

scholarly journals Experience-independent transformation of single-cell 3D genome structure and transcriptome during postnatal development of the mammalian brain

2020 ◽  
Author(s):  
Longzhi Tan ◽  
Wenping Ma ◽  
Honggui Wu ◽  
Yinghui Zheng ◽  
Dong Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Genome Structure ◽  
Sensory Experience ◽  
Mammalian Genome ◽  
Brain Cells ◽  
List Type ◽  
3D Genome ◽  
Allele Specific ◽  
3D Genome Structure

SUMMARYBoth transcription and 3D organization of the mammalian genome play critical roles in neurodevelopment and its disorders. However, 3D genome structures of single brain cells have not been solved; little is known about the dynamics of single-cell transcriptome and 3D genome after birth. Here we generate a transcriptome atlas of 3,517 cells and a 3D genome atlas of 3,646 cells from the developing mouse cortex and hippocampus, using our high-resolution MALBAC-DT and Dip-C methods. In adults, 3D genome “structure types” delineate all major cell types, with high correlation between A/B compartments and gene expression. During development, both transcriptome and 3D genome are extensively transformed in the first postnatal month. In neurons, 3D genome is rewired across multiple scales, correlated with gene expression modules and independent of sensory experience. Finally, we examine allele-specific structure of imprinted genes, revealing local and chromosome-wide differences. These findings uncover a previously unknown dimension of neurodevelopment.HIGHLIGHTSTranscriptomes and 3D genome structures of single brain cells (both neurons and glia) in the developing mouse forebrainCell type identity encoded in the 3D wiring of the mammalian genome (“structure types”)Major transformation of both transcriptome and 3D genome during the first month of life, independent of sensory experienceAllele-specific 3D structure at 7 imprinted gene loci, including one that spans a whole chromosome

scholarly journals Radiation-induced DNA damage and repair effects on 3D genome organization

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jacob T. Sanders ◽  
Trevor F. Freeman ◽  
Yang Xu ◽  
Rosela Golloshi ◽  
Mary A. Stallard ◽  
...  
Keyword(s):  
Dna Damage ◽  
Gene Expression Regulation ◽  
Genome Structure ◽  
Cell Types ◽  
Dimensional Structure ◽  
X Rays ◽  
3D Genome ◽  
Radiation Induced ◽  
The Impact ◽  
3D Genome Structure

AbstractThe three-dimensional structure of chromosomes plays an important role in gene expression regulation and also influences the repair of radiation-induced DNA damage. Genomic aberrations that disrupt chromosome spatial domains can lead to diseases including cancer, but how the 3D genome structure responds to DNA damage is poorly understood. Here, we investigate the impact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells and ataxia telangiectasia mutated (ATM) patient cells. We irradiate fibroblasts, lymphoblasts, and ATM-deficient fibroblasts with 5 Gy X-rays and perform Hi-C at 30 minutes, 24 hours, or 5 days after irradiation. We observe that 3D genome changes after irradiation are cell type-specific, with lymphoblastoid cells generally showing more contact changes than irradiated fibroblasts. However, all tested repair-proficient cell types exhibit an increased segregation of topologically associating domains (TADs). This TAD boundary strengthening after irradiation is not observed in ATM deficient fibroblasts and may indicate the presence of a mechanism to protect 3D genome structure integrity during DNA damage repair.

scholarly journals Mapping 3D genome architecture through in situ DNase Hi-C

2016 ◽  
Vol 11 (11) ◽  
pp. 2104-2121 ◽  
Author(s):  
Vijay Ramani ◽  
Darren A Cusanovich ◽  
Ronald J Hause ◽  
Wenxiu Ma ◽  
Ruolan Qiu ◽  
...  
Keyword(s):  
Genome Architecture ◽  
3D Genome

scholarly journals Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer

2020 ◽  
Author(s):  
Tejaswi Iyyanki ◽  
Baozhen Zhang ◽  
Qiushi Jin ◽  
Hongbo Yang ◽  
Tingting Liu ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Cancer Cell ◽  
Genome Structure ◽  
Epigenetic Mechanism ◽  
Open Chromatin ◽  
3D Genome ◽  
Genome Wide ◽  
Specific Regulation ◽  
And Migration ◽  
3D Genome Structure

AbstractMuscle-invasive bladder cancers have recently been characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. For example, FOXA1, GATA3, and PPARG have been shown to be essential for luminal subtype-specific regulation and subtype switching, while TP63 and STAT3 are critical for basal subtype bladder cancer. Despite these advances, the underlying epigenetic mechanism and 3D chromatin architecture for subtype-specific regulation in bladder cancers remains largely unknown. Here, we determined the genome-wide transcriptome, enhancer landscape, TF binding profiles (FOXA1 and GATA3) in luminal and basal subtypes of bladder cancers. Furthermore, we mapped genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors, for the first time in bladder cancer. We showed that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct TF binding at distal-enhancers of luminal and basal bladder cancers. Finally, we identified a novel clinically relevant transcriptional factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other luminal-specific genes (such as FOXA1, GATA3, and PPARG) and affects cancer cell proliferation and migration. In summary, our work shows a subtype-specific epigenomic and 3D genome structure in urinary bladder cancers and suggested a novel link between the circadian TF NPAS2 and a clinical bladder cancer subtype.

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