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 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.

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 Order and stochasticity in the folding of individual Drosophila genomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sergey V. Ulianov ◽  
Vlada V. Zakharova ◽  
Aleksandra A. Galitsyna ◽  
Pavel I. Kos ◽  
Kirill E. Polovnikov ◽  
...  
Keyword(s):  
Random Walk ◽  
High Resolution ◽  
3D Genome ◽  
Topologically Associating Domains ◽  
Chromatin Folding ◽  
A Cell ◽  
Single Nucleus ◽  
High Level ◽  
Cell To Cell Variability

AbstractMammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

scholarly journals Organizational principles of 3D genome architecture

2018 ◽  
Vol 19 (12) ◽  
pp. 789-800 ◽  
Author(s):  
M. Jordan Rowley ◽  
Victor G. Corces
Keyword(s):  
Genome Architecture ◽  
3D Genome ◽  
Organizational Principles

3D genome architecture from populations to single cells

2015 ◽  
Vol 31 ◽  
pp. 36-41 ◽  
Author(s):  
Mayra Furlan-Magaril ◽  
Csilla Várnai ◽  
Takashi Nagano ◽  
Peter Fraser
Keyword(s):  
Single Cells ◽  
Genome Architecture ◽  
3D Genome

scholarly journals Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Olga Raskina
Keyword(s):  
Transposable Elements ◽  
Mobile Element ◽  
Plant Genome ◽  
Aegilops Speltoides ◽  
Genome Architecture ◽  
Different Types ◽  
In The Wild ◽  
Species Specific ◽  
Current Species

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

scholarly journals Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell

2018 ◽  
Vol 13 (5) ◽  
pp. 1034-1061 ◽  
Author(s):  
David Lando ◽  
Srinjan Basu ◽  
Tim J Stevens ◽  
Andy Riddell ◽  
Kai J Wohlfahrt ◽  
...  
Keyword(s):  
Single Cell ◽  
Fluorescence Imaging ◽  
Genome Architecture ◽  
3D Genome

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 CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Cell ◽  
2015 ◽  
Vol 163 (7) ◽  
pp. 1611-1627 ◽  
Author(s):  
Zhonghui Tang ◽  
Oscar Junhong Luo ◽  
Xingwang Li ◽  
Meizhen Zheng ◽  
Jacqueline Jufen Zhu ◽  
...  
Keyword(s):  
Genome Architecture ◽  
3D Genome

scholarly journals A CTCF Code for 3D Genome Architecture

Cell ◽  
2015 ◽  
Vol 162 (4) ◽  
pp. 703-705 ◽  
Author(s):  
Michael H. Nichols ◽  
Victor G. Corces
Keyword(s):  
Genome Architecture ◽  
3D Genome
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