3D genome architecture — of loops and globules

2014 ◽  
Vol 15 (12) ◽  
pp. 780-780
Author(s):  
Linda Koch
Keyword(s):  
Genome Architecture ◽  
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 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

scholarly journals RNA gradients: Shapers of 3D genome architecture

2022 ◽  
Vol 74 ◽  
pp. 7-12
Author(s):  
Britta A.M. Bouwman ◽  
Nicola Crosetto ◽  
Magda Bienko
Keyword(s):  
Genome Architecture ◽  
3D Genome

scholarly journals β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

2020 ◽  
Author(s):  
Syed Raza Mahmood ◽  
Xin Xie ◽  
Nadine Hosny El Said ◽  
Kristin C. Gunsalus ◽  
Piergiorgio Percipalle
Keyword(s):  
Chromatin Remodeling ◽  
Genomic Analysis ◽  
Chromatin Accessibility ◽  
Genome Architecture ◽  
Dependent Manner ◽  
Chromatin Remodelers ◽  
3D Genome ◽  
Polycomb Proteins ◽  
Crucial Component ◽  
Development And Differentiation

Abstractβ-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings support a novel role for β-actin-dependent chromatin remodeling in shaping the chromatin landscape and regulating genes involved in development and differentiation.

scholarly journals SARS-CoV-2 Restructures the Host Chromatin Architecture

2021 ◽  
Author(s):  
Ruoyu Wang ◽  
Joo-Hyung Lee ◽  
Feng Xiong ◽  
Jieun Kim ◽  
Lana Al Hasani ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Host Cells ◽  
Interferon Response ◽  
Genome Architecture ◽  
3D Genome ◽  
Chromatin Architecture ◽  
Severe Infections ◽  
Global Reduction ◽  
Host Chromatin

SARS-CoV-2 has made >190-million infections worldwide, thus it is pivotal to understand the viral impacts on host cells. Many viruses can significantly alter host chromatin, but such roles of SARS-CoV-2 are largely unknown. Here, we characterized the three-dimensional (3D) genome architecture and epigenome landscapes in human cells after SARS-CoV-2 infection, revealing remarkable restructuring of host chromatin architecture. High-resolution Hi-C 3.0 uncovered widespread A compartmental weakening and A-B mixing, together with a global reduction of intra-TAD chromatin contacts. The cohesin complex, a central organizer of the 3D genome, was significantly depleted from intra-TAD regions, supporting that SARS-CoV-2 disrupts cohesin loop extrusion. Calibrated ChIP-Seq verified chromatin restructuring by SARS-CoV-2 that is particularly manifested by a pervasive reduction of euchromatin modifications. Built on the rewired 3D genome/epigenome maps, a modified activity-by-contact model highlights the transcriptional weakening of antiviral interferon response genes or virus sensors (e.g., DDX58) incurred by SARS-CoV-2. In contrast, pro-inflammatory genes (e.g. IL-6) high in severe infections were uniquely regulated by augmented H3K4me3 at their promoters. These findings illustrate how SARS-CoV-2 rewires host chromatin architecture to confer immunological gene deregulation, laying a foundation to characterize the long-term epigenomic impacts of this virus.

scholarly journals Advancements in mapping 3D genome architecture

Methods ◽  
2020 ◽  
Vol 170 ◽  
pp. 75-81 ◽  
Author(s):  
Daniel J. McKay ◽  
Alexis V. Stutzman ◽  
Jill M. Dowen
Keyword(s):  
Genome Architecture ◽  
3D Genome
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