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

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 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

scholarly journals Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

2019 ◽  
Author(s):  
Hyeon-Jin Kim ◽  
Galip Gürkan Yardımcı ◽  
Giancarlo Bonora ◽  
Vijay Ramani ◽  
Jie Liu ◽  
...  
Keyword(s):  
Single Cell ◽  
Topic Modeling ◽  
Biological Information ◽  
Chromatin Interaction ◽  
Cell Type ◽  
3D Genome ◽  
Genome Wide ◽  
Significant Barrier ◽  
Chromatin Structural ◽  
Cell Type Specific

AbstractSingle-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics.

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

Fluorescence imaging-based methods for single-cell protein analysis

2019 ◽  
Vol 411 (19) ◽  
pp. 4339-4347
Author(s):  
Siwen Wang ◽  
Fei Ji ◽  
Zhonghan Li ◽  
Min Xue
Keyword(s):  
Single Cell ◽  
Fluorescence Imaging ◽  
Protein Analysis ◽  
Single Cell Protein ◽  
Cell Protein

scholarly journals Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

2020 ◽  
Vol 12 (9) ◽  
pp. 1616-1622
Author(s):  
Susan A Smith ◽  
Xyrus X Maurer-Alcalá ◽  
Ying Yan ◽  
Laura A Katz ◽  
Luciana F Santoferrara ◽  
...  
Keyword(s):  
Single Cell ◽  
Functional Annotation ◽  
Trophic Ecology ◽  
Genome Architecture ◽  
Ecological Research ◽  
Model Species ◽  
Dna Elimination ◽  
Genomic Biology ◽  
Transcriptome Resource ◽  
And Inversion

Abstract Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.

scholarly journals Single cell fluorescence imaging of glycan uptake by intestinal bacteria

2019 ◽  
Vol 13 (7) ◽  
pp. 1883-1889 ◽  
Author(s):  
Jan-Hendrik Hehemann ◽  
Greta Reintjes ◽  
Leeann Klassen ◽  
Adam D. Smith ◽  
Didier Ndeh ◽  
...  
Keyword(s):  
Single Cell ◽  
Fluorescence Imaging ◽  
Intestinal Bacteria

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.

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