Multiplexed imaging of nucleome architectures in single cells of mammalian tissue.

Nature Communications
Miao LiuSiyuan Wang

Abstract

The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged in the same cell and how they are mutually correlated in different cell types in mammalian tissue are largely unknown. Here, we develop Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We apply this method in mouse fetal liver, and identify de novo cell-type-specific chromatin architectures associated with gene expression, as well as cell-type-independent principles of chromatin organization. Polymer simulation shows that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our results illustrate a multi-faceted picture and physical principles of chromatin organization.

References

Jun 12, 2003·Nucleic Acids Research·Jean-Marie RouillardErdogan Gulari
Aug 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Makoto MiyazakiJames M Ntambi
Oct 3, 2006·Nature Methods·Ivan RasnikTaekjip Ha
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 20, 2010·Cold Spring Harbor Perspectives in Biology·Thomas Cremer, Marion Cremer
Apr 3, 2010·PLoS Genetics·Attila NémethGernot Längst
Dec 24, 2010·Cytogenetic and Genome Research·N A YamadaA R Brothman
Oct 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Shelagh BoyleWendy A Bickmore
Dec 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Brian J BeliveauChao-ting Wu
Mar 19, 2013·Cell·Wendy A Bickmore, Bas van Steensel
Jul 24, 2013·Annual Review of Genomics and Human Genetics·Wendy A Bickmore
Apr 1, 2014·Cell·Michael LevineRobert Tjian
Jun 7, 2014·Cell Stem Cell·David U GorkinBing Ren
Jun 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Siyuan WangXiaowei Zhuang
Jul 8, 2014·Current Opinion in Genetics & Development·Giancarlo BonoraMatthew Denholtz
Apr 22, 2015·FEBS Letters·Melike Lakadamyali, Maria Pia Cosma
Aug 27, 2015·Genome Biology·Takashi NaganoPeter Fraser
Mar 12, 2016·Cell·Job Dekker, Leonid Mirny
May 6, 2016·Annual Review of Biophysics·Baohui ChenBo Huang
Sep 15, 2016·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey R MoffittXiaowei Zhuang
Jun 22, 2017·Nature·Amy R StromGary H Karpen
Nov 21, 2017·Nucleic Acids Research·Daniel R ZerbinoPaul Flicek
Feb 24, 2018·Cell·Xiaoping HanGuoji Guo

❮ Previous
Next ❯

Citations

Nov 28, 2020·Nature Reviews. Genetics·Benjamin Carter, Keji Zhao
Dec 12, 2020·Genome Génome / Conseil National De Recherches Canada·Hilmar Strickfaden
Aug 10, 2020·Molecular Cell·Andrews Akwasi AgblekeDushan Wadduwage
Apr 30, 2021·Frontiers in Molecular Biosciences·Chengwei Zhang, Jing Huang
May 26, 2021·Seminars in Cell & Developmental Biology·Sergey V Ulianov, Sergey V Razin

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE70181
32

Methods Mentioned

BETA
single-cell
single-cell Hi–C
fluorescence microscopy
PCR
electron microscopy
RNA-seq

Software Mentioned

MINA
BLAST
MERFISH
Cufflinks
MERIFSH
OligoArray2
Tophat
MATLAB

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.