The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

AbstractThree-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

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Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.774719 ◽

2021 ◽

Vol 9 ◽

Author(s):

Suresh Kumar ◽

Simardeep Kaur ◽

Karishma Seem ◽

Santosh Kumar ◽

Trilochan Mohapatra

Keyword(s):

Gene Expression ◽

Environmental Stress ◽

Genome Organization ◽

Regulation Of Gene Expression ◽

Three Dimensional ◽

Regulatory Elements ◽

Chromosome Conformation ◽

3D Genome ◽

Chromatin Architecture ◽

Capture Techniques

The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.

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PHi-C: deciphering Hi-C data into polymer dynamics

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa020 ◽

2020 ◽

Vol 2 (2) ◽

Author(s):

Soya Shinkai ◽

Masaki Nakagawa ◽

Takeshi Sugawara ◽

Yuichi Togashi ◽

Hiroshi Ochiai ◽

...

Keyword(s):

Live Cell Imaging ◽

Cell Imaging ◽

Simulation Method ◽

Live Cell ◽

Polymer Dynamics ◽

Interaction Parameters ◽

Physical Interaction ◽

Chromosome Conformation ◽

3D Genome ◽

Genome Features

Abstract Genomes are spatiotemporally organized within the cell nucleus. Genome-wide chromosome conformation capture (Hi-C) technologies have uncovered the 3D genome organization. Furthermore, live-cell imaging experiments have revealed that genomes are functional in 4D. Although computational modeling methods can convert 2D Hi-C data into population-averaged static 3D genome models, exploring 4D genome nature based on 2D Hi-C data remains lacking. Here, we describe a 4D simulation method, PHi-C (polymer dynamics deciphered from Hi-C data), that depicts 4D genome features from 2D Hi-C data by polymer modeling. PHi-C allows users to interpret 2D Hi-C data as physical interaction parameters within single chromosomes. The physical interaction parameters can then be used in the simulations and analyses to demonstrate dynamic characteristics of genomic loci and chromosomes as observed in live-cell imaging experiments. PHi-C is available at https://github.com/soyashinkai/PHi-C.

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Chromosome Conformation Paints Reveal the Role of Lamina Association in Genome Organization and Regulation

10.1101/122226 ◽

2017 ◽

Cited By ~ 14

Author(s):

Teresa R Luperchio ◽

Michael EG Sauria ◽

Xianrong Wong ◽

Marie-Cécile Gaillard ◽

Peter Tsang ◽

...

Keyword(s):

Single Cells ◽

Regulation Of Gene Expression ◽

Three Dimensional ◽

Nuclear Lamina ◽

Peripheral Zone ◽

Integrated Analysis ◽

Chromosome Conformation ◽

Transcription Start Sites ◽

Repressive Regime

SummaryNon-random, dynamic three-dimensional organization of the nucleus is important for regulation of gene expression. Numerous studies using chromosome conformation capture strategies have uncovered ensemble organizational principles of individual chromosomes, including organization into active (A) and inactive (B) compartments. In addition, large inactive regions of the genome appear to be associated with the nuclear lamina, the so-called Lamina Associated Domains (LADs). However, the interrelationship between overall chromosome conformation and association of domains with the nuclear lamina remains unclear. In particular, the 3D organization of LADs within the context of the entire chromosome has not been investigated. In this study, we describe “chromosome conformation paints” to determine the relationship in situ between LAD and non-LAD regions of the genome in single cells. We find that LADs organize into constrained and compact regions at the nuclear lamina, and these findings are supported by an integrated analysis of both DamID and Hi-C data. Using a refined algorithm to identify active (A) and inactive (B) compartments from Hi-C data, we demonstrate that the LADs correspond to the B compartment. We demonstrate that in situ single cell chromosome organization is strikingly predicted by integrating both Hi-C and DamID data into a chromosome conformation model. In addition, using the chromosome conformation paints, we demonstrate that LAD (and B-compartment) organization is dependent upon both chromatin state and Lamin A/C. Finally, we demonstrate that small regions within LADs escape the repressive regime at the peripheral zone to interact with the A-compartment and are enriched for both transcription start sites (TSSs) and active enhancers.

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Cost-Effective High-Speed, Three-Dimensional Live-Cell Imaging of HIV-1 Transfer at the T Cell Virological Synapse

SSRN Electronic Journal ◽

10.2139/ssrn.3956819 ◽

2021 ◽

Author(s):

Alice Sandmeyer ◽

Lili Wang ◽

Wolfgang Hübner ◽

Marcel Müller ◽

Benjamin Chen ◽

...

Keyword(s):

T Cell ◽

Live Cell Imaging ◽

High Speed ◽

Cell Imaging ◽

Three Dimensional ◽

Cost Effective ◽

Live Cell ◽

Virological Synapse ◽

Hiv 1

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CRISPR-mediated Multiplexed Live Cell Imaging of Nonrepetitive Genomic Loci

10.1101/2020.03.03.974923 ◽

2020 ◽

Author(s):

Patricia A. Clow ◽

Nathaniel Jillette ◽

Jacqueline J. Zhu ◽

Albert W. Cheng

Keyword(s):

Live Cell Imaging ◽

Cell Imaging ◽

Repetitive Sequences ◽

Binary Sequence ◽

Three Dimensional ◽

Live Cell ◽

Live Cells ◽

Imaging Method ◽

Genomic Locus ◽

Time Dynamics

AbstractThree-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and low signal-to-noise ratios (SNRs), and are thus mostly applicable to repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method, with an enhanced SNR, that allows for one nonrepetitive genomic locus to be labeled using a single sgRNA. We constructed Casilio dual-color probes to visualize the dynamic interactions of cohesin-bound elements in single live cells. By forming a binary sequence of multiple Casilio probes (PISCES) across a continuous stretch of DNA, we track the dynamic 3D folding of a 74kb genomic region over time. This method offers unprecedented resolution and scalability for delineating the dynamic 4D nucleome.One Sentence SummaryCasilio enables multiplexed live cell imaging of nonrepetitive DNA loci for illuminating the real-time dynamics of genome structures.

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Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae

10.1101/339010 ◽

2018 ◽

Cited By ~ 1

Author(s):

David J Winter ◽

Austen RD Ganley ◽

Carolyn A Young ◽

Ivan Liachko ◽

Christopher L Schardl ◽

...

Keyword(s):

Genome Structure ◽

Regulation Of Gene Expression ◽

Three Dimensional ◽

Structural Features ◽

Dimensional Structure ◽

In Planta ◽

Repeat Elements ◽

Symbiotic Relationships ◽

3D Genome ◽

Transcriptional Changes

AbstractStructural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organization influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus,Epichloë festucae. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that anEpichloëspecies needs to maintain symbiotic relationships with its grass host. Our results reveal a unique “patchwork” genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

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ER sheet persistence is coupled to myosin 1c–regulated dynamic actin filament arrays

Molecular Biology of the Cell ◽

10.1091/mbc.e13-12-0712 ◽

2014 ◽

Vol 25 (7) ◽

pp. 1111-1126 ◽

Cited By ~ 36

Author(s):

Merja Joensuu ◽

Ilya Belevich ◽

Olli Rämö ◽

Ilya Nevzorov ◽

Helena Vihinen ◽

...

Keyword(s):

Actin Filament ◽

Actin Filaments ◽

Network Architecture ◽

Live Cell Imaging ◽

Cell Imaging ◽

Three Dimensional ◽

Actin Depolymerization ◽

Specific Subset ◽

3D Network ◽

3D Electron Microscopy

The endoplasmic reticulum (ER) comprises a dynamic three-dimensional (3D) network with diverse structural and functional domains. Proper ER operation requires an intricate balance within and between dynamics, morphology, and functions, but how these processes are coupled in cells has been unclear. Using live-cell imaging and 3D electron microscopy, we identify a specific subset of actin filaments localizing to polygons defined by ER sheets and tubules and describe a role for these actin arrays in ER sheet persistence and, thereby, in maintenance of the characteristic network architecture by showing that actin depolymerization leads to increased sheet fluctuation and transformations and results in small and less abundant sheet remnants and a defective ER network distribution. Furthermore, we identify myosin 1c localizing to the ER-associated actin filament arrays and reveal a novel role for myosin 1c in regulating these actin structures, as myosin 1c manipulations lead to loss of the actin filaments and to similar ER phenotype as observed after actin depolymerization. We propose that ER-associated actin filaments have a role in ER sheet persistence regulation and thus support the maintenance of sheets as a stationary subdomain of the dynamic ER network.

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The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

Genes ◽

10.3390/genes11030289 ◽

2020 ◽

Vol 11 (3) ◽

pp. 289 ◽

Cited By ~ 2

Author(s):

Ping Hong ◽

Hao Jiang ◽

Weize Xu ◽

Da Lin ◽

Qian Xu ◽

...

Keyword(s):

Target Genes ◽

High Efficiency ◽

New Technology ◽

Three Dimensional ◽

Large Data ◽

Regulatory Elements ◽

Chromosome Conformation Capture ◽

Genome Chromosome ◽

Chromosome Conformation ◽

3D Genome

It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.

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Nucleoplasmic Lamin C Rapidly Accumulates at Sites of Nuclear Envelope Rupture with BAF and cGAS

10.1101/2022.01.05.475028 ◽

2022 ◽

Author(s):

Yohei Kono ◽

Stephen A. Adam ◽

Karen Reddy ◽

Yixian Zheng ◽

Ohad Medalia ◽

...

Keyword(s):

Nuclear Envelope ◽

Live Cell Imaging ◽

Cell Imaging ◽

Nuclear Lamina ◽

Structural Components ◽

Cell Nuclei ◽

Embryonic Fibroblasts ◽

Nuclear Lamins ◽

Laser Microirradiation

In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that lamin C but not the other lamin isoforms rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The immunoglobulin-like fold domain and the NLS were required for the recruitment from the nucleoplasm to the rupture sites with the Barrier-to-autointegration factor (BAF). The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP (cGAMP) synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF and cGAS concertedly accumulate at sites of NE rupture for repair.

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