scholarly journals Interchromosomal interactions: A genomic love story of kissing chromosomes

2018 ◽  
Vol 218 (1) ◽  
pp. 27-38 ◽  
Author(s):  
Philipp G. Maass ◽  
A. Rasim Barutcu ◽  
John L. Rinn
Keyword(s):  
Gene Expression ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Specific Gene ◽  
Love Story ◽  
Fundamental Properties ◽  
Disease States ◽  
Gene Positioning

Nuclei require a precise three- and four-dimensional organization of DNA to establish cell-specific gene-expression programs. Underscoring the importance of DNA topology, alterations to the nuclear architecture can perturb gene expression and result in disease states. More recently, it has become clear that not only intrachromosomal interactions, but also interchromosomal interactions, a less studied feature of chromosomes, are required for proper physiological gene-expression programs. Here, we review recent studies with emerging insights into where and why cross-chromosomal communication is relevant. Specifically, we discuss how long noncoding RNAs (lncRNAs) and three-dimensional gene positioning are involved in genome organization and how low-throughput (live-cell imaging) and high-throughput (Hi-C and SPRITE) techniques contribute to understand the fundamental properties of interchromosomal interactions.

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

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

scholarly journals CRISPR-mediated Multiplexed Live Cell Imaging of Nonrepetitive Genomic Loci

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.

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

2014 ◽  
Vol 25 (7) ◽  
pp. 1111-1126 ◽  
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.

Tissue-specific gene expression in chondrocytes grown on three-dimensional hyaluronic acid scaffolds

Biomaterials ◽  
2003 ◽  
Vol 24 (19) ◽  
pp. 3265-3275 ◽  
Author(s):  
Davide Girotto ◽  
Serena Urbani ◽  
Paola Brun ◽  
Davide Renier ◽  
Rolando Barbucci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hyaluronic Acid ◽  
Three Dimensional ◽  
Specific Gene ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression

scholarly journals Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters

2014 ◽  
Vol 42 (11) ◽  
pp. e90-e90 ◽  
Author(s):  
Ilchung Shin ◽  
Judhajeet Ray ◽  
Vinayak Gupta ◽  
Muslum Ilgu ◽  
Jonathan Beasley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Live Cell Imaging ◽  
Promoter Activity ◽  
Cell Imaging ◽  
Live Cell ◽  
Pol Ii

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Three-Dimensional Unstained Live-Cell Imaging Using Stimulated Parametric Emission Microscopy

2009 ◽  
Vol 48 (9) ◽  
pp. 097003 ◽  
Author(s):  
Hieu M. Dang ◽  
Takehito Kawasumi ◽  
Gen Omura ◽  
Toshiyuki Umano ◽  
Shin'ichiro Kajiyama ◽  
...  
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Three Dimensional ◽  
Live Cell ◽  
Emission Microscopy

Analysis of the influence of subcellular localization of the HIV Rev protein on Rev-dependent gene expression by multi-fluorescence live-cell imaging

2006 ◽  
Vol 312 (4) ◽  
pp. 443-456 ◽  
Author(s):  
Horst Wolff ◽  
Kamyar Hadian ◽  
Manja Ziegler ◽  
Claudia Weierich ◽  
Susanne Kramer-Hammerle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Subcellular Localization ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Rev Protein ◽  
Fluorescence Live Cell Imaging

scholarly journals Three-Dimensional Genome Organization in Breast and Gynecological Cancers: How Chromatin Folding Influences Tumorigenic Transcriptional Programs

Cells ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 75
Author(s):  
Stephanie I. Nuñez-Olvera ◽  
Jonathan Puente-Rivera ◽  
Rosalio Ramos-Payán ◽  
Carlos Pérez-Plasencia ◽  
Yarely M. Salinas-Vera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Function ◽  
Three Dimensional ◽  
Gene Mutations ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Gene Promoters ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rnas ◽  
Insulator Elements

A growing body of research on the transcriptome and cancer genome has demonstrated that many gynecological tumor-specific gene mutations are located in cis-regulatory elements. Through chromosomal looping, cis-regulatory elements interact which each other to control gene expression by bringing distant regulatory elements, such as enhancers and insulators, into close proximity with promoters. It is well known that chromatin connections may be disrupted in cancer cells, promoting transcriptional dysregulation and the expression of abnormal tumor suppressor genes and oncogenes. In this review, we examine the roles of alterations in 3D chromatin interactions. This includes changes in CTCF protein function, cancer-risk single nucleotide polymorphisms, viral integration, and hormonal response as part of the mechanisms that lead to the acquisition of enhancers or super-enhancers. The translocation of existing enhancers, as well as enhancer loss or acquisition of insulator elements that interact with gene promoters, is also revised. Remarkably, similar processes that modify 3D chromatin contacts in gene promoters may also influence the expression of non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which have emerged as key regulators of gene expression in a variety of cancers, including gynecological malignancies.

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