The lack of safe and efficient gene-delivery methods is a limiting obstacle to human gene therapy. Synthetic gene-delivery agents, although safer than recombinant viruses, generally do not possess the required efficacy. In recent years, a variety of effective polymers have been designed specifically for gene delivery, and much has been learned about their structure–function relationships. With the growing understanding of polymer gene-delivery mechanisms and continued efforts of creative polymer chemists, it is likely that polymer-based gene-delivery systems will become an important tool for human gene therapy.

Design and development of polymers for gene delivery

The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation.

/pdf/chromosome-territories-nuclear-architecture-and-gene-36775rhtfg.pdf

Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

tion of gene expression and other nuclear functions — namely the architecture of the nucleus as a whole. In particular, we describe evidence for a compartmentalized nuclear architecture in the mammalian cell nucleus based on chromosome territories (CTs) and an interchromatin compartment (IC) that contains macromolecular complexes that are required for replication, transcription, splicing and repair (summarized in FIG. 1). Other nuclear components, such as the nucleolus, nuclear lamina and pores, are not reviewed here (for reviews, see REFS 15,16), and although the focus of this review is the mammalian nucleus, the nuclear architecture of other organisms will be mentioned where appropriate. During the past two decades, various new methods have expanded the cell biologist’s ‘toolkit’ for the study of nuclear architecture and function (BOX 1). These methods have provided the basis for detailed studies of CTs, as well as for studies of the topology and dynamics of non-chromatin domains in the nucleus of fixed and, more recently, living cells. Computer simulations of CTs and nuclear architecture are also being used to make quantitative predictions that can be tested experimentally. On the basis of Despite all the celebrations associated with the sequencing of the human genome, and the genomes of other model organisms, our abilities to interpret genome sequences are quite limited. For example, we cannot understand the orchestrated activity — and the silencing — of many thousands of genes in any given cell just on the basis of DNA sequences, such as promoter and enhancer elements. How are the profound differences in gene activities established and maintained in a large number of cell types to ensure the development and functioning of a complex multicellular organism? To answer this question fully, we need to understand how genomes are organized in the nucleus, the basic principles of nuclear architecture and the changes in nuclear organization that occur during cellular differentiation. During recent years, EPIGENETIC mechanisms of gene regulation, such as DNA methylation and histone modification, have entered the centre stage of chromatin research. Modifications of DNA and nucleosomes, however, as well as boundaries and insulators, that affect gene regulation at the chromatin level are not the focus of this article. Instead, we review experimental data and models for a higher level of the regulaCHROMOSOME TERRITORIES, NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS

Nuclear architecture and gene regulation in mammalian cells

Protons dictate the charge and structure of macromolecules and are used as energy currency by eukaryotic cells. The unique function of individual organelles therefore depends on the establishment and stringent maintenance of a distinct pH. This, in turn, requires a means to sense the prevailing pH and to respond to deviations from the norm with effective mechanisms to transport, produce or consume proton equivalents. A dynamic, finely tuned balance between proton-extruding and proton-importing processes underlies pH homeostasis not only in the cytosol, but in other cellular compartments as well.

/pdf/sensors-and-regulators-of-intracellular-ph-35e35yleyy.pdf

Sensors and regulators of intracellular pH

5. Cyanine-Based pHi Indicators 2717 5.1. Design of pH-Sensitive Cyanine Dyes 2717 5.2. Near-Neutral Cyanine-Based pH Indicators 2718 5.3. Acidic Cyanine-Based pH Indicators 2719 6. Miscellaneous Small Molecule pHi Indicators 2719 6.1. Various Indicators for Near-Neutral pH Values 2719 6.1.1. Europium Complex 2719 6.1.2. Fluorene Derivative 2719 6.1.3. 1,4-Dihydroxyphthalonitrile (1,4-DHPN) 2720 6.1.4. 8-Hydroxypyrene-1,3,6-trisulfonic acid (HPTS) 2720

Fluorescent indicators for intracellular pH.

https://hal.archives-ouvertes.fr/hal-01604987/document

Size-dependent DNA Mobility in Cytoplasm and Nucleus

Fluorescence recovery after photobleaching (FRAP) was used to quantify the translational diffusion of microinjected FITC-dextrans and Ficolls in the cytoplasm and nucleus of MDCK epithelial cells and Swiss 3T3 fibroblasts. Absolute diffusion coefficients (D) were measured using a microsecond-resolution FRAP apparatus and solution standards. In aqueous media (viscosity 1 cP), D for the FITC-dextrans decreased from 75 to 8.4 × 10−7 cm2/s with increasing dextran size (4–2,000 kD). D in cytoplasm relative to that in water (D/Do) was 0.26 ± 0.01 (MDCK) and 0.27 ± 0.01 (fibroblasts), and independent of FITC-dextran and Ficoll size (gyration radii [RG] 40–300 Å). The fraction of mobile FITC-dextran molecules (fmob), determined by the extent of fluorescence recovery after spot photobleaching, was >0.75 for RG 300 Å. The independence of D/Do on FITC-dextran and Ficoll size does not support the concept of solute “sieving” (size-dependent diffusion) in cytoplasm. Photobleaching measurements using different spot diameters (1.5–4 μm) gave similar D/Do, indicating that microcompartments, if present, are of submicron size. Measurements of D/Do and fmob in concentrated dextran solutions, as well as in swollen and shrunken cells, suggested that the low fmob for very large macromolecules might be related to restrictions imposed by immobile obstacles (such as microcompartments) or to anomalous diffusion (such as percolation). In nucleus, D/Do was 0.25 ± 0.02 (MDCK) and 0.27 ± 0.03 (fibroblasts), and independent of solute size (RG 40–300 Å). Our results indicate relatively free and rapid diffusion of macromolecule-sized solutes up to approximately 500 kD in cytoplasm and nucleus.

/pdf/translational-diffusion-of-macromolecule-sized-solutes-in-psk59y7be4.pdf

Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus.

Chains of magnetosomes extracted from AMB-1 magnetotactic bacteria are shown to be highly efficient for cancer therapy when they are exposed to an alternative magnetic field. When a suspension containing MDA-MB-231 breast cancer cells was incubated in the presence of various amounts of extracted chains of magnetosomes, the viability of these cells remained high in the absence of an alternative magnetic field. By contrast, when this suspension was exposed to an alternative magnetic field of frequency 183 kHz and field strengths of 20, 40, or 60 mT, up to 100% of these cells were destroyed. The antitumoral activity of the extracted chains of magnetosomes is demonstrated further by showing that they can be used to fully eradicate a tumor xenografted under the skin of a mouse. For that, a suspension containing ∼1 mg of extracted chains of magnetosomes was administered within the tumor and the mouse was exposed to three heat cycles of 20 min, during which the tumor temperature was raised to ∼43 °C. We also dem...

Chains of magnetosomes extracted from AMB-1 magnetotactic bacteria for application in alternative magnetic field cancer therapy.

Direct measurement of trans-Golgi pH in living cells and regulation by second messengers.

Intracellular pH has been measured by laser microspectrofluorimetry, using the pH-sensitive dyes SNARF-1, SNARF-calcein and SNARF-1-dextran. By this technique it was possible to accurately determine pH in volumes as small as 0.5 x 0.5 x 1 microns 3. The probes were loaded into the cells either by diffusion of their acetoxymethylester derivatives (SNARF-1-AM, SNARF-calcein-AM) or by microinjection (SNARF-1-dextran). When the five types of cells were studied in RPMI medium, the nuclear pH was consistently found to be 0.3 to 0.5 units above that of the cytosol. Although the presence of pores in the nuclear membrane has been taken as evidence that free diffusion of ions and small molecules can occur in and out the nucleus, we conclude that the nuclear membrane of these cells presents a permeability barrier to H+. The pH gradient was not observed in cells suspended in PBS.

Olivier Seksek

Papers

Size-dependent DNA Mobility in Cytoplasm and Nucleus

Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus.

Chains of magnetosomes extracted from AMB-1 magnetotactic bacteria for application in alternative magnetic field cancer therapy.

Direct measurement of trans-Golgi pH in living cells and regulation by second messengers.

Nuclear pH gradient in mammalian cells revealed by laser microspectrofluorimetry.