Analysis of the transcriptional activity of model piggyBac transgenes stably integrated into different loci of the genome of CHO cells in the absence of selection pressure.

CHO cells are most commonly used for the synthesis of recombinant proteins in biopharmaceutical production. When stable producer cell lines are obtained, the locus of transgene integration into the genome has a great influence on the level of its expression. Therefore, the identification of genomic loci ensuring a high level of protein production is very important. Here, we used the TRIP assay to study the influence of the local chromatin environment on the activity of transgenes in CHO cells. For this purpose, reporter constructs encoding eGFP under the control of four promoters were stably integrated into the genome of CHO cells using the piggyBac transposon. Each individual transgene contained a unique tag, a DNA barcode, and the resulting polyclonal cell population was cultured for almost a month without any selection. Next, using the high-throughput sequencing, genomic localizations of barcodes, as well as their abundances in the population and transcriptional activities were identified. In total, ~640 transgenes more or less evenly distributed across all chromosomes of CHO cells were characterized. More than half of the transgenes were completely silent. The most active transgenes were identified to be inserted in gene promoters and 5' UTRs. Transgenes carrying Chinese hamster full-length promoter of the EF-1α gene showed the highest activity. Transgenes with a truncated version of the same promoter and with the mouse PGK gene promoter were on average 10 and 19 times less active, respectively. In total, combinations of genomic loci of CHO cells and transgene promoters that together provide different levels of transcriptional activity of the model reporter construct were described.

[Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation].

Position effect variegation (PEV) is a phenomenon wherein the expression level of a gene strongly depends on its genomic position. PEV can be observed when a gene is moved via a chromosome rearrangement or identical genetic constructs are inserted into different regions of the genome. The eukaryotic genome has a domain organization, and gene activity within a domain depends not only on the nucleotide sequence of a gene, but also on the state of surrounding chromatin, thus being regulated epigenetically. Chromatin is a complex of DNA, RNA, and associated structural and regulatory proteins. The epigenetic status of chromatin depends on the replication time of a given genomic region, particular regulatory DNA motifs, and contacts with the inner nuclear envelope (lamina) and other chromosome regions (topologically associated domains). PEV results from the changes in the epigenetic state of a gene and provides a unique tool to study the molecular and biochemical processes that underlie the establishment and switching of epigenetic states. Understanding the molecular mechanisms of PEV in human is of clinical importance, in particular, for the detection and treatment of retroviral infections because the local chromatin state may determine the latent/active state transition of an infection, such as HIV. In addition, a large number of human neurodegenerative diseases are caused by epigenetic gene inactivation due to expansion of short repeats. Finally, to apply gene therapy methods, it is important to develop approaches that ensure a necessary level of transgene expression with sufficient accuracy.

An Inducible DamID System for Profiling Interactions of Nuclear Lamina Protein Component Lamin B1 with Chromosomes in Mouse Cells.

At the level of DNA organization into chromatin, there are mechanisms that define gene expression profiles in specialized cell types. Genes within chromatin regions that are located at the nuclear periphery are generally expressed at lower levels; however, the nature of this phenomenon remains unclear. These parts of chromatin interact with nuclear lamina proteins like Lamin B1 and, therefore, can be identified in a given cell type by chromatin profiling of these proteins. In this study, we created and tested a Dam Identification (DamID) system induced by Cre recombinase using Lamin B1 and mouse embryonic fibroblasts. This inducible system will help to generate genome-wide profiles of chromatin proteins in given cell types and tissues with no need to dissect tissues from organs or separate cells from tissues, which is achieved by using specific regulatory DNA elements and due to the high sensitivity of the method.

Genomic mapping of chromatin proteins by using Daminv modification of an FLP-dependent DamID approach.

To identify interactions of chromatin proteins with the genome of the cell type of interest that is a part of heterologous tissues and organs of Drosophila, an FLP-dependent DamID approach was recently developed [4], which does not require sorting of cells or nuclei. Here, a modification of this approach, Daminv, is described. The modified approach was validated by generating the binding pattern of the LAM protein, a component of the inner membrane of the nuclear envelope, with the genome of glial cells of the Drosophila larval central brains.

PATHWAYS OF SPINDLE FORMATION IN DROSOPHILA MITOTIC AND MEIOTIC CELLS.

Spindle assembly relies on three main classes of microtubules (MTs): MTs nucleated by the centrosomes, MTs nucleated near the chromosomes/kinetochores and MTs nucleated from preexisting MTs through the augmin-based pathway. Here, we review the roles of these microtubule generation pathways in Drosophila spindle assembly. The extant results indicate that female meiotic cells, male meiotic cells, larval brain cells and S2 tissue culture cells exploit specific pathway combinations for generating the MTs necessary for spindle formation. Thus, different Drosophila cell types have specific modes of spindle assembly, which might be related to specific functional and developmental requirements.

FACTORS GOVERNING THE PATTERN OF SPINDLE MICROTUBULE REGROWTH AFTER TUBULIN DEPOLYMERIZATION.

We analyzed the pattern of spindle microtubule (MT) regrowth after cold- or colcemid-induced MT depolymerization in Drosophila S2 cells. Cold-induced MT disassembly at low temperature (­2 °C) destroyed kinetochore-driven MT regrowth without affecting astral MT formation. Conversely, colcemid-induced MT depolymerization strongly impaired centrosome-dependent MT nucleation, allowing kinetochore-driven MT regrowth. Collectively, these results indicate that the kinetochore- and the centrosome-mediated MT assembly pathways exploit molecular mechanisms that are at least in part different.