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Introduction Historically, retrotransposons were first characterized as 'controlling elements' of neighboring genes (McClintock 1956). Our understanding of the biology of retrotransposal elements and the mechanisms of retrotransposition, as well as [...], A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100-300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2-3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as 'evolutionary junkyard' or 'fossils', this enigmatic 'dark matter' of the genome possesses many yet to be discovered properties. Key words: retrotransposons, SINE, genomic boundaries, Pol III transcription, TFIIIC, chromatin architecture, intrachromosomal interactions, tRNA genes. Le genome eucaryote typique comprend une riche variete d'elements repetitifs. Les plus abondants sont les retrotransposons, des retro-elements mobiles qui utilisent la transcriptase inverse et les ARN intermediates pour se relocaliser ailleurs a l'interieur des genomes cellulaires. La grande majorite du contenu du genome repetitif des mammiferes origine de la retrotransposition d'elements transposables membres des superfamilles SINE (elements nucleates courts dissemines de 100-300 pb qui derivent de l'ARN structural 7SL ou de l'ARNt), LINE (elements nucleates longs dissemines de 7 kb) et LTR (longues repetitions terminales de 2-3 kb). Grossierement appelee << ADN depotoir >> ou << fossile >>, cette << matiere noire >> du genome possede plusieurs proprietes qu'il reste largement a decouvrir. Mots-cles : retrotransposons, SINE, bornes genomiques, transcription par Pol III, TFIIIC, architecture de la chromatine, interactions intrachromosomiques, genes des ARNt. [Traduit par la Redaction]

The functional consequences of molecular sensor and molecular adaptor actions of corepressor/coactivator complexes in integrating signal dependent programs of transcriptional responses at the molecular level are reviewed. This strategy imposes a temporal order for modifying programs of transcriptional regulation in response to the cellular milieu, which is used to mediate developmental/homeostatic and pathological events.

Research shows that induction of the Ets domain repressor, METS, during macrophage differentiation, arrests the terminal cell cycle by repressing transcription of the cell cycle control genes. Data indicate that METS selectively represses Ets target genes mediateing Ras-dependent proliferation witthout affecting the genes involved in the Ras-dependent differentiation.

Operating at multiple levels of control, mesenchymal stemcells fromadipose tissue (ADSCs) communicate with organ systems to adjust immune response, provide signals for differentiation, migration, enzymatic reactions, and to equilibrate the regenerative demands of balanced tissue homeostasis. The identification of the mechanisms by which ADSCs accomplish these functions for dermatological rejuvenation and wound healing has great potential to identify novel targets for the treatment of disorders and combat aging. Herein, we review new insights into the role of adipose-derived stem cells in the maintenance of dermal and epidermal homeostasis, and recent advances in clinical applications of ADSCs related to dermatology. [ABSTRACT FROM AUTHOR]

Insulators are regulatory elements that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity. Although there are several examples of transposable element (TE)-derived insulators, the contribution of TEs to human insulators has not been systematically explored. Mammalian-wide interspersed repeats (MIRs) are a conserved family of TEs that have substantial regulatory capacity and share sequence characteristics with tRNA-related insulators. We sought to evaluate whether MIRs can serve as insulators in the human genome. We applied a bioinformatic screen using genome sequence and functional genomic data from CD4+ T cells to identify a set of 1,178 predicted MIR insulators genome-wide. These predicted MIR insulators were computationally tested to serve as chromatin barriers and regulators of gene expression in CD4+ T cells. The activity of predicted MIR insulators was experimentally validated using in vitro and in vivo enhancer-blocking assays. MIR insulators are enriched around genes of the T-cell receptor pathway and reside at T-cell-specific boundaries of repressive and active chromatin. A total of 58% of the MIR insulators predicted here show evidence of T-cell-specific chromatin barrier and gene regulatory activity. MIR insulators appear to be CCCTC-binding factor (CTCF) independent and show a distinct local chromatin environment with marked peaks for RNA Pol III and a number of histone modifications, suggesting that MIR insulators recruit transcriptional complexes and chromatin modifying enzymes in situ to help establish chromatin and regulatory domains in the human genome. The provisioning of insulators by MIRs across the human genome suggests a specific mechanism by which TE sequences can be used to modulate gene regulatory networks. [ABSTRACT FROM AUTHOR]

The DEAD-box RNA helicase DDX3 is a multifunctional protein involved in all aspects of RNA metabolism, including transcription, splicing, mRNA nuclear export, translation, RNA decay and ribosome biogenesis. In addition, DDX3 is also implicated in cell cycle regulation, apoptosis, Wnt-ß-catenin signaling, tumorigenesis, and viral infection. Notably, recent studies suggest that DDX3 is a component of anti-viral innate immune signaling pathways. Indeed, DDX3 contributes to enhance the induction of anti-viral mediators, interferon (IFN) regulatory factor 3 and type I IFN.However, DDX3 seems to be an important target for several viruses, such as human immunodeficiency virus type 1 (HIV-1), hepatitis C virus (HCV), hepatitis B virus (HBV), and poxvirus. DDX3 interacts with HIV-1 Rev or HCV Core protein and modulates its function. At least, DDX3 is required for both HIV-1 and HCV replication. Therefore, DDX3 could be a novel therapeutic target for the development of drug against HIV-1 and HCV. [ABSTRACT FROM AUTHOR]

Recent analyses suggest that transposable element-derived transcripts are processed to yield a variety of small RNA species that play critical functional roles in gene regulation and chromatin organization as well as genome stability and maintenance. Here we report a mass spectrometry analysis of an RNA-affinity complex isolation using a piRNA homologous sequence derived from Alu retrotransposal RNA. Our data point to potential roles for piALU RNAs in DNA repair, cell cycle and chromatin regulations. [ABSTRACT FROM AUTHOR]

Multiple enzymatic activities are required for transcriptional initiation. The enzyme DNA topoisomerase II associates with gene promoter regions and can generate breaks in double-stranded DNA (dsDNA). Therefore, it is of interest to know whether this enzyme is critical for regulated gene activation. We report that the signal-dependent activation of gene transcription by nuclear receptors and other classes of DNA binding transcription factors, including activating protein 1, requires DNA topoisomerase IIβ-dependent, transient, site-specific dsDNA break formation. Subsequent to the break, poly(adenosine diphosphate-ribose) polymerase-1 enzymatic activity is induced, which is required for a nucleosome-specific histone H1-high-mobility group B exchange event and for Local changes of chromatin architecture. Our data mechanistically rink DNA topoisomerase IIβ-dependent dsDNA breaks and the components of the DNA damage and repair machinery in regulated gene transcription. [ABSTRACT FROM AUTHOR]

Human adipose-derived mesenchymal stem (stromal) cells (hADSC) represent an attractive source of the cells for numerous therapeutic applications in regenerative medicine. These cells are also an efficient model to study biological pathways of stem cell action, tissue injury and disease. Like any other primary somatic cells in culture, industrial-scale expansion of mesenchymal stromal cells (MSC) leads to the replicative exhaustion/senescence as defined by the "Hayflick limit." The senescence is not only greatly effecting in vivo potency of the stem cell cultures but also might be the cause and the source of clinical inconsistency arising from infused cell preparations. In this light, the characterization of hADSC replicative and stressor-induced senescence phenotypes is of great interest.This chapter summarizes some of the essential protocols and assays used at our laboratories and clinic for the human fat procurement, isolation, culture, differentiation, and characterization of mesenchymal stem cells from adipose tissue and the stromal vascular fraction. Additionally, we provide manuals for characterization of hADSC senescence in a culture based on stem cells immunophenotype, proliferation rate, migration potential, and numerous other well-accepted markers of cellular senescence. Such methodological framework will be immensely helpful to design standards and surrogate measures for hADSC-based therapeutic applications.

Emerging evidence is shedding light on a large and complex network of epigenetic modifications at play in human stem cells. This "epigenetic landscape" governs the fine-tuning and precision of gene expression programs that define the molecular basis of stem cell pluripotency, differentiation and reprogramming. This review will focus on recent progress in our understanding of the processes that govern this landscape in stem cells, such as histone modification, DNA methylation, alterations of chromatin structure due to chromatin remodeling and non-coding RNA activity. Further investigation into stem cell epigenetics promises to provide novel advances in the diagnosis and treatment of a wide array of human diseases.