Distinct Mechanisms for Induction and Tolerance Regulate the Immediate Early Genes Encoding Interleukin 1β and Tumor Necrosis Factor α

Interleukin-1β and Tumor Necrosis Factor α play related, but distinct, roles in immunity and disease. Our study revealed major mechanistic distinctions in the Toll-like receptor (TLR) signaling-dependent induction for the rapidly expressed genes (IL1B and TNF) coding for these two cytokines. Prior to induction, TNF exhibited pre-bound TATA Binding Protein (TBP) and paused RNA Polymerase II (Pol II), hallmarks of poised immediate-early (IE) genes. In contrast, unstimulated IL1B displayed very low levels of both TBP and paused Pol II, requiring the lineage-specific Spi-1/PU.1 (Spi1) transcription factor as an anchor for induction-dependent interaction with two TLR-activated transcription factors, C/EBPβ and NF-κB. Activation and DNA binding of these two pre-expressed factors resulted in de novo recruitment of TBP and Pol II to IL1B in concert with a permissive state for elongation mediated by the recruitment of elongation factor P-TEFb. This Spi1-dependent mechanism for IL1B transcription, which is unique for a rapidly-induced/poised IE gene, was more dependent upon P-TEFb than was the case for the TNF gene. Furthermore, the dependence on phosphoinositide 3-kinase for P-TEFb recruitment to IL1B paralleled a greater sensitivity to the metabolic state of the cell and a lower sensitivity to the phenomenon of endotoxin tolerance than was evident for TNF. Such differences in induction mechanisms argue against the prevailing paradigm that all IE genes possess paused Pol II and may further delineate the specific roles played by each of these rapidly expressed immune modulators. © 2013 Adamik et al

The RNA Helicase Rm62 Cooperates with SU(VAR)3-9 to Re-Silence Active Transcription in Drosophila melanogaster

Gene expression is highly dynamic and many genes show a wide range in expression over several orders of magnitude. This regulation is often mediated by sequence specific transcription factors. In addition, the tight packaging of DNA into chromatin can provide an additional layer of control resulting in a dynamic range of gene expression covering several orders of magnitude. During transcriptional activation, chromatin barriers have to be eliminated to allow an efficient progression of the RNA polymerase. This repressive chromatin structure has to be re-established quickly after it has been activated in order to tightly regulate gene activity. We show that the DExD/H box containing RNA helicase Rm62 is targeted to a site of rapid induction of transcription where it is responsible for an increased degree of methylation at H3K9 at the heat shock locus after removal of the heat shock stimulus. The RNA helicase interacts with the well-characterized histone methyltransferase SU(VAR)3-9 via its N-terminus, which provides a potential mechanism for the targeting of H3K9 methylation to highly regulated genes. The recruitment of SU(VAR)3-9 through interaction with a RNA helicase to a site of active transcription might be a general mechanism that allows an efficient silencing of highly regulated genes thereby enabling a cell to fine tune its gene activity over a wide range

Stress-Induced PARP Activation Mediates Recruitment of Drosophila Mi-2 to Promote Heat Shock Gene Expression

Eukaryotic cells respond to genomic and environmental stresses, such as DNA damage and heat shock (HS), with the synthesis of poly-[ADP-ribose] (PAR) at specific chromatin regions, such as DNA breaks or HS genes, by PAR polymerases (PARP). Little is known about the role of this modification during cellular stress responses. We show here that the nucleosome remodeler dMi-2 is recruited to active HS genes in a PARP–dependent manner. dMi-2 binds PAR suggesting that this physical interaction is important for recruitment. Indeed, a dMi-2 mutant unable to bind PAR does not localise to active HS loci in vivo. We have identified several dMi-2 regions which bind PAR independently in vitro, including the chromodomains and regions near the N-terminus containing motifs rich in K and R residues. Moreover, upon HS gene activation, dMi-2 associates with nascent HS gene transcripts, and its catalytic activity is required for efficient transcription and co-transcriptional RNA processing. RNA and PAR compete for dMi-2 binding in vitro, suggesting a two step process for dMi-2 association with active HS genes: initial recruitment to the locus via PAR interaction, followed by binding to nascent RNA transcripts. We suggest that stress-induced chromatin PARylation serves to rapidly attract factors that are required for an efficient and timely transcriptional response

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency

The SWI/SNF BAF chromatin remodeling complex generates a repressive nucleosome structure at the HIV LTR conducive to establishment and maintenance of HIV latency, while PBAF augments HIV transcription

Effects of DNA supercoiling on chromatin architecture

Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo

Consideration of irradiation effect in components design illustration of a way to introduce an environmental effect in the design process

International audienceDuring the last years, a particular attention has been paid to the consideration and evaluation of environmental effects in the design of mechanical components, particularly the consequences of Pressure Water Reactors environment on fatigue damages. In the frame of RCC-MRx design code, developed for Sodium Fast Reactors (SFR), Research Reactors (RR) and Fusion Reactors (FR-ITER), the specific features are creep damage (covered by the design rules responding to the needs of fast breeder reactors and high temperatures) and irradiated material (covered by the design rules responding to the needs of research reactors developed mainly for the JHR project).The purpose of this paper is to detail the way to consider an environmental effect such as irradiation in the material design rules. It covers- the background of these rules, linked with the changes in materials behavior,- their content, in term of damage impact,- and the challenges to be met for their development to other applications

Development of a standard for fusion needs example of introduction of Eurofer in RCC-MRX

International audienceThe 2018 edition of the RCC-MRx Code [1] will be issuedby the end of the 2018, in French and English versions byAFCEN (Association Francaise pour les regles de Conceptionet de Construction des Materiels des Chaudieres Electronucleaires).This Code set up design and construction rules ofresearch reactor components (coming from the RCC-MX 2008code developed within the context of the Jules HorowitzReactor project), and to components operating at hightemperature and to the Vacuum Vessel of ITER (coming fromthe RCC-MR 2007).The extension of the scope of the code to innovativesystems such as fusion reactors leads to revisit the backgroundof the code to define the requirements to introduce a newprocess or a new material.The developed methodology has been applied to theintroduction of the Fe9%Cr1%WTaV steel (Eurofer), todayin the Probationary Phase Rules of RCC-MRx. It was the firsttime to introduce a new material into the code, new in thesense of non-existing in any current standardization. Thisprocess, still in progress, highlights the need to have aminimum of information on the expectation of the coderegarding the material data.This paper describes the different steps of the introductionof the Eurofer in the RCC-MRx code as well as the toolsdeveloped to facilitate the process

Assessing participation in a community-based health planning and services programme in Ghana

Background Community participation is increasingly seen as a pre-requisite for successful health service uptake. It is notoriously difficult to assess participation and little has been done to advance tools for the assessment of community participation. In this paper we illustrate an approach that combines a 'social psychology of participation' (theory) with 'spider-grams' (method) to assess participation and apply it to a Community-based Health Planning and Services (CHPS) programme in rural Ghana. Methods We draw on data from 17 individual in-depth interviews, two focus group discussions and a community conversation with a mix of service users, providers and community health committee members. It was during the community conversation that stakeholders collectively evaluated community participation in the CHPS programme and drew up a spider-gram. Results Thematic analysis of our data shows that participation was sustained through the recognition and use of community resources, CHPS integration with pre-existing community structures, and alignment of CHPS services with community interests. However, male dominance and didactic community leadership and management styles undermined real opportunities for broad-based community empowerment, particularly of women, young people and marginalised men. Conclusion We conclude that combining the 'spider-gram' tool and the 'social psychology of participation' framework provide health professionals with a useful starting point for assessing community participation and developing recommendations for more participatory and empowering health care programmes