Development of a New Model System to Study Long-Distance Interactions Supported by Architectural Proteins.

Chromatin architecture is critical for the temporal and tissue-specific activation of genes that determine eukaryotic development. The functional interaction between enhancers and promoters is controlled by insulators and tethering elements that support specific long-distance interactions. However, the mechanisms of the formation and maintenance of long-range interactions between genome regulatory elements remain poorly understood, primarily due to the lack of convenient model systems. Drosophila became the first model organism in which architectural proteins that determine the activity of insulators were described. In Drosophila, one of the best-studied DNA-binding architectural proteins, Su(Hw), forms a complex with Mod(mdg4)-67.2 and CP190 proteins. Using a combination of CRISPR/Cas9 genome editing and attP-dependent integration technologies, we created a model system in which the promoters and enhancers of two reporter genes are separated by 28 kb. In this case, enhancers effectively stimulate reporter gene promoters in cis and trans only in the presence of artificial Su(Hw) binding sites (SBS), in both constructs. The expression of the mutant Su(Hw) protein, which cannot interact with CP190, and the mutation inactivating Mod(mdg4)-67.2, lead to the complete loss or significant weakening of enhancer-promoter interactions, respectively. The results indicate that the new model system effectively identifies the role of individual subunits of architectural protein complexes in forming and maintaining specific long-distance interactions in the D. melanogaster model.

Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids.

In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

Boundary bypass activity in the abdominal-B region of the Drosophila bithorax complex is position dependent and regulated.

Expression of Abdominal-B (Abd-B) in abdominal segments A5-A8 is controlled by four regulatory domains, iab-5-iab-8. Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements (Mcp, Fab-7, Fab-7 and Fab-8). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can 'jump over' intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation.

Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems.

In higher eukaryotes, the regulation of developmental gene expression is determined by enhancers, which are often located at a large distance from the promoters they regulate. Therefore, the architecture of chromosomes and the mechanisms that determine the functional interaction between enhancers and promoters are of decisive importance in the development of organisms. Mammals and the model animal Drosophila have homologous key architectural proteins and similar mechanisms in the organization of chromosome architecture. This review describes the current progress in understanding the mechanisms of the formation and regulation of long-range interactions between enhancers and promoters at three well-studied key regulatory loci in Drosophila.

Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila.

The spatial organization of chromosomes is involved in regulating the majority of intranuclear processes in higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play a key role in regulation of gene expression in mammals. According to modern views, a cohesin complex mostly determines the architecture of mammalian chromosomes by forming chromatin loops on anchors created by the CTCF DNA-binding architectural protein. The role of the cohesin complex in chromosome architecture is poorly understood in Drosophila, and CTCF is merely one of many Drosophila architectural proteins with a proven potential to organize specific long-range interactions between regulatory elements in the genome. The review compares the mechanisms responsible for long-range interactions and chromosome architecture between mammals and Drosophila.

Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes.

In higher eukaryotes, enhancers determine the activation of developmental gene transcription in specific cell types and stages of embryogenesis. Enhancers transform the signals produced by various transcription factors within a given cell, activating the transcription of the targeted genes. Often, developmental genes can be associated with dozens of enhancers, some of which are located at large distances from the promoters that they regulate. Currently, the mechanisms underlying specific distance interactions between enhancers and promoters remain poorly understood. This review briefly describes the properties of enhancers and discusses the mechanisms of distance interactions and potential proteins involved in this process.

Involvement of top-down networks in the perception of facial emotions: A magnetoencephalographic investigation.

Conscious perception of the emotional valence of faces has been proposed to involve top-down and bottom-up information processing. Yet, the underlying neuronal mechanisms of these two processes and the implementation of their cooperation is still unclear. According to the global workspace model, higher level cognitive processing of visual emotional stimuli relies on both bottom-up and top-down processing. Using masking stimuli in a visual backward masking paradigm with delays at the perceptual threshold, at which stimuli can only partly be detected, suggests that only top-down processing differs between correctly and incorrectly perceived stimuli, while bottom-up visual processing is not compromised and comparable for both conditions. Providing visual stimulation near the perceptual threshold in the backward masking paradigm thus enabled us to compare differences in top-down modulation of the visual information of correctly and incorrectly recognized facial emotions in 12 healthy individuals using magnetoencephalography (MEG). For correctly recognized facial emotions, we found a right-hemispheric fronto-parietal network oscillating in the high-beta and low-gamma band and exerting top-down control as determined by the causality measure of phase slope index (PSI). In contrast, incorrect recognition was associated with enhanced coupling in the gamma band between left frontal and right parietal regions. Our results indicate that the perception of emotional face stimuli relies on the right-hemispheric dominance of synchronized fronto-parietal gamma-band activity.

Mapping the D.melanogaster En1A Enhancer Modules Responsible for Transcription Activation and Long-Distance Enhancer-Promoter Interactions.

The structure of the new enhancer En1A of the 1A region of the X chromosome of D. melanogaster was investigated. Two distinct regulatory elements were found. The first element is responsible for transcription activation, and the second element provides specific interaction with the promoter of the yellow gene. The findings support the hypothesis of a modular structure for enhancers, including certain sequences that bind transcription activators and special communication elements providing long-distance enhancer-promoter interaction.

Data collection and advanced statistical analysis in phytotoxic activity of aerial parts exudates of Salvia spp

In order to define the phytotoxic potential of Salvia species a database was developed for fast and efficient data collection in screening studies of the inhibitory activity of Salvia exudates on the germination of Papaver rhoeas L. and Avena sativa L.. The structure of the database is associated with the use of algorithms for calculating the usual germination indices reported in the literature, plus the newly defined indices (Weighted Average Damage, Differential Weighted Average Damage, Germination Weighted Average Velocity) and other variables usually recorded in experiments of phytotoxicity (LC50, LC90). Furthermore, other algorithms were designed to calculate the one-way ANOVA followed by Duncan's multiple range test to highlight automatically significant differences between the species. The database model was designed in order to be suitable also for the development of further analysis based on the artificial neural network approach, using Self-Organising Maps (SOM).