Silent State Research Articles

Foreground and Background in Mental Models.

Foreground and Background in Mental Models.

Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability

The ETV6-RUNX1 onco-fusion arises in utero, initiating a clinically silent pre-leukemic state associated with the development of pediatric B-acute lymphoblastic leukemia (B-ALL). We characterize the ETV6-RUNX1 regulome by integrating chromatin immunoprecipitation- and RNA-sequencing and show that ETV6-RUNX1 functions primarily through competition for RUNX1 binding sites and transcriptional repression. In pre-leukemia, this results in ETV6-RUNX1 antagonization of cell cycle regulation by RUNX1 as evidenced by mass cytometry analysis of B-lineage cells derived from ETV6-RUNX1 knock-in human pluripotent stem cells. In frank leukemia, knockdown of RUNX1 or its co-factor CBFβ results in cell death suggesting sustained requirement for RUNX1 activity which is recapitulated by chemical perturbation using an allosteric CBFβ-inhibitor. Strikingly, we show that RUNX1 addiction extends to other genetic subtypes of pediatric B-ALL and also adult disease. Importantly, inhibition of RUNX1 activity spares normal hematopoiesis. Our results suggest that chemical intervention in the RUNX1 program may provide a therapeutic opportunity in ALL.

A Human iPSC Model Reveals Specific Upregulation of Linker Histone H1-0 in ETV6::RUNX1+ Preleukemia and B Cell Precursor Acute Lymphoblastic Leukemia

The ETV6::RUNX1 translocation is the most common chromosomal rearrangement associated with pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). As previously shown, ETV6::RUNX1 leads to a distinct clinically silent preleukemic state in utero that manifests in impaired early B cell differentiation. Acquisition of secondary oncogenic mutations gives rise to overt leukemia in 0.2% of children carrying ETV6::RUNX1. In-depth characterization of ETV6::RUNX1+ preleukemia is essential to gain an understanding of leukemic transformation and develop preventive strategies. Here, we identify dysregulation of the epigenetic regulator H1-0 in ETV6::RUNX1+ preleukemia and BCP-ALL. Utilizing CRISPR/Cas9 genome editing, we generated monoclonal ETV6::RUNX1+ human induced pluripotent stem cell (hiPSC) lines with stable ETV6::RUNX1 expression driven by the endogenous ETV6 promoter. To assess the preleukemic setting mediated by ETV6::RUNX1, we performed RNA sequencing (RNA-seq) analysis of ETV6::RUNX1+ and matching wild-type (WT) hiPSCs of two donors. We identified 20 differentially expressed genes in ETV6::RUNX1+ hiPSCs of both donors compared to the respective WT hiPSCs (up: 15, down: 5, absolute fold change ≥ 2, p ≤ 0.05). Interestingly, our RNA-seq analysis revealed consistent upregulation of H1-0 (mean: 2.43-fold), a linker histone involved in chromatin remodeling, cell proliferation and differentiation. Elevated H1-0 levels in the ETV6::RUNX1+ hiPSC lines were confirmed by quantitative real-time PCR and immunoblot (Figure 1A). To determine H1-0 levels in ETV6::RUNX1+ B cell precursors, we analyzed published gene expression microarray and RNA-seq data sets. Both ETV6::RUNX1+ CD34+ cells (n = 10) derived from umbilical cord blood (Polak et al. Haematologica 2019) and ETV6::RUNX1+ CD34+CD19+ cells (n = 4) generated by hematopoietic differentiation of hiPSCs (Böiers et al. Developmental Cell 2018) showed significant upregulation of H1-0 compared to the respective control cells lacking ETV6::RUNX1 (unpaired t-test, p = 0.0087 and p = 0.0076, respectively). Additionally, we differentiated ETV6::RUNX1+ and WT hiPSCs into CD34+CD45+ hematopoietic progenitor cells and performed single-cell RNA-seq analysis. We identified coexpression of H1-0 with cyclin-dependent kinase inhibitor genes CDKN1A and CDKN1B, indicating a slow or non-cycling phenotype of H1-0+ cells. Next, we examined H1-0 mRNA levels in gene expression data sets of pediatric and adult leukemia patients (St. Jude PeCan database (n = 876), Jerchel et al. Haematologica 2018 (n = 654), MILE study (n = 1299)). H1-0 expression was found to be significantly elevated in ETV6::RUNX1+ BCP-ALL patient samples compared to other leukemia entities, especially TCF3::PBX1+ ALL (ordinary one-way ANOVA, p ≤ 0.0001), KMT2A rearranged ALL (p ≤ 0.0001) and chronic lymphoblastic leukemia (CLL, p ≤ 0.0001). Strikingly, H1-0 expression was 22.37-fold lower in CLL compared to ETV6::RUNX1+ BCP-ALL (Figure 1B). This observation prompted us to investigate H1-0 expression in B cell developmental stages using published data sets. Interestingly, we found that H1-0 levels decrease during early B cell development in both normal bone marrow (Black et al. Nucleic Acids Research 2018) and umbilical cord blood-derived cells (Novershtern et al. Cell 2011). Additionally, analysis of single-cell RNA-seq data of early B cell precursors derived from healthy bone marrow (Mehtonen et al. Genome Medicine 2020) and fetal liver (Developmental Cell Atlas Newcastle University) revealed that relative numbers of H1-0 expressing cells per differentiation state decreased along the pseudotime B cell development trajectory. Taken together, our study identifies H1-0 upregulation as a specific alteration present already at the ETV6::RUNX1+ preleukemic state. High H1-0 expression was associated with slower proliferation and increased stemness. This phenotype might explain the persistence of in utero generated preleukemic ETV6::RUNX1+ clones residing in the bone marrow of approximately 5% of healthy children for years. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Diptoindonesin G is a middle domain HSP90 modulator for cancer treatment

HSP90 inhibitors can target many oncoproteins simultaneously, but none have made it through clinical trials due to dose-limiting toxicity and induction of heat shock response, leading to clinical resistance. We identified diptoindonesin G (dip G) as an HSP90 modulator that can promote degradation of HSP90 clients by binding to the middle domain of HSP90 (Kd= 0.13± 0.02μM) without inducing heat shock response. This is likely because dip G does not interfere with the HSP90-HSF1 interaction like N-terminal inhibitors, maintaining HSF1 in a transcriptionally silent state. We found that binding of dip G to HSP90 promotes degradation of HSP90 client protein estrogen receptor α (ER), a major oncogenic driver protein in most breast cancers. Mutations in the ER ligand-binding domain (LBD) are an established mechanism of endocrine resistance and decrease the binding affinity of mainstay endocrine therapies targeting ER, reducing their ability to promote ER degradation or transcriptionally silence ER. Because dip G binds to HSP90 and does not bind to the LBD of ER, unlike endocrine therapies, it is insensitive to ER LBD mutations that drive endocrine resistance. Additionally, we determined that dip G promoted degradation of WT and mutant ER with similar efficacy, downregulated ER- andmutant ER-regulated gene expression, and inhibited WT and mutant cell proliferation. Our data suggest that dip G is not only a molecular probe to study HSP90 biology and the HSP90 conformation cycle, but also a new therapeutic avenue for various cancers, particularly endocrine-resistant breast cancer harboring ER LBD mutations.

Sleep and wake in a model of the thalamocortical system with Martinotti cells.

The mechanisms leading to the alternation between active (UP) and silent (DOWN) states during sleep slow waves (SWs) remain poorly understood. Previous models have explained the transition to the DOWN state by a progressive failure of excitation because of the build-up of adaptation currents or synaptic depression. However, these models are at odds with recent studies suggesting a role for presynaptic inhibition by Martinotti cells (MaCs) in generating SWs. Here, we update a classical large-scale model of sleep SWs to include MaCs and propose a different mechanism for the generation of SWs. In the wake mode, the network exhibits irregular and selective activity with low firing rates (FRs). Following an increase in the strength of background inputs and a modulation of synaptic strength and potassium leak potential mimicking the reduced effect of acetylcholine during sleep, the network enters a sleep-like regime in which local increases of network activity trigger bursts of MaC activity, resulting in strong disfacilitation of the local network via presynaptic GABAB1a -type inhibition. This model replicates findings on slow wave activity (SWA) during sleep that challenge previous models, including low and skewed FRs that are comparable between the wake and sleep modes, higher synchrony of transitions to DOWN states than to UP states, the possibility of triggering SWs by optogenetic stimulation of MaCs, and the local dependence of SWA on synaptic strength. Overall, this work points to a role for presynaptic inhibition by MaCs in the generation of DOWN states during sleep.

Deterministic and Stochastic Components of Cortical Down States: Dynamics and Modulation.

Slow oscillations are an emergent activity of the cerebral cortex network consisting of alternating periods of activity (Up states) and silence (Down states). Up states are periods of persistent cortical activity that share properties with that of underlying wakefulness. However, the occurrence of Down states is almost invariably associated with unconsciousness, both in animal models and clinical studies. Down states have been attributed relevant functions, such as being a resetting mechanism or breaking causal interactions between cortical areas. But what do Down states consist of? Here, we explored in detail the network dynamics (e.g., synchronization and phase) during these silent periods in vivo (male mice), in vitro (ferrets, either sex), and in silico, investigating various experimental conditions that modulate them: anesthesia levels, excitability (electric fields), and excitation/inhibition balance. We identified metastability as two complementary phases composing such quiescence states: a highly synchronized "deterministic" period followed by a low-synchronization "stochastic" period. The balance between these two phases determines the dynamical properties of the resulting rhythm, as well as the responsiveness to incoming inputs or refractoriness. We propose detailed Up and Down state cycle dynamics that bridge cortical properties emerging at the mesoscale with their underlying mechanisms at the microscale, providing a key to understanding unconscious states.SIGNIFICANCE STATEMENT The cerebral cortex expresses slow oscillations consisting of Up (active) and Down (silent) states. Such activity emerges not only in slow wave sleep, but also under anesthesia and in brain lesions. Down states functionally disconnect the network, and are associated with unconsciousness. Based on a large collection of data, novel data analysis approaches and computational modeling, we thoroughly investigate the nature of Down states. We identify two phases: a highly synchronized "deterministic" period, followed by a low-synchronization "stochastic" period. The balance between these two phases determines the dynamic properties of the resulting rhythm and responsiveness to incoming inputs. This finding reconciles different theories of slow rhythm generation and provides clues about how the brain switches from conscious to unconscious brain states.

The Relevance of Non-verbal Communication in the Covid’19 Nigerian Environment

Human beings, in their various environments, communicate their ideas, feelings, and life experiences through verbal or non-verbal means. The way people speak, move their bodies, gesticulate, and handle spatial relationships are important to all kinds of interpersonal communication. In most non-verbal communication situations, as experienced in the Nigerian environment during the Covid'19 pandemic, we observed that interlocutors, even in their silent states, use nonlinguistic forms to communicate meanings (through space and body language). This paper examined the imperatives of space and body language during the Covid'19 era. Much of what has occupied the interest of scholarship has been verbal (speaking and writing) rather than non-verbal communication. But the Covid'19 challenges have opened a fresh vista of attention to the other modes of communicating messages to a target audience. This paper wondered how easy and possible it was to employ appropriate multi-modal media of information dissemination targeted at controlling the ugly situation, saving the lives of people, and achieving fidelity of desired action in such a multilingual/cultural environment as Nigeria. This triggered the researchers' selection and evaluation of some of the communications made through space (proxemics), body language (kinesics), and other non-verbal symbolic modes, their imperatives, and challenges during this period. The analysis was anchored on the multimodal theory of discourse which is an approach that takes into account multiple modes of communication and how they interact with one another to produce meaning. The study is qualitative in nature and allows the interpretation of data according to the context of use. It is hoped that the findings of the paper shall not only expose the important place of non-verbal communication but will also add to the corpus of knowledge concerning the dynamics of human communication in general.

Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control.

Transcriptional silencing through the Polycomb silencing machinery utilizes a "read-write" mechanism involving histone tail modifications. However, nucleation of silencing and long-term stable transmission of the silenced state also requires P-olycomb Repressive Complex 2 (PRC2) accessory proteins, whose molecular role is poorly understood. The Arabidopsis VEL proteins are accessory proteins that interact with PRC2 to nucleate and propagate silencing at the FLOWERING LOCUS C (FLC) locus, enabling early flowering in spring. Here, we report that VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. Plant VEL proteins thus facilitate assembly of dynamic multivalent Polycomb complexes required for inheritance of the silenced state.

Neuromorphic quantum computing.

Quantum computation builds on the use of correlations. Correlations could also play a central role for artificial intelligence, neuromorphic computing or "biological computing." As a step toward a systematic exploration of "correlated computing" we demonstrate that neuromorphic computing can perform quantum operations. Spiking neurons in the active or silent states are connected to the two states of Ising spins. A quantum density matrix is constructed from the expectation values and correlations of the Ising spins. We show for a two qubit system that quantum gates can be learned as a change of parameters for neural network dynamics. These changes respect restrictions which ensure the quantum correlations. Our proposal for probabilistic computing goes beyond Markov chains and is not based on transition probabilities. Constraints on classical probability distributions relate changes made in one part of the system to other parts, similar to entangled quantum systems.

The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells.

Neurons critically depend on regulated RNA localization and tight control of spatio-temporal gene expression to maintain their morphological and functional integrity. Mutations in the kinesin motor protein gene KIF1C cause Hereditary Spastic Paraplegia, an autosomal recessive disease leading to predominant degeneration of the long axons of central motoneurons. In this study we aimed to gain insight into the molecular function of KIF1C and understand how KIF1C dysfunction contributes to motoneuron degeneration. We used affinity proteomics in neuronally differentiated neuroblastoma cells (SH-SY5Y) to identify the protein complex associated with KIF1C in neuronal cells; candidate interactions were then validated by immunoprecipitation and mislocalization of putative KIF1C cargoes was studied by immunostainings. We found KIF1C to interact with all core components of the exon junction complex (EJC); expression of mutant KIF1C in neuronal cells leads to loss of the typical localization distally in neurites. Instead, EJC core components accumulate in the pericentrosomal region, here co-localizing with mutant KIF1C. These findings suggest KIF1C as a neuronal transporter of the EJC. Interestingly, the binding of KIF1C to the EJC is RNA-mediated, as treatment with RNAse prior to immunoprecipitation almost completely abolishes the interaction. Silica-based solid-phase extraction of UV-crosslinked RNA-protein complexes furthermore supports direct interaction of KIF1C with RNA, as recently also demonstrated for kinesin heavy chain. Taken together, our findings are consistent with a model where KIF1C transports mRNA in an EJC-bound and therefore transcriptionally silenced state along neurites, thus providing the missing link between the EJC and mRNA localization in neurons.

New HATNA(CN)6 ligand in the design of dianion magnetic assemblies with lanthanides {Cryptand(K+)}2{HATNA(CN)6·3LnIII(TMHD)3}2− (Ln = Gd, Tb and Dy)

Hexaazatrinaphthylenehexacarbonitrile ligand, HATNA(CN)6, when reduced to dianion state, forms crystalline {Cryptand[2.2.2](K+)}2{HATNA(CN)6}2−·2C6H4Cl2 (1) salt whose structure, optical and magnetic properties are studied. The HATNA(CN)6}2− dianions absorb light in the whole visible and a wide NIR range from 900 up to 2200 nm and have singlet EPR silent ground state. The dianions form trinuclear {Cryptand[2.2.2](K+)}2{HATNA(CN)6·3LnIII(TMHD)3}2−·3C6H5CH3 complexes where Ln is Gd (2), Tb (3) and Dy (4), and TMHD is 2,2,6,6-tetramethyl-3,5-heptanedionate. The {HATNA(CN)6}2− dianions are strongly distorted in coordination assemblies and have the length of the La-N{HATNA(CN)6} bonds of 2.58–2.66 Å. Dianions preserve low-energy absorption at the coordination of three metal complexes with maxima of the bands at 1440–1460 nm. DFT calculations support strong acceptor properties of HATNA(CN)6 and the non-degenerated LUMO for this ligand. As a result, dianions have singlet ground state whereas triplet state is positioned higher by 139 meV only (1620 K) and is thermally unattainable at 300 K. Coordination of the lanthanide complexes increases the singlet–triplet gap up to 210 meV (2440 K). Complexes 2–4 show weak antiferromagnetic coupling between high-spin lanthanide ions. J value estimated by PHI program for the gadolinium-complex is close to zero. Among 2–4 only gadolinium-containing complex 2 manifests an EPR signal with a complicated structure which can be approximated with D = 0.19 and E = 0.02 cm−1.

Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells.

Much has been learned about the mechanisms of action of pluripotency factors Oct4 and Sox2. However, as with other regulators of cell identity, little is known about the impact of disrupting their binding motifs in a native environment or the characteristics of genes they regulate. By quantitatively examining dynamic ranges of gene expression instead of focusing on conventional measures of differential expression, we found that Oct4 and Sox2 enhancer binding is strongly enriched near genes subject to large dynamic ranges of expression among cell types, with binding sites near these genes usually within superenhancers. Mutagenesis of representative Oct4:Sox2 motifs near such active, dynamically regulated genes revealed critical roles in transcriptional activation during reprogramming, with more limited roles in transcriptional maintenance in the pluripotent state. Furthermore, representative motifs near silent genes were critical for establishing but not maintaining the fully silent state, while genes whose transcript levels varied by smaller magnitudes among cell types were unaffected by nearby Oct4:Sox2 motifs. These results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation during mammalian development, but are less important than expected for maintaining transcriptional states.

Energy-efficient and intelligent cooperative spectrum sensing algorithm in cognitive radio networks

Green communication is the demand of current and future wireless communication. As the next-generation communication network, cognitive radio network also needs to meet the requirements of green communication. Therefore, improving energy efficiency is an inevitable requirement for the development of cognitive radio networks. However, there is a need to compromise sensing performance while improving energy efficiency. To take into account the two important indicators of sensing performance and energy efficiency, a grouping algorithm is proposed in this article, which can effectively improve the energy efficiency while improving the spectrum sensing performance. The algorithm obtains the initial value of the reliability of the nodes through training, and sorts them according to the highest reliability value, then selects an even number of nodes with the highest reliability value, and divides the selected nodes into two groups, and the two groups of nodes take turns in Alternate work. At this time, other nodes not participating in cooperative spectrum sensing are in a silent state, waiting for the instruction of the fusion center. The experimental results show that compared with the traditional algorithm, the proposed algorithm has a great improvement in the two indicators of sensing performance and energy efficiency.

Distinct silencer states generate epigenetic states of heterochromatin

Heterochromatic loci can exhibit different transcriptional states in genetically identical cells. A popular model posits that the inheritance of modified histones is sufficient for inheritance of the silenced state. However, silencing inheritance requires silencers and therefore cannot be driven by the inheritance of modified histones alone. To address these observations, we determined the chromatin architectures produced by strong and weak silencers in Saccharomyces. Strong silencers recruited Sir proteins and silenced the locus in all cells. Strikingly, weakening these silencers reduced Sir protein recruitment and stably silenced the locus in some cells; however, this silenced state could probabilistically convert to an expressed state that lacked Sir protein recruitment. Additionally, changes in the constellation of silencer-bound proteins or the concentration of a structural Sir protein modulated the probability that a locus exhibited the silenced or expressed state. These findings argued that distinct silencer states generate epigenetic states and regulate their dynamics.

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.

Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.

Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus.

Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.

Effects of Soundscape on Flow State during Diabolo Exercise.

“Soundscape” is defined as “an acoustic environment as perceived or experienced and/or understood by a person or people, in context.” The research focuses on the physical properties of sound, paying attention to the relationship between the soundscape and people. Sports provide a comprehensive context, including the athletes, their behavior, the environment, spectators, and other elements. Soundscape in sports has many important functions, such as indicating the movement process, promoting positive emotions, and enhancing the entertainment atmosphere. It is also related to the physical and mental health of people who are exercising. As a technical sport with multidimensional soundscape qualities, diabolo is very popular among older adults in China due to its easy portability and operation. In order to explore the influence mechanism of the soundscape on the mental health of older players and better guide the shaping of soundscapes at sports venues, this paper focuses on soundscape perception and proposes a two-channel (direct and indirect) model of the influence of the diabolo soundscape on the psychological perception of older players. At the same time, we introduce the flow state as an indicator to evaluate mental health, and use the Short Flow State Scale (SFSS) to measure the flow state. By setting up a control experiment using the diabolo with and without sound and using the two-channel (direct and indirect) influence model to compare the differences in flow state scores under the two states, we analyzed the influence mechanism of the diabolo soundscape on the flow state of elderly groups. The results show that the scores of various flow state dimensions and total flow scores in the silent state of diabolo exercise are significantly lower than those in the sound state (p < 0.05 and p < 0.001), and the main differences are in the three dimensions of unambiguous feedback, sense of control, and autotelic experience. The two-channel influence model can effectively explain the differences in older adults’ flow state, which provides a new comprehensive perspective to study the effect of the soundscape in sports on people’s mental health.

Imaging translational control by Argonaute with single-molecule resolution in live cells

A major challenge to our understanding of translational control has been deconvolving the individual impact specific regulatory factors have on the complex dynamics of mRNA translation. MicroRNAs (miRNAs), for example, guide Argonaute and associated proteins to target mRNAs, where they direct gene silencing in multiple ways that are not well understood. To better deconvolve these dynamics, we have developed technology to directly visualize and quantify the impact of human Argonaute2 (Ago2) on the translation and subcellular localization of individual reporter mRNAs in living cells. We show that our combined translation and Ago2 tethering sensor reflects endogenous miRNA-mediated gene silencing. Using the sensor, we find that Ago2 association leads to progressive silencing of translation at individual mRNA. Silencing was occasionally interrupted by brief bursts of translational activity and took 3–4 times longer than a single round of translation, consistent with a gradual increase in the inhibition of translation initiation. At later time points, Ago2-tethered mRNAs cluster and coalesce with P-bodies, where a translationally silent state is maintained. These results provide a framework for exploring miRNA-mediated gene regulation in live cells at the single-molecule level. Furthermore, our tethering-based, single-molecule reporter system will likely have wide-ranging application in studying RNA-protein interactions.

Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins.

The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycombrepressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.

The Influence of Sustained Mercury Exposure on Prothrombin Time and Partial Thromboplastin Time among Sudanese Gold Mining Workers

Background: Gold mining is the world's leading source of anthropogenic mercury pollution, negatively impacting not only miners but also the surrounding inhabitants; it has many effects on human health, especially cardiovascular problems, which lead to coagulation disorders and an increase in morbidity and mortality rate. The present study aimed to determine the prothrombin time (PT) and partial thromboplastin time (PTT) among Sudanese gold mining workers exposed to mercury. Methods and Results: This cross-sectional study was carried out among mining workers in the Red Sea state. A total of 50 mining workers were enrolled in the case group, and 50 non-mining apparently healthy subjects were the control group. About 5 ml of whole blood samples were collected in 3.2% sodium citrate blood collection tubes. Platelet poor plasma (PPP) for prothrombin time (PT) and partial thromboplastin time (PTT) measurements was obtained by using high-speed centrifugation. PT and PTT tests were performed using a standard method (Practical-Haemostasis.com.) with a Helena C2 coagulometer (Germany) and reagents manufactured by the Bio-med trademark (China). The mean age of miners was 33.5±11.5 years and occupation time - 1.94±2.1 years. The mean value of PTT was greater in the case group than in the control group (42.43±6.18 sec vs. 37.76±5.33 sec, P=0.000). In the age subgroup &lt;40 years, the PT level was longer than in the age subgroup &gt;40 years: 14.04±1.38 sec vs. 13.15±1.35 sec (P=0.045), respectively. The correlation analysis revealed a significant, direct correlation between PTT and occupation time (r=0.357, P=0.011). Conclusion: Prolonged coagulation time, notably PTT, has been revealed among mining workers, implying that these workers may have a clinically silent state of coagulation abnormalities.