The Human Transcription Factors.

Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them. Major classes of human TFs differ markedly in their evolutionary trajectories and expression patterns, underscoring distinct functions. TFs likewise underlie many different aspects of human physiology, disease, and variation, highlighting the importance of continued effort to understand TF-mediated gene regulation.

Systematic analysis of binding of transcription factors to noncoding variants.

Many sequence variants have been linked to complex human traits and diseases1, but deciphering their biological functions remains challenging, as most of them reside in noncoding DNA. Here we have systematically assessed the binding of 270 human transcription factors to 95,886 noncoding variants in the human genome using an ultra-high-throughput multiplex protein-DNA binding assay, termed single-nucleotide polymorphism evaluation by systematic evolution of ligands by exponential enrichment (SNP-SELEX). The resulting 828 million measurements of transcription factor-DNA interactions enable estimation of the relative affinity of these transcription factors to each variant in vitro and evaluation of the current methods to predict the effects of noncoding variants on transcription factor binding. We show that the position weight matrices of most transcription factors lack sufficient predictive power, whereas the support vector machine combined with the gapped k-mer representation show much improved performance, when assessed on results from independent SNP-SELEX experiments involving a new set of 61,020 sequence variants. We report highly predictive models for 94 human transcription factors and demonstrate their utility in genome-wide association studies and understanding of the molecular pathways involved in diverse human traits and diseases.

The interaction landscape between transcription factors and the nucleosome.

Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.

Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences.

RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-throughput RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequences, whereas ∼30% preferred structured motifs folding into stem-loops. We also found that many RBPs can bind to multiple distinctly different motifs. Analysis of the matches of the motifs in human genomic sequences suggested novel roles for many RBPs. We found that three cytoplasmic proteins-ZC3H12A, ZC3H12B, and ZC3H12C-bound to motifs resembling the splice donor sequence, suggesting that these proteins are involved in degradation of cytoplasmic viral and/or unspliced transcripts. Structural analysis revealed that the RNA motif was not bound by the conventional C3H1 RNA-binding domain of ZC3H12B. Instead, the RNA motif was bound by the ZC3H12B's PilT N terminus (PIN) RNase domain, revealing a potential mechanism by which unconventional RBDs containing active sites or molecule-binding pockets could interact with short, structured RNA molecules. Our collection containing 145 high-resolution binding specificity models for 86 RBPs is the largest systematic resource for the analysis of human RBPs and will greatly facilitate future analysis of the various biological roles of this important class of proteins.

High-precision and wide-wavelength range FBG demodulation method based on spectrum correction and data fusion.

Optical fiber sensing technology plays an important role in the application of the sensing layer of the Internet of Things. The core of this technology is the demodulation of the fiber Bragg grating (FBG) sensing system. Since the FBG sensor utilizes the wavelength change to respond to the measured size, it is of great significance to improve the accuracy of the FBG wavelength demodulation. However, the demodulation performance of the current FBG wavelength demodulation method still has much room for improvement in terms of accuracy and stability. To this end, we propose a composite gas cell demodulation scheme based on spectrum correction and data fusion by using differential photodetectors, fitting extrapolation, data fusion methods, etc. The issue of low demodulation accuracy arising due to noise, temperature drift, spectral distortion, etc., was addressed to improve the demodulation performance of the FBG. In the experiment, four FBGs with different center wavelengths were used to verify their demodulation accuracy in the range of 1510-1590 nm. The maximum repeatability error of the FBG wavelength was measured to be 2.51 pm, and the linearity was as high as 99.9% or more; under the working environment of -20 °C to 60 °C, the maximum full-scale error did not exceed ±1.71 pm, which is improved by 54.3% compared with the traditional method.

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.

In some dimeric cases of transcription factor (TF) binding, the specificity of dimeric motifs has been observed to differ notably from what would be expected were the two factors to bind to DNA independently of each other. Current motif discovery methods are unable to learn monomeric and dimeric motifs in modular fashion such that deviations from the expected motif would become explicit and the noise from dimeric occurrences would not corrupt monomeric models. We propose a novel modeling technique and an expectation maximization algorithm, implemented as software tool MODER, for discovering monomeric TF binding motifs and their dimeric combinations. Given training data and seeds for monomeric motifs, the algorithm learns in the same probabilistic framework a mixture model which represents monomeric motifs as standard position-specific probability matrices (PPMs), and dimeric motifs as pairs of monomeric PPMs, with associated orientation and spacing preferences. For dimers the model represents deviations from pure modular model of two independent monomers, thus making co-operative binding effects explicit. MODER can analyze in reasonable time tens of Mbps of training data. We validated the tool on HT-SELEX and ChIP-seq data. Our findings include some TFs whose expected model has palindromic symmetry but the observed model is directional.

Multiparameter functional diversity of human C2H2 zinc finger proteins.

C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions. Here, we report a multifaceted functional analysis of 131 human C2H2-ZF proteins, encompassing DNA binding sites, interacting proteins, and transcriptional response to genetic perturbation. We confirm the expected diversity in DNA binding motifs and genomic binding sites, and provide motif models for 78 previously uncharacterized C2H2-ZF proteins, most of which are unique. Surprisingly, the diversity in protein-protein interactions is nearly as high as diversity in DNA binding motifs: Most C2H2-ZF proteins interact with a unique spectrum of co-activators and co-repressors. Thus, multiparameter diversification likely underlies the evolutionary success of this large class of human proteins.

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.

Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF-DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions. Statistical machine-learning models combined with feature-selection techniques helped to reveal the nucleotide position-dependent DNA shape readout in TF-binding sites and the TF family-specific position dependence. Based on these results, we proposed novel DNA shape logos to visualize the DNA shape preferences of TFs. Overall, this work suggests a way of obtaining mechanistic insights into TF-DNA binding without relying on experimentally solved all-atom structures.

Nuclear export factor 3 is involved in regulating the expression of TGF-ß3 in an mRNA export activity-independent manner in mouse Sertoli cells.

The NXF (nuclear export factor) family members are implicated in the transport of mRNA from the nucleus to the cytoplasm. Recently, some members of the NXF family have been reported to play divergent functional roles, such as post-transcriptional regulation, translational control, regulation of mRNA stability and trafficking. However, little is known about the roles of NXF3 in spermatogenesis. In the present study, we found that mouse NXF3, specifically expressed in principal cells in segment II of the caput epididymis, as well as Sertoli cells in the mouse testis, was required to mediate TGF-ß (transforming growth factor ß)-induced down-regulation of Tgfb3/TGF-ß3 mRNA expression and protein secretion in Sertoli cells. In addition, NXF3 was also involved in TGF-ß-induced transcriptional regulation of other genes associated with Sertoli cell maturation and the restructuring of the Sertoli cell BTB (blood-testis barrier), such as Gata1 (GATA-binding protein 1), Wt1 (Wilms's tumour homologue 1), Cldn11 (claudin11) and Cdkn1a (cyclin-dependent kinase inhibitor 1A or p21(Cip1)). The transcriptional regulation of NXF3 was mediated through physical interaction with STRAP (serine/threonine kinase receptor-associated protein), where NXF3 inhibited the complex formation among Smad7, STRAP and activated type I TGF-ß receptor. Taken together, our data provide mechanistic insights into the roles of NXF3 in TGF-ß-mediated expression of Tgfb3 and other genes. NXF3 may be implicated in Sertoli cell maturation and the extensive restructuring of the Sertoli cell BTB.

Occupational fatigue and health of gas station workers: A review.

BACKGROUND: Occupational health factors such as shift work, sleep, fatigue, and work environment jeopardise the health and safety of gas station workers. This calls for new research to investigate how the working environment and characteristics impact the occupational health of workers at gas stations. However, minimal research has been conducted in this field, especially those involving psychological and behavioural factors, occupational stress, and so forth. OBJECTIVE: This review was performed to investigate the present condition of the occupational risk of gas station workers in this safety-critical position. METHODS: Five databases (Web of Science, ScienceDirect, PubMed, Google Scholar, and PsycINFO) were searched for relevant peer-reviewed studies. Results were selected according to these criteria: studies on fatigue, shift work, sleep, and physical and mental health of gas station employees; published on or before November 11, 2021; papers in English. RESULTS: Twenty studies were considered for the final analysis. The results showed that shift work at gas stations leads to psychological and physiological problems. The psychological consequences included anxiety, stress, and depression, while the physiological consequences included biochemical changes and lifestyle consequences. CONCLUSION: Shift work and the specific working environment of gas station employees adversely affect their sleep, stress levels, physical and mental health, and turnover intention. This systematic review allowed us to consider the occupational risk factors that can lead to sickness or accidents and contribute to reducing these risk factors. Realistic countermeasures ought to be established and interventions must be explored to mitigate risks to life, property, and the environment in operating gas stations.

Subfertile effects of quinestrol and levonorgestrel in male rats.

The contraceptive regimen consisting of levonorgestrel and quinestrol (EP-1) has been shown to be effective in several types of wild rodents. In the present study, we investigated the effect of EP-1 and its two components on fertility and spermatogenesis to elucidate the mechanisms underlying its contraceptive effect. Sprague-Dawley rats were treated with 0.33 mgkg(-1) quinestrol (E group), 0.67 mgkg(-1) levonorgestrel (P group) or their combination (EP group) for 7 days and then killed on Days 21 or 42 after treatment for tissue analysis. On Day 21, the weight of the cauda epididymis decreased significantly, while the weight of the adrenal gland increased significantly in the E and EP groups compared with the weights in the control group. In addition, there was a significant decrease in sperm number in the E and EP groups compared with the control group and there was less staining for the androgen receptor and Wilms' tumour nuclear protein 1 in the E and EP groups. The primary defects in E- or EP-treated rats were abnormal spermiogenesis, lack of elongating spermatids, and pachytene spermatocyte arrest. Analysis of MutL homologue 1 revealed that EP treatment inhibited chromosome recombination during meiosis, but did not cause obvious genetic abnormalities. These data demonstrate that quinestrol, alone or in combination with levonorgestrel, induces subfertility in male rats mainly by interfering with germ cell differentiation. Thus, EP-1 or E alone may be effective contraceptive regimens for fertility control in rodents.

The emerging roles of piezo1 channels in animal models of multiple sclerosis.

Multiple sclerosis (MS) is a chronic inflammatory, demyelinating, and neurodegenerative disease in the central nervous system (CNS). Its pathogenesis is quite complex: Accumulated evidence suggests that biochemical signals as well as mechanical stimuli play important roles in MS. In both patients and animal models of MS, brain viscoelasticity is reduced during disease progression. Piezo mechanosensitive channels are recently discovered, and their three-dimensional structure has been solved. Both the membrane dome mechanism and the membrane footprint hypothesis have been proposed to explain their mechanosensitivity. While membrane-mediated forces alone appear to be sufficient to induce Piezo gating, tethers attached to the membrane or to the channel itself also seem to play a role. Current research indicates that Piezo1 channels play a key role in multiple aspects of MS pathogenesis. Activation of Piezo1 channels in axon negatively regulates CNS myelination. in addition, the inhibition of Piezo1 in CD4+ T cells and/or T regulatory cells (Treg) attenuates experimental autoimmune encephalitis (EAE) symptoms. Although more work has to be done to clarify the roles of Piezo1 channels in MS, they might be a promising future drug target for MS treatment.

Interaction between Nickel Oxide and Support Promotes Selective Catalytic Reduction of NOx with C3 H6.

Selective catalytic reduction of nitrogen oxides (NOx ) with C3 H6 (C3 H6 -SCR) was investigated over NiO catalysts supported on different metal-oxides. A NiAlOx mixed oxide phase was formed over NiO/γ-Al2 O3 catalyst, inducing an immediate interaction between NiOx and AlOx species. Such interaction resulted in a charge transfer from Ni to Al site and the formation of Ni species in high oxidation state. In comparison to other NiO-loaded catalysts, NiO/γ-Al2 O3 catalyst exhibited the highest NOx conversion at temperature higher than 450 °C, but a poor C3 H6 oxidation activity due to the decreased nucleophilicity for surface oxygen species. By temperature-programed NO oxidation, it is indicated that nitrate species were rapidly formed and stably maintained at high temperature over NiO/γ-Al2 O3 catalyst. In situ transient reactions further verified the Langmuir-Hinshelwood mechanism for C3 H6 -SCR, where both gaseous NO and C3 H6 were adsorbed and activated on catalyst surface and reacted to generate N2 . Due to the strong metal-support interaction over NiO/γ-Al2 O3 catalyst, both nitrate and Cx Hy Oz intermediates were well preserved to attain high C3 H6 -SCR activity.

Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing.

The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.

Variation in crossover interference levels on individual chromosomes from human males.

Crossovers (COs) generated by homologous recombination ensure the proper segregation of chromosomes during meiosis. COs exhibit interference, which leads to widely spaced COs along chromosomes. Strong positive CO interference has been found in humans. However, little is known about the extent of human CO interference. In this study, variations in CO interference over the entire human genome and among individuals were analyzed by immunofluorescence combined with fluorescence in situ hybridization of testicular biopsies from 10 control men. These methods allow for direct identification of the frequency and location of COs in specific chromosomes of pachytene cells. The strength of CO interference was estimated by fitting the frequency distribution of inter-CO distances to the gamma model. Positive interference among CO on chromosomes was observed in these men, and the strength of inter-arm interference was significantly stronger than that for intra-arm CO. In addition, interference was observed to act across the centromere. Significant inter-individual and inter-chromosomal variations in the levels of interference were found, with smaller chromosomes exhibiting stronger interference. Discontinuous chromosome regions (gaps) and unsynapsed chromosome regions (splits) in chromosome 9 had both cis and trans effects on CO interference levels. This is the first report that the interference level varies significantly across the whole genome and that, at least in the human male, anomalies in chromosome synapsis play an important role in altering CO interference levels.

A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae.

Pseudomonas syringae is a Gram-negative and model pathogenic bacterium that causes plant diseases worldwide. Here, we set out to identify binding motifs for all 301 annotated transcription factors (TFs) of P. syringae using HT-SELEX. We successfully identify binding motifs for 100 TFs. We map functional interactions between the TFs and their targets in virulence-associated pathways, and validate many of these interactions and functions using additional methods such as ChIP-seq, electrophoretic mobility shift assay (EMSA), RT-qPCR, and reporter assays. Our work identifies 25 virulence-associated master regulators, 14 of which had not been characterized as TFs before.

[Distribution Characteristics and Health Risk Assessment of Heavy Metals in a Soil-Rice System in an E-waste Dismantling Area].

This study selected Guiyu Town, Guangdong Province as the research area, the content of 15 kinds of metals (As, Be, Cd, Co, Cr, Cu, Hg, Li, Mn, Ni, Sb, Sn, Pb, V, and Zn) in the soil was determined, and the content of heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn in the rice of this research area was identified. Multivariate statistical analysis and a human health risk assessment model were used to investigate the distribution characteristics and health risk of heavy metals in a soil-rice system. The results showed that Hg, Sb, and Sn in the surface soil surrounding the electronic waste dismantling area have obvious accumulation effect. The average content of Cd and Hg exceeds the Ⅱ standard limit of the "Environmental Quality Standard for Soil" (GB 156182-1995), and that Guiyu Town is more seriously polluted than Chendian Town and Simapu Town. The multivariate statistical analysis showed that Cu, Sb, Ni, Zn, Sn, Pb, and Hg originated from the surrounding electronic waste dismantling activities, Cd and Be originated from other man-made sources of pollution, and V, Li, Cr, Co, As, and Mn originated from natural sources. Heavy metal evaluation concentration in the soil-rice system by heavy metal migration accumulated in rice are in compliance with national food hygiene standards, and the enrichment ability is Cd > Zn > Cu > Ni > As > Cr > Hg > Pb. Soil heavy metal health risk assessment results showed that children are more susceptible to heavy metal pollution, and handling-oral ingestion is the main way of soil exposure risk. The non-carcinogenic risk and carcinogenic risk of heavy metals in the soil of each town are acceptable. The health risk in Guiyu Town through ingestion of rice is mainly from the elements that include As, Cr, Cu, and Ni.

[Seasonal Characteristics and Ecological Risk Assessment of Heavy Metals in PM10 Around Electroplating Plants].

PM10 samples were collected from 45 sites around the electroplating factories in five towns in Dongguan at different times during all four seasons in 2015. The contents of 12 heavy metals (HMs) from the PM10 samples were analyzed by ICP-MS. The seasonal and spatial distribution characteristics and the ecological risk were analyzed to provide a scientific foundation for the relevant department to make decisions regarding the environmental hazard, risk assessment and, pollution control. The results showed that PM10 concentrations in the towns were lower than national standard level-Ⅱ, and the air pollution was heavier in winter than summer. The HM concentrations were higher in autumn and winter, and As, Cd, and Cr concentrations were higher than national standard (GB3095-2012). The concentrations of HMs in Humen, Shatian, and Dalingshan were much higher. The results for the enrichment factor and the geoaccumulation index indicated that Cd, Sb, Hg, and Co were in the extreme degree of pollution category, Pb and Zn were in the slight to extreme degree of pollution category, and Ni, Cr, Mn, and V were described as uncontaminated. The average potential ecological risk assessment (RI) of the HMs from the PM10 samples was more than 600, which suggested an extremely serious ecological risk in the study area.