XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells

X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

Ataxia Telangiectasia Mutated Signaling Delays Skin Pigmentation upon UV Exposure by Mediating MITF Function toward DNA Repair Mode

Skin pigmentation is paused after sun exposure; however, the mechanism behind this pausing is unknown. In this study, we found that the UVB-induced DNA repair system, led by the ataxia telangiectasia mutated (ATM) protein kinase, represses MITF transcriptional activity of pigmentation genes while placing MITF in DNA repair mode, thus directly inhibiting pigment production. Phosphoproteomics analysis revealed ATM to be the most significantly enriched pathway among all UVB-induced DNA repair systems. ATM inhibition in mouse or human skin, either genetically or chemically, induces pigmentation. Upon UVB exposure, MITF transcriptional activation is blocked owing to ATM-dependent phosphorylation of MITF on S414, which modifies MITF activity and interactome toward DNA repair, including binding to TRIM28 and RBBP4. Accordingly, MITF genome occupancy is enriched in sites of high DNA damage that are likely repaired. This suggests that ATM harnesses the pigmentation key activator for the necessary rapid, efficient DNA repair, thus optimizing the chances of the cell surviving. Data are available from ProteomeXchange with the identifier PXD041121.

FGFR3 is expressed by human primordial germ cells and is repressed after meiotic initiation to form primordial oocytes

Human germ cell development is a highly regulated process beginning soon after embryo implantation with the specification of primordial germ cells (PGCs) and ending in adulthood with the differentiation of gametes. Here, we show that fibroblast growth factor receptor 3 (FGFR3) is expressed by human PGCs during the first and second trimester, becoming repressed as PGCs differentiate into primordial oocytes. Using fluorescence-activated cell sorting (FACS) with antibodies that recognize FGFR3 followed by single-cell RNA sequencing, we show that isolating FGFR3-positive cells enriches for human PGCs. Taken together, FGFR3 could be used in future studies as a strategy to identify maturing PGCs in vitro.

Uptake, translocation, weathering and speciation of gold nanoparticles in potato, radish, carrot and lettuce crops

Extensive use of nanomaterials in agriculture will inevitably lead to their release to the environment in significant loads. Thus, understanding the fate of nanoparticles in the soil-plant environment, and potential presence and consequent implication of nanoparticles in food and feed products, is required. We study plant uptake of gold nanoparticles from soil, and their distribution, translocation and speciation (in terms of particle size change and release of ionic Au) in the different plant tissues of four important crops (potato, radish, carrot and lettuce). Our new analytical protocol and experiments show the feasibility of determining the presence, concentration and distribution of nanoparticles in different plant parts, which differ from plant to plant. Critically, we identify the evident capacity of plants to break down (or substantially change the properties of) nanoparticles in the rhizosphere prior to uptake, as well as the evident capacity of plants to reorganize ionic metals as nanoparticles in their tissues. This could lead to nanoparticle exposure through consumption of crops.

UV-Protection Timer Controls Linkage between Stress and Pigmentation Skin Protection Systems

Skin sun exposure induces two protection programs: stress responses and pigmentation, the former within minutes and the latter only hours afterward. Although serving the same physiological purpose, it is not known whether and how these programs are coordinated. Here, we report that UVB exposure every other day induces significantly more skin pigmentation than the higher frequency of daily exposure, without an associated increase in stress responses. Using mathematical modeling and empirical studies, we show that the melanocyte master regulator, MITF, serves to synchronize stress responses and pigmentation and, furthermore, functions as a UV-protection timer via damped oscillatory dynamics, thereby conferring a trade-off between the two programs. MITF oscillations are controlled by multiple negative regulatory loops, one at the transcriptional level involving HIF1α and another post-transcriptional loop involving microRNA-148a. These findings support trait linkage between the two skin protection programs, which, we speculate, arose during furless skin evolution to minimize skin damage.

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UV exposure frequency reveals a trade-off between skin protection programs

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MITF dynamics synchronize skin stress responses and pigmentation

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MITF serves as a UV-protection timer

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Two negative regulatory loops involving miR-148a and HIF1α underlie MITF dynamics

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

Transcription factors (TFs) have to find their binding sites, which are distributed throughout the genome. Facilitated diffusion is currently the most widely accepted model for this search process. Based on this model the TF alternates between one-dimensional sliding along the DNA, and three-dimensional bulk diffusion. In this view, the non-specific associations between the proteins and the DNA play a major role in the search dynamics. However, little is known about how the DNA properties around the motif contribute to the search. Accumulating evidence showing that TF binding sites are embedded within a unique environment, specific to each TF, leads to the hypothesis that the search process is facilitated by favorable DNA features that help to improve the search efficiency. Here, we review the field and present the hypothesis that TF-DNA recognition is dictated not only by the motif, but is also influenced by the environment in which the motif resides.

A widespread role of the motif environment in transcription factor binding across diverse protein families

Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Recent in vitro binding assays, which exclude the effects of the cellular environment, also demonstrate selective TF binding. An intriguing conjecture is that the surroundings of cognate binding sites have unique characteristics that distinguish them from other sequences containing a similar motif that are not bound by the TF. To test this hypothesis, we conducted a comprehensive analysis of the sequence and DNA shape features surrounding the core-binding sites of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respectively. Comparing the nucleotide content of the regions around the TF-bound sites to the counterpart unbound regions containing the same consensus motifs revealed significant differences that extend far beyond the core-binding site. Specifically, the environment of the bound motifs demonstrated unique sequence compositions, DNA shape features, and overall high similarity to the core-binding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate binding sites.

Deconvolving the recognition of DNA shape from sequence

Protein-DNA binding is mediated by the recognition of the chemical signatures of the DNA bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of sequence, it is difficult to dissociate these modes of recognition. Here, we tease them apart in the context of Hox-DNA binding by mutating residues that, in a co-crystal structure, only recognize DNA shape. Complexes made with these mutants lose the preference to bind sequences with specific DNA shape features. Introducing shape-recognizing residues from one Hox protein to another swapped binding specificities in vitro and gene regulation in vivo. Statistical machine learning revealed that the accuracy of binding specificity predictions improves by adding shape features to a model that only depends on sequence, and feature selection identified shape features important for recognition. Thus, shape readout is a direct and independent component of binding site selection by Hox proteins.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.

Covariation between homeodomain transcription factors and the shape of their DNA binding sites

Protein–DNA recognition is a critical component of gene regulatory processes but the underlying molecular mechanisms are not yet completely understood. Whereas the DNA binding preferences of transcription factors (TFs) are commonly described using nucleotide sequences, the 3D DNA structure is recognized by proteins and is crucial for achieving binding specificity. However, the ability to analyze DNA shape in a high-throughput manner made it only recently feasible to integrate structural information into studies of protein–DNA binding. Here we focused on the homeodomain family of TFs and analyzed the DNA shape of thousands of their DNA binding sites, investigating the covariation between the protein sequence and the sequence and shape of their DNA targets. We found distinct homeodomain regions that were more correlated with either the nucleotide sequence or the DNA shape of their preferred binding sites, demonstrating different readout mechanisms through which homeodomains attain DNA binding specificity. We identified specific homeodomain residues that likely play key roles in DNA recognition via shape readout. Finally, we showed that adding DNA shape information when characterizing binding sites improved the prediction accuracy of homeodomain binding specificities. Taken together, our findings indicate that DNA shape information can generally provide new mechanistic insights into TF binding.

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA sequence and shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist). The results of rigorous validations of the HT predictions based on DNA structures solved by X-ray crystallography and NMR spectroscopy, hydroxyl radical cleavage data, statistical analysis and cross-validation, and molecular dynamics simulations provide strong confidence in this approach. The DNAshape web server is freely available at http://rohslab.cmb.usc.edu/DNAshape/.

Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes

3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology.

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.

Predicting nucleic acid binding interfaces from structural models of proteins

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure.

SFmap: a web server for motif analysis and prediction of splicing factor binding sites

Alternative splicing (AS) is a post-transcriptional process considered to be responsible for the huge diversity of proteins in higher eukaryotes. AS events are regulated by different splicing factors (SFs) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites in genomic data (http://sfmap.technion.ac.il). SFmap implements the COS(WR) algorithm, which computes similarity scores for a given regulatory motif based on information derived from its sequence environment and its evolutionary conservation. Input for SFmap is a human genomic sequence or a list of sequences in FASTA format that can either be uploaded from a file or pasted into a window. SFmap searches within a given sequence for significant hits of binding motifs that are either stored in our database or defined by the user. SFmap results are provided both as a text file and as a graphical web interface.

To be or not to be: the effects of aging stereotypes on the will to live

This study examined whether stereotypes of aging might contribute to decisions the elderly make about when to die. Old and young participants (N=64) were subliminally primed with either negative or positive stereotypes of old age and then responded to hypothetical medical situations involving potentially fatal illnesses. Consistent with our prediction, the aged participants primed with negative stereotypes tended to refuse life-prolonging interventions, whereas the old participants primed with positive age stereotypes tended to accept the interventions. This priming effect did not emerge among the young participants for whom the stereotypes were less relevant. The results suggest that societally-transmitted negative stereotypes of aging can weaken elderly people's will to live.

Enhanced transport of pesticides in a field trial with treated sewage sludge

This study was designed to provide high-density data on spatial distribution of three herbicides with different physiochemical characteristics in a sludge-amended and non-amended control field over the course of an irrigation season. The field experiment was carried out on a sandy loam Hamra Red Mediterranean soil (Rhodoxeralf) at Bet Dagan, Israel. After a single 50 mm irrigation event, the mean centers of mass (COM) in the control field were at 15.6, 14.9, and 17 cm for bromacil, atrazine and terbuthylazine, respectively; in the sludge-amended field, mean COMs were at 28.8, 31.2, and 34.1 cm, respectively. After 500 mm of irrigation in the control field, the COM depth distribution of the three pesticides was inversely correlated with octanol-water (Kow) distribution coefficients and soil sorption coefficients (Koc), and positively correlated with aqueous solubilities. After 500 mm irrigation in the sludge-amended field, the mean terbuthylazine COM was at 19.8 cm versus 13.8 cm for the control field, demonstrating a sustained enhanced effect on terbuthylazine transport. Downward transport of atrazine was also enhanced by sludge amendment, albeit less than terbuthylazine. Bromacil was preferentially accumulated in the upper soil layers of the sludge-amended field as compared with the control field after 500 mm irrigation. The enhanced transport of all three pesticides in the sludge-amended field after a single irrigation event is attributed to development of preferential flow pathways around hydrophobic clods of sludge. Enhanced transport of terbuthylazine, and to a lesser extent, atrazine, throughout the irrigation season, is attributed to their transport as complexes with dissolved, colloidal and suspended organic matter derived from sludge degradation.

Temporal changes in kerosene content and composition in field soil as a result of leaching

A field experiment was designed to determine the combined effect of leaching and natural attenuation on the redistribution dynamics of kerosene--a volatile petroleum hydrocarbon mixture (VPHM)--and of its selected individual components in the soil subsurface. Variables included the composition of contaminant spilled, the soil water content before contamination and the leaching pattern. Temporal changes in the residual kerosene concentration and composition in the soil subsurface of the experimental field during 39 days and leaching by 500 mm of irrigation water were determined to a depth of 100 cm. The main processes controlling contaminant attenuation were volatilization and redistribution with depth. Soil hydration status was found to affect the attenuation, redistribution and composition of VPHM in the porous media. An initial relative increase of n-alkanes in the subsurface compared with the total VPHM in the first leaching period was a result of the volatilization of low vapor pressure compounds. The redistribution of individual components in the soil profile during leaching was in accordance with their physico-chemical properties.

Experimental investigation of the influence of the relative position of the scattering layer on image quality: the shower curtain effect

The imaging quality of optical systems in a turbid environment is influenced not only by the content of the turbid layer between the object and the optical receiver but also by the inhomogeneity of that medium. This is important, particularly when imaging is performed through clouds, nonhomogeneous layers of dust, or over vertical or slant paths through the atmosphere. Forward small-angle scattering influences image quality and blur more severely when the scattering layer is closer to the receiver. In this study it is the influence of the relative position of the scattering layer on the image quality and modulation transfer function (MTF) that is investigated. The scattering layer in controlled laboratory experiments consists of calibrated polystyrene particles of known size and quantity in a small cuvette. A point source was imaged by a computerized imaging system through a layer containing polystyrene particles, and the point-spread function (PSF) was recorded. The aerosol MTF was calculated using the measured PSF. The MTF was measured as a function of changing relative distance of the scattering layer from the receiver, whereas the object-plane-to-receiver distance was constant. The experimental results were compared to theoretical shower curtain effect models based on the solution from radiative transfer theory under the small-angle approximation. Although the general trend of the experimental results certainly agrees with the theoretical models, it could be that the small-angle approximation method might be of limited validity at such low spatial frequencies. Aggregation also causes some disagreement with predictions from theory.

Basal membrane labyrinths in the healing stages of chick nutritional encephalopathy

Chicks were fed a diet rich in oxidized oil and deficient in alpha-tocopherol. As soon as nutritional encephalopathy developed the animals were immediately put on to a normal diet, and kept alive for up to 166 days. Examination of the cerebellum showed multiple foci of healed encephalomalacia with EM appearance of basal membrane labyrinths between astroglial cells and around blood vessels. The possible origin of the basement membrane material in this conditions was considered and compared with similar formations in normal animals, in CNS tumour explants, and after portocaval anastomosis as well as after spinal cord lesions.