Binding Sites For Regulatory Proteins Research Articles

Asymmetric allostery in estrogen receptor-α homodimers drives responses to the ensemble of estrogens in the hormonal milieu

The estrogen receptor-α (ER) is thought to function only as a homodimer but responds to a variety of environmental, metazoan, and therapeutic estrogens at subsaturating doses, supporting binding mixtures of ligands as well as dimers that are only partially occupied. Here, we present a series of flexible ER ligands that bind to receptor dimers with individual ligand poses favoring distinct receptor conformations-receptor conformational heterodimers-mimicking the binding of two different ligands. Molecular dynamics simulations showed that the pairs of different ligand poses changed the correlated motion across the dimer interface to generate asymmetric communication between the dimer interface, the ligands, and the surface binding sites for epigenetic regulatory proteins. By examining the binding of the same ligand in crystal structures of ER in the agonist vs. antagonist conformers, we also showed that these allosteric signals are bidirectional. The receptor conformer can drive different ligand binding modes to support agonist vs. antagonist activity profiles, a revision of ligand binding theory that has focused on unidirectional signaling from the ligand to the coregulator binding site. We also observed differences in the allosteric signals between ligand and coregulator binding sites in the monomeric vs. dimeric receptor, and when bound by two different ligands, states that are physiologically relevant. Thus, ER conformational heterodimers integrate two different ligand-regulated activity profiles, representing different modes for ligand-dependent regulation of ER activity.

Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code.

Codon degeneracy of amino acid sequences permits an additional "mRNP code" layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids. We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach. To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information. The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.

Bovine pyruvate carboxylase gene proximal promoter activity is regulated by saturated and unsaturated fatty acids in Madin-Darby bovine kidney cells

An increase in bovine pyruvate carboxylase (PC; EC 6.4.1.1) at calving and during feed restriction corresponds with increased circulating nonesterified fatty acids as a consequence of negative energy balance. Regulation of PC mRNA and effect of specific combinations of saturated and unsaturated fatty acid profiles has yet to be explored. Our objective was to determine the effects of chain length, degree of saturation, and copresence of saturated and unsaturated fatty acids on activity of bovine PC promoter 1 (PCP1). For these experiments, Madin-Darby bovine kidney cells were transfected with a full-length bovine PCP1 construct from -1002 to +3 bp relative to the bovine PC gene transcription start site (bovine PCP1(-1002_+3)) ligated to a Firefly luciferase reporter, or with one of a series of nested 5' serial truncations (bovine PCP1(-773_+3), bovine PCP1(-494_+3), or bovine PCP1(-222_+3)). Cells were exposed for 23 h to either individual fatty acids (C16:0, C18:0, or C18:3n-3 cis) bound to BSA or to fatty acid mixtures in ratios of 90:10, 75:25, 50:50, or 25:75, corresponding to combinations of C16:0: C18:3n-3 cis or C18:0: C18:3n-3 cis. Total fatty acid concentration was 1.00 mM. Exposure to either C16:0 or C18:3n-3 cis alone elicited a significant increase in capacity to drive bovine PCP1(-1002_+3) activity compared with 1% BSA in Dulbecco's Modified Eagle's Medium control treatment (2.29, 2.89, and 1.00 ± 0.26 fold of promoter induction for C16:0, C18:3n-3 cis, and control, respectively). Treatment with C18:3n-3 cis alone caused a greater increase in promoter activity compared with C16:0 alone, indicating a lesser response to C16:0 alone for bovine PCP1(-1002_+3). Interestingly, inclusion of C18:3n-3 cis, at any level of fatty acid ratios examined, in combination with C16:0 increased promoter activity of bovine PCP1(-773_+3) or bovine PCP1(-222_+3) compared with treatment with C16:0 alone or control. Data from the bovine PCP1 truncation and fatty acid copresence experiments reveal the potential for response elements of unsaturated fatty acids or fatty acid ligands in several bovine PCP1 promoter regions. In silico analysis of bovine PCP1 identified putative peroxisome proliferator-activated receptor α and sterol regulatory element binding protein binding sites which may be implicated in fatty acid signaling to alter bovine PCP1 activity. Pyruvate carboxylase promoter 1 activity that is mediated by unsaturated fatty acids acting through elements within -1002 and -222 bp of bovine PCPI may determine PC response during periods of negative energy balance in dairy cows.

The Dark Side of Actin: Cardiac actin variants highlight the role of allostery in disease development

Mutations in the α-cardiac actin ACTC1 gene cause dilated or hypertrophic cardiomyopathy. These diseases are the result of changes in protein interactions between ACTC protein and force-generating β-myosin or the calcium-dependent cardiac-tropomyosin (cTm) and cardiac troponin (cTn) regulatory complex, altering the overall contractile force. The T126I and S271F ACTC variants possess amino acid substitutions on the other side of actin relative to the myosin or regulatory protein binding sites on what we call the “dark side” of actin. The T126I change results in hyposensitivity to calcium, in accordance with the calcium sensitivity pathway of cardiomyopathy development while the S271F change alters the maximum in vitro motility sliding speed, reflecting a change in maximum force. These results demonstrate the role of actin allostery in the cardiac disease development.

Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns

BackgroundThe binding sites of transcription factors (TFs) and the localisation of histone modifications in the human genome can be quantified by the chromatin immunoprecipitation assay coupled with next-generation sequencing (ChIP-seq). The resulting chromatin feature data has been successfully adopted for genome-wide enhancer identification by several unsupervised and supervised machine learning methods. However, the current methods predict different numbers and different sets of enhancers for the same cell type and do not utilise the pattern of the ChIP-seq coverage profiles efficiently.ResultsIn this work, we propose a PRobabilistic Enhancer PRedictIoN Tool (PREPRINT) that assumes characteristic coverage patterns of chromatin features at enhancers and employs a statistical model to account for their variability. PREPRINT defines probabilistic distance measures to quantify the similarity of the genomic query regions and the characteristic coverage patterns. The probabilistic scores of the enhancer and non-enhancer samples are utilised to train a kernel-based classifier. The performance of the method is demonstrated on ENCODE data for two cell lines. The predicted enhancers are computationally validated based on the transcriptional regulatory protein binding sites and compared to the predictions obtained by state-of-the-art methods.ConclusionPREPRINT performs favorably to the state-of-the-art methods, especially when requiring the methods to predict a larger set of enhancers. PREPRINT generalises successfully to data from cell type not utilised for training, and often the PREPRINT performs better than the previous methods. The PREPRINT enhancers are less sensitive to the choice of prediction threshold. PREPRINT identifies biologically validated enhancers not predicted by the competing methods. The enhancers predicted by PREPRINT can aid the genome interpretation in functional genomics and clinical studies.

Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation

SUMMARYRepetitive elements are abundantly distributed in mammalian genomes. Here, we reveal a striking association between repeat subtypes and gene function. SINE, L1, and low-complexity repeats demarcate distinct functional categories of genes and may dictate the time and level of gene expression by providing binding sites for different regulatory proteins. Importantly, imaging and sequencing analysis show that L1 repeats sequester a large set of genes with specialized functions in nucleolus- and lamina-associated inactive domains that are depleted of SINE repeats. In addition, L1 transcripts bind extensively to its DNA in embryonic stem cells (ESCs). Depletion of L1 RNA in ESCs leads to relocation of L1-enriched chromosomal segments from inactive domains to the nuclear interior and de-repression of L1-associated genes. These results demonstrate a role of L1 DNA and RNA in gene silencing and suggest a general theme of genomic repeats in orchestrating the function, regulation, and expression of their host genes.

Gene-environment interactions between polymorphic loci of MMPs and obesity in essential hypertension in women.

The prevalence of essential hypertension (ЕH) is increasing every year, both in Russia and around the world. Genetic and environmental risk factors are involved in the development of hypertension, and obesity plays an important role. Therefore, the study of gene-ecological interactions in the development of hypertension seems to be relevant. to study the gene-environment interactions between polymorphic loci of MMP and obesity in essential hypertension in women. The study was conducted in a case-control design. The sample included 584 subjects: 375 patients with EH and 209 women in the control group. All individuals included in the study were genotyped for eight polymorphic loci of MMPs. The study of the gene-environmental interactions during the formation of hypertension was performed using the GMDR method (Generalized Multifactor Dimensionality Reduction, http://www.ssg.uab.edu/gmdr). rs11568818 MMР7 and rs11225395 MMР8 polymorphic loci were found to be involved in the development of arterial hypertension in women without obesity (p<0.050). Fifteen three-, four-, and five-factor models of gene-environmental interactions of 8 MMPs with obesity, associated with EH (p=0.01), were found. It is shown that the analyzed SNPs are located in the DNA regions that bind to histones, marking promoters and enhancers, in the region of hypersensitivity to DNAse-1, in the binding sites of regulatory proteins and transcription factors. The loci of MMPs rs17577, rs11568818, rs1320632 and rs11225395 have cis-eQTL-value. They affecting the expression of the genes of MMP7, SNX21, SLC12A5 and RP11-817J15.3. SNP rs11568818 MMP7 and rs11225395 MMP8 and gene-environmental interactions of MMPs rs1799750, rs243865, rs3025058, rs11568818, rs1320632, rs11225395, rs17577, rs652438 with obesity are involved in the development of essential hypertension in women.

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins.

Gene regulation plays an important role in all cells. Transcriptional, post-transcriptional (or RNA processing), translational, and post-translational steps are used to regulate specific genes. Sequence-specific nucleic acid-binding proteins target specific sequences to control spatial or temporal gene expression. The binding sites in nucleic acids are typically characterized by mutational analysis. However, numerous proteins of interest have no known binding site for such characterization. Here we describe an approach to identify previously unknown binding sites for RNA-binding proteins. It involves iterative selection and amplification of sequences starting with a randomized sequence pool. Following several rounds of these steps-transcription, binding, and amplification-the enriched sequences are sequenced to identify a preferred binding site(s). Success of this approach is monitored using in vitro binding assays. Subsequently, in vitro and in vivo functional assays can be used to assess the biological relevance of the selected sequences. This approach allows identification and characterization of a previously unknown binding site(s) for any RNA-binding protein for which an assay to separate protein-bound and unbound RNAs exists.

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses

Transmembrane and Coiled-Coil Domains 1 (TMCO1) protein is encoded by TMCO1 gene consists of 7 exons. Previous studies have identified multiple TMCO1 variants in patients with cerebro-facio-thoracic dysplasia (CFTD) and TMCO1 locus was also shown to be associated with primary open angle glaucoma (POAG). However, there are limited number of research exist reporting associations of the TMCO1 gene sequence variants and majority of the findings affirm the pathogenicity of the nonsense and frameshift TMCO1 variants and their associations with clinical phenotypes. Thus functional properties of the single nucleotide variants causing amino acid changes in the TMCO1 are yet to be comprehensively elucidated. In this study, we evaluated the effects of amino acid substitutions on protein structure, identified their putative roles in post-translational modifications (PTM) and in regulatory mechanism for TMCO1 protein. We classified 41 missense variants as pathogenic based on combined scores of common in silico tools (SIFT, MutationTaster2, Polyphen2). Of these 41 variants, four (p.K211Q, p.K105E, p.S235F, p.K237R) were identified to be located in PTMs and regulatory protein binding sites; thus they were proposed to be putative functional variants. Moreover, rs1387528611 (p.Lys128Gln) had also strong evidence (RegulomeDB score=2b) for its possible regulatory function. The results of our in silico analyses highlight the functional importance of the missense TMCO1 variants that may contribute to the TMCO1-associated disease phenotypes and further in vivo evaluation yet to be needed to uncover their role in human diseases.

Comparison between Effects of Retroactivity and Resource Competition upon Change in Downstream Reporter Genes of Synthetic Genetic Circuits.

Reporter genes have contributed to advancements in molecular biology. Binding of an upstream regulatory protein to a downstream reporter promoter allows quantification of the activity of the upstream protein produced from the corresponding gene. In studies of synthetic biology, analyses of reporter gene activities ensure control of the cell with synthetic genetic circuits, as achieved using a combination of in silico and in vivo experiments. However, unexpected effects of downstream reporter genes on upstream regulatory genes may interfere with in vivo observations. This phenomenon is termed as retroactivity. Using in silico and in vivo experiments, we found that a different copy number of regulatory protein-binding sites in a downstream gene altered the upstream dynamics, suggesting retroactivity of reporters in this synthetic genetic oscillator. Furthermore, by separating the two sources of retroactivity (titration of the component and competition for degradation), we showed that, in the dual-feedback oscillator, the level of the fluorescent protein reporter competing for degradation with the circuits’ components is important for the stability of the oscillations. Altogether, our results indicate that the selection of reporter promoters using a combination of in silico and in vivo experiments is essential for the advanced design of genetic circuits.

Damage-responsive elements in Drosophila regeneration.

One of the most important questions in regenerative biology is to unveil how and when genes change expression and trigger regeneration programs. The resetting of gene expression patterns during response to injury is governed by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using genome-wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings indicate there is global coregulation of gene expression as well as a regeneration program driven by different types of regulatory elements. Novel enhancers acting exclusively within damaged tissue cooperate with enhancers co-opted from other tissues and other developmental stages, as well as with endogenous enhancers that show increased activity after injury. Together, these enhancers host binding sites for regulatory proteins that include a core set of conserved transcription factors that control regeneration across metazoans.

A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates.

Gene regulation plays an important role in development. Numerous DNA- and RNA-binding proteins bind their target sequences with high specificity to control gene expression. These regulatory proteins control gene expression either at the level of DNA (transcription) or at the level of RNA (pre-mRNA splicing, polyadenylation, mRNA transport, decay, and translation). Identification of regulatory sequences helps understand not only how a gene is switched on or off, but also which downstream genes are regulated by a particular regulatory protein. Here, we describe a one-step approach that allows saturation mutagenesis of a protein binding site in RNA. It involves doping DNA template with non-wild-type nucleotides within the binding site, synthesis of separate RNAs with each phosphorothioate nucleotide, and isolation of the bound fraction following incubation with protein. Interference from non-wild-type nucleotides results in their preferential exclusion from the protein-bound fraction. This is monitored by gel electrophoresis following selective chemical cleavage with iodine of phosphodiester bonds containing phosphorothioates (phosphorothioate mutagenesis or PTM). This single-step saturation mutagenesis approach is applicable to the characterization of any protein binding site in RNA.

A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates

A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates

Structure and Function of the Campylobacter jejuni Chromosome Replication Origin.

Campylobacter jejuni is the leading bacterial cause of foodborne infections worldwide. However, our understanding of its cell cycle is poor. We identified the probable C. jejuni origin of replication (oriC) – a key element for initiation of chromosome replication, which is also important for chromosome structure, maintenance and dynamics. The herein characterized C. jejuni oriC is monopartite and contains (i) the DnaA box cluster, (ii) the DnaA-dependent DNA unwinding element (DUE) and (iii) binding sites for regulatory proteins. The cluster of five DnaA boxes and the DUE were found in the dnaA-dnaN intergenic region. Binding of DnaA to this cluster of DnaA-boxes enabled unwinding of the DUE in vitro. However, it was not sufficient to sustain replication of minichromosomes, unless the cluster was extended by additional DnaA boxes located in the 3′ end of dnaA. This suggests, that C. jejuni oriC requires these boxes to initiate or to regulate replication of its chromosome. However, further detailed mutagenesis is required to confirm the role of these two boxes in initiation of C. jejuni chromosome replication and thus to confirm partial localization of C. jejuni oriC within a coding region, which has not been reported thus far for any bacterial oriC. In vitro DUE unwinding by DnaA was inhibited by Cj1509, an orphan response regulator and a homolog of HP1021, that has been previously shown to inhibit replication in Helicobacter pylori. Thus, Cj1509 might play a similar role as a regulator of C. jejuni chromosome replication. This is the first systematic analysis of chromosome replication initiation in C. jejuni, and we expect that these studies will provide a basis for future research examining the structure and dynamics of the C. jejuni chromosome, which will be crucial for understanding the pathogens’ life cycle and virulence.

Nebulin Stiffens the Thin Filament and Augments Crossbridge Interaction - An X-Ray Diffraction Study on Intact Muscle

Nebulin, the giant sarcomeric protein is thought to play a role in thin filament length regulation but little is known about nebulin's influence on the thin filament structure in skeletal muscle. In the present work we compared the ultrastructure of relaxed and contracting intact soleus muscle dissected from conditional nebulin-knockout (cKO) and control (Ctrl) mice by using small-angle X-ray diffraction. Although the spacing of the actin subunit repeats (27.3 Å meridional reflection) was equal in both groups in relaxed muscles, during contraction the normalized percent change is more than the double in cKO (0.0054%/kPa) compared to that of the control (0.0020%/kPa). The myofibrillar area was determined by a detailed cross-sectional ultrastructural analysis thereby making the stiffness calculation of single thin filaments possible. The stiffness for 1-μm-long actin was calculated to be 38.7 pN/nm in Ctrl muscle and 14.8 pN/nm in cKO soleus. Furthermore, significantly shorter left-handed thin filament helical pitch (59 Å meridional reflection) was found in the absence of nebulin in passive muscles (58.88 Å in cKO vs. 59.14 Å in Ctrl); the shorter 59 Å helical pitch was maintained during contraction. Through the equatorial 1,0 and 1,1 intensities we found significantly less mass attached to the thin filaments in passive cKO muscles and inefficient myosin mass transfer during their contraction. According to our findings, nebulin plays a role in the passive state of muscle by fine-adjusting the 59 Å helical pitch of the thin filaments thereby modulating the binding sites of regulatory proteins along the long pitch groove of actin. Further, nebulin stiffens the thin filament which is critically important for skeletal muscle force development, explaining why the absence of the nebulin in nemaline myopathy patients leads to muscle weakness.

T2. IDENTIFICATION OF PATHOGENIC VARIANTS IN PROTEIN CODING GENES

Background A central aim of precision medicine is to target treatments to the underlying causes of disease. To accurately target treatments we must be able to recognize pathogenic genetic variants. Current methods prioritize variants that directly alter protein sequence (missense and loss of function) but not variants that may cause disease by changing the processing of final transcripts. The difficulty in capturing this effect results in overlooking synonymous and intronic variants when searching for disease risk in sequenced genomes. Methods The TraP score was constructed using three main components: 1) Information acquisition – details of the harboring gene and it’s transcripts are gathered for each variant. 2) Feature calculation - possible changes to sequence motifs are evaluated, including changes to exon-intron boundaries, creation of cryptic splice sites, creations and disruptions of cis-acting binding sites for splicing regulatory proteins, interactions between selected features such as original and new splice sites and others. Overall, 42 features and 14 general properties (chromosome, strand, coordinate, etc.) are collected for each variant. 3) Modeling – the incorporation of selected features into a random forest model. The model is trained on a set of 75 pathogenic synonymous variants and 402 benign variants. Pathogenic variants are strongly associated with rare disease, whereas the 402 benign variants are de novo mutations identified from healthy individuals. Results The Transcript-inferred Pathogenicity score (TraP) presented here was constructed to reliably identify non-coding mutations that cause disease. Trap is strongly negatively correlated with allele frequency in both synonymous and intronic regions, suggesting that the higher the TraP score the stronger the selection against these variants in the population. Moreover, synonymous variants with high TraP scores have significantly lower minor allele frequencies than even missense variants, indicating that Trap identifies a subset of synonymous variants under stronger purifying selection. TraP identifies known pathogenic variants in synonymous and intronic ClinVar datasets (AUC = 0.88 and 0.83, respectively), dismissing benign variants with extremely high specificity of above 99%. Applied to exomes of 281 epilepsy family trios, TraP pinpoints synonymous de novo variants in known epilepsy genes. TraP’s high performance and specificity clearly outperforms existing methods and allows the prioritization of synonymous and intronic variants for use in gene discovery and the interpretation of personal genomes. Discussion Exome sequencing studies consider rare non-synonymous variants as disease candidates, while other variant types are mostly ignored. Some existing methods are able to prioritize synonymous and intronic variants, yet lack the specificity required for detection of causal variants. TraP discards over 99% of non-coding variants as benign while strongly identifying true pathogenic variants. TraP identifies pathogenic variants that are not conserved, yet have rare population frequencies. Doing so without prior population frequency information and in contrast to the GERP++ and CADD scores, suggests that TraP identifies pathogenic events that were not selected against during vertebrate evolution, but are selected against in human population. This conclusion is supported by the highest complexity of alternative splicing found in primates and by the species-specific nature of splicing regulation.

Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies.

Hidden Markov model (HMM) is widely used for modeling spatially correlated genomic data (series data). In genomics, datasets of this kind are generated from genome-wide mapping studies through high-throughput methods such as chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq). When multiple regulatory protein binding sites or related epigenetic modifications are mapped simultaneously, the correlation between data series can be incorporated into the latent variable inference in a multivariate form of HMM, potentially increasing the statistical power of signal detection. In this chapter, we review the challenges of multivariate HMMs and propose a computationally tractable method called sparsely correlated HMMs (scHMM). We illustrate the method and the scHMM package using an example mouse ChIP-seq dataset.

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci.

Identification of the relationship between the variability of the expression of signaling pathway genes in the human brain and the affinity of TATA-binding protein to their promoters

Variations in gene expression are the subject of a wide range of research aimed at the reconstruction of regulatory protein binding sites on DNA, regulatory gene regions, gene networks, signaling pathways, and many other entities that are able to modify gene expression. Pearson’s coefficient of variation (Cv, the ratio of the standard deviation to the mean) is the measure of variations in gene expression that is the most used in the fields of intense biomedical and breeding research. In turn, only one common genomic regulatory signal has been identified in all eukaryotes, namely, the TATA box, together with three other, less conservative, obligatory elements of core promoters accompanying it: DPE, BPE, and INR. We applied the equation for TATA box Binding Protein (TBP) affinity to TATA boxes deduced from our experimental data to the analysis of high-throughput sequencing data on 35609 mRNAs in 946 human brain segments taken from the Allen Brain Atlas. The analysis revealed a significant correlation between the affinity of TBP binding to promoters of signaling pathways genes and in silico estimates of Pearson’s Cv of the expression of these genes. This finding may help scientists analyze high-throughput sequencing data in order to identify more candidate factors modifying gene expression.