Regulatory Variations Research Articles

Lipotransfer: the potential from bench to bedside.

The development of autologous fat grafting to augment or reconstruct tissue defects has become an increasingly popular modality among plastic surgeons. Despite its popularity, a standardized fat grafting protocol has yet to be developed. Great variations exist with regard to almost all the technical features, yielding a reported fat graft survivability that ranges from 40% to 80%. Recent bench approaches have been proposed to improve the long-term viability of fat grafts: although promising results have been shown, empirical evidence has yet to prove the superiority of one particular method. Nevertheless, currently available literature still provides some evidence for optimal results in differing clinical scenarios, in the wait of validating and ultimate studies.The issues of enriched fat grafting techniques and variations in harvesting and delivery in the background of US regulatory constraints demand alterations and variations in techniques. These only complicate the process of validation of any single technique. However, recent studies have brought us closer to making informed decisions on technical choices in lipotransfer. These are elaborated on in this review.

Genetic factors underlying discordance in chromatin accessibility between monozygotic twins.

BackgroundOpen chromatin is implicated in regulatory processes; thus, variations in chromatin structure may contribute to variations in gene expression and other phenotypes. In this work, we perform targeted deep sequencing for open chromatin, and array-based genotyping across the genomes of 72 monozygotic twins to identify genetic factors regulating co-twin discordance in chromatin accessibility.ResultsWe show that somatic mutations cause chromatin discordance mainly via the disruption of transcription factor binding sites. Structural changes in DNA due to C:G to A:T transversions are under purifying selection due to a strong impact on chromatin accessibility. We show that CpGs whose methylation is specifically regulated during cellular differentiation appear to be protected from high mutation rates of 5′-methylcytosines, suggesting that the spectrum of CpG variations may be shaped fully at the developmental level but not through natural selection. Based on the association mapping of within-pair chromatin differences, we search for cases in which twin siblings with a particular genotype had chromatin discordance at the relevant locus. We identify 1,325 chromatin sites that are differentially accessible, depending on the genotype of a nearby locus, suggesting that epigenetic differences can control regulatory variations via interactions with genetic factors. Poised promoters present high levels of chromatin discordance in association with either somatic mutations or genetic-epigenetic interactions.ConclusionOur observations illustrate how somatic mutations and genetic polymorphisms may contribute to regulatory, and ultimately phenotypic, discordance.

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions

The fibrillins and latent transforming growth factor binding proteins (LTBPs) form a superfamily of extracellular matrix (ECM) proteins characterized by the presence of a unique domain, the 8-cysteine transforming growth factor beta (TGFβ) binding domain. These proteins are involved in the structure of the extracellular matrix and controlling the bioavailability of TGFβ family members. Genes encoding these proteins show differential expression in mesenchymal cell types which synthesize the extracellular matrix. We have investigated the promoter regions of the seven gene family members using the FANTOM5 CAGE database for human. While the protein and nucleotide sequences show considerable sequence similarity, the promoter regions were quite diverse. Most genes had a single predominant transcription start site region but LTBP1 and LTBP4 had two regions initiating different transcripts. Most of the family members were expressed in a range of mesenchymal and other cell types, often associated with use of alternative promoters or transcription start sites within a promoter in different cell types. FBN3 was the lowest expressed gene, and was found only in embryonic and fetal tissues. The different promoters for one gene were more similar to each other in expression than to promoters of the other family members. Notably expression of all 22 LTBP2 promoters was tightly correlated and quite distinct from all other family members. We located candidate enhancer regions likely to be involved in expression of the genes. Each gene was associated with a unique subset of transcription factors across multiple promoters although several motifs including MAZ, SP1, GTF2I and KLF4 showed overrepresentation across the gene family. FBN1 and FBN2, which had similar expression patterns, were regulated by different transcription factors. This study highlights the role of alternative transcription start sites in regulating the tissue specificity of closely related genes and suggests that this important class of extracellular matrix proteins is subject to subtle regulatory variations that explain the differential roles of members of this gene family.

Moving Life Science Ethics Debates Beyond National Borders: Some Empirical Observations

The life sciences are increasingly being called on to produce "socially robust" knowledge that honors the social contract between science and society. This has resulted in the emergence of a number of "broad social issues" that reflect the ethical tensions in these social contracts. These issues are framed in a variety of ways around the world, evidenced by differences in regulations addressing them. It is important to question whether these variations are simply regulatory variations or in fact reflect a contextual approach to ethics that brings into question the existence of a system of "global scientific ethics". Nonetheless, within ethics education for scientists these broad social issues are often presented using this scheme of global ethics due to legacies of science ethics pedagogy. This paper suggests this may present barriers to fostering international discourse between communities of scientists, and may cause difficulties in harmonizing (and transporting) national regulations for the governance of these issues. Reinterpreting these variations according to how the content of ethical principles is attributed by communities is proposed as crucial for developing a robust international discourse. To illustrate this, the paper offers some empirical fieldwork data that considers how the concept of dual-use (as a broad social issue) was discussed within African and UK laboratories. Demonstrating that African scientists reshaped the concept of dual-use according to their own research environmental pressures and ascribed alternative content to the principles that underpin it, suggests that the limitations of a "global scientific ethics" system for these issues cannot be ignored.

DiGSNP: a web tool for Disease-Gene-SNP hierarchical prioritization

DiGSNP: a web tool for Disease-Gene-SNP hierarchical prioritization

Effects of cis and trans regulatory variations on the expression divergence of heat shock response genes between yeast strains

Phenotypic variation among individuals in a population can be due to DNA sequence variation in protein coding regions or in regulatory elements. Recently, many studies have indicated that mutations in regulatory elements may be the major cause of phenotypic evolution. However, the mechanisms for evolutionary changes in gene expression are still not well understood. Here, we studied the relative roles of cis and trans regulatory changes in Saccharomyces cerevisiae cells to cope with heat stress. It has been found that the expression level of ~300 genes was induced at least two fold and that of ~500 genes was repressed at least two fold in response to heat shock. From the former set of genes, we randomly selected 65 genes that showed polymorphism(s) between the BY and RM strains for pyrosequencing analysis to explore the relative contributions of cis and trans regulatory variations to the expression divergence between BY and RM. Our data indicated that the expression divergence between BY and RM was mainly due to trans regulatory variations under either the normal condition or the heat stress condition. However, the relative contribution of trans regulatory variation was decreased from 76.9% to 61.5% after the heat shock stress. These results indicated that the cis regulatory variation may play an important role in the adaption to heat stress. In our data, 43.1% (28 genes) of the 65 genes showed the same trend of cis or trans variation effect after the heat shock stress, 35.4% (23 genes) showed an increased cis variation effect and 21.5% (14 genes) showed an increased trans variation effect after the heat shock stress. Thus, our data give insights into the relative roles of cis and trans variations in response to heat shock in yeast.

Regulatory variations in the era of next-generation sequencing: Implications for clinical molecular diagnostics

With the successful identification of many protein-coding genes, the focus has now shifted toward deciphering functions of non-protein-coding regions that direct spatiotemporal and quantitative aspects of protein expression. Recent advances in our understanding of the regulatory architecture of the human genome coincide with growing evidence that changes in regulatory sequences are associated with human disease. Several recent reviews have highlighted disease-causing potential of aberrations in transcriptional and splicing regulatory elements as well as non-protein-coding RNA. Although changes in regulatory sequences generally produce milder biological effects than their protein-coding counterparts, many act as independent risk factors for common complex disorders or as genetic modifiers for "primary" disease-causing loci. Here, we review bioinformatics and experimental approaches that are used to identify regulatory sequences and assess pathogenicity of regulatory changes. We describe the current state of knowledge on disease-causing changes in regulatory sequences, challenge protein-centric views, and discuss complexities and solutions pertaining to the interpretation of regulatory changes in the next-generation sequencing era.

The World of Regulatory Influence

Models of firms’ influence over the regulatory agencies that oversee them have traditionally been constrained by several factors, including a lack of direct measures of “influence,” an inability to account for variations in the institutional environment within which firms operate, and a nearly singular focus on industry-level measures of interest group strengths. In this paper, we employ a global database and novel measures to provide a fresh look at the determinants of firms’ influence over regulatory agencies. We find that in addition to traditional industry-level determinants, important country-level institutional and firm-level determinants affect firms’ regulatory agency influence. We also find that regulatory process variations affect firms’ influence over regulators. With these empirical estimates in hand, we generate a Regulatory Influence Index that ranks influence levels of typical firms that operate in each sample country in the dataset, and then discuss the substantial country-level variation in regulatory agency influence that obtains.

The impact of cis-acting polymorphisms on the human phenotype

Cis-acting polymorphisms that affect gene expression are now known to be frequent, although the extent and mechanisms by which such variation affects the human phenotype are, as yet, only poorly understood. Key signatures of cis-acting variation are differences in gene expression that are tightly associated with regulatory SNPs or expression Quantitative Trait Loci (eQTL) and an imbalance of allelic expression (AEI) in heterozygous samples. Such cis-acting sequence differences appear often to have been under selection within and between populations and are also thought to be important in speciation. Here we describe the example of lactase persistence. In medical research, variants that affect regulation in cis have been implicated in both monogenic and polygenic disorders, and in the metabolism of drugs. In this review we suggest that by further understanding common regulatory variations and how they interact with other genetic and environmental variables it will be possible to gain insight into important mechanisms behind complex disease, with the potential to lead to new methods of diagnosis and treatments.

Metabolic regulatory variations in rats due to acute cold stress & Tinospora Cordifolia intervention: high resolution 1H NMR approach

Acute cold stress may trigger systemic biochemical and physiological changes in the living organisms, which leads to rapid loss of homeostasis. These changes may reverse due to self-regulatory mechanism of the organism or by the intervention of suitable medication in the form of herbs. The present study was undertaken to assess the alterations in metabolites levels arising due to acute cold stress and to monitor the restoration of these changes by suitable herb intervention. Male Sprague-Dawley rats were exposed to acute cold stress of −10°C for 3 h and urine samples were collected and analyzed by NMR spectroscopy in conjugation with Principal Component Analysis (PCA). The study revealed highly significant biochemical changes in urinary metabolites and also demonstrated the protective effects of Tinospora Cordifolia (Tc) extract on the stressed rats. These changes suggest the involvement of various metabolic pathways such as Tricarboxylic Acid (TCA) cycle, gut microbiota, renal function, catecholamines and muscle metabolism in the metabolic alterations induced by cold stress and the compensation required to restore homeostasis. The present study forms the basis of future studies to establish potential biomarkers for cold stress in humans and lay down the optimum dosage of Tc to be administered for providing immunity to the body as prophylactic and mitigating agent against environmental insult such as cold stress.

Laws of Attraction

Past research recognizes that firms exploit regulatory variations to their advantage but depicts such regulatory arbitrage as a dyadic process between firms and regulators. We extend this account by including a firm’s non-market rivals and suggest that firms view regulatory differences as part of a corporate political opportunity structure and exploit regulatory variations to disadvantage their rivals. Empirically, we focus on variations in right-to-work (RTW) laws that signal the pro-business climate in a state; these laws exist in 22 U.S. states. Using a spatial-regression discontinuity design, we analyze how Walmart locates new stores in the face of anti-Walmart activists and exploits regulatory discontinuities on the borders between RTW and non-RTW states. We find that Walmart is more likely to propose new stores, and to open those stores even if they are protested, at the borders of RTW states, compared with the borders of neighboring non-RTW states. We conclude with a discussion of implications for the study of regulation, social movements, and organizations.

Variation in the ADH1B proximal promoter affects expression

The primary pathway of metabolism of dietary alcohol is via its oxidation in liver by alcohol dehydrogenases (ADH). Differences in the ADH enzyme activity or levels of enzyme present could affect the risk for alcoholism. Regulatory variations have been shown to affect the promoter activity and thereby affect the risk for alcoholism. In this study the functional effects of the two SNPs (rs1159918 and rs1229982) in the proximal promoter region of ADH1B that were associated with alcoholism were explored. We examined the effects of five naturally occurring haplotypes on the promoter activity. We observed that a C to A change at rs1229982 increased promoter activity 1.4-fold.

Structure and Assembly of Escherichia coli Capsules

The capsule is a cell surface structure composed of long-chain polysaccharides that envelops many isolates of Escherichia coli. It protects the cell against host defenses or physical environmental stresses, such as desiccation. The component capsular polysaccharides (CPSs) are major surface antigens in E. coli. They are named K antigens (after the German word Kapsel). Due to variations in CPS structures, more than 80 serologically unique K antigens exist in E. coli. Despite the hypervariability in CPS structures, only two capsule-assembly strategies exist in E. coli. These have led to the assignment of group 1 and group 2 capsules, and many of the key elements of the corresponding assembly pathways have been resolved. Structural features, as well as genetic and regulatory variations, give rise to additional groups 3 and 4. These employ the same biosynthesis processes described in groups 2 and 1, respectively. Each isolate possesses a distinctive set of cytosolic and inner-membrane enzymes, which generate a precise CPS structure, defining a given K serotype. Once synthesized, a multiprotein complex is needed to translocate the nascent CPS across the Gram-negative cell envelope to the outer surface of the outer membrane, where the capsule structure is assembled. While the translocation machineries for group 1 and group 2 CPSs are fundamentally different from one another, they possess no specificity for a given CPS structure. Each is conserved in all isolates producing capsules belonging to a particular group.

DNA Variants in Region for Noncoding Interfering Transcript of Dihydrofolate Reductase Gene and Outcome in Childhood Acute Lymphoblastic Leukemia

Dihydrofolate reductase (DHFR) is the major target of methotrexate, a key component in childhood acute lymphoblastic leukemia (ALL) treatment. We recently reported an association of DHFR promoter polymorphisms with ALL outcome. Lower event-free survival correlated with haplotype *1, defined by A(-317) and C(-1610) alleles. Haplotype *1 was also associated higher DHFR expression. Here, we analyzed adjacent 400-bp region participating in DHFR regulation as both a major promoter and a noncoding minor transcript. Six polymorphisms were identified, of which five were single nucleotide polymorphisms and one was length polymorphism composed of variable number of 9-bp elements and 9-bp insertion/deletion. Haplotype analysis including all promoter polymorphisms revealed diversification of haplotype *1 into five subtypes (*1a-*1e). DNA variations of major promoter/noncoding transcript region and haplotype *1 subtypes were subsequently analyzed for the association with ALL outcome. Lower event-free survival was associated with an A allele of G(308)A polymorphism (P = 0.02) and with *1b haplotype (P = 0.01). This association was particularly striking in high-risk patients (P = 0.001) and was subsequently confirmed in independent patient cohort (P = 0.02). Haplotype *1b was the only haplotype *1 subtype associated with higher mRNA levels. The study provides a new insight into DHFR regulatory variations predisposing to an event in ALL patients.

Multiplex parallel pair‐end‐ditag sequencing approaches in system biology

Characterization of all the functional components constituted in human genome relies in our ability to completely elucidate the genetic/epigenetic regulatory networks, chromatin states, nuclear architectures, and genome variations. Such endeavors demand for the development of robust and effective genomic technologies. In the past few years, the availability of disruptive next generation DNA sequencing technologies has offered new promise for whole genome interrogation. However, despite the massive parallel and ultra-high throughput capacity, the common nature of short read lengths found within these platforms limits their applications for many types of whole genome-based analyses. To overcome such constrain, pair end ditag (PET) based sequencing concept was conceived as an immediate solution to expand the information content and extend the linear coverage. By sequencing paired end signatures from any desired DNA fragment and mapping them to the reference genome, PET strategy allows the accurate demarcation of target DNA boundaries and defines their locations on the genomic landscape. Furthermore, the ability to delineate relationship between two ends of a DNA molecule enables the full scale discovery of unconventional gene products, genome rearrangements, and chromatin interactions. Coupling with the massively parallel and ultra-high throughput sequencing platforms, such unique features of PET strategy have the potential to revolutionize the approaches used to decipher regulatory networks in system biology, define the genome organizations, and characterize genome variations; which ultimately leads to the development of strategies for personalized medicine.

New putative cis-acting regulatory variations in the CFTR gene

New putative cis-acting regulatory variations in the CFTR gene

Detection, Distribution, and Pathologic Significance of BK Virus Strains Isolated From Patients With Kidney Transplants, With and Without Polyomavirus-Associated Nephropathy

BK virus strains or regulatory region sequence variations may play a role in the pathogenesis of polyomavirus-associated nephropathy (PVAN), although no definite relationship has yet been demonstrated. To investigate the pathologic significance of BK virus strains and regulatory region sequence variations. Eight (3.5%) of 226 patients with renal transplants developed PVAN; the remaining 218 cases were used as controls. From the patients who developed PVAN, 70 urine samples, 63 blood samples, and 17 renal biopsy samples were taken, and 682 urine samples, 677 blood samples, and 101 renal biopsy samples were taken from the control cases. Amplification and sequence analyses of regulatory region were obtained, and the sequences were analyzed using the Basic Local Alignment Search Tool program. The WWT strain was more frequently detected in PVAN cases than in the control cases (urine: 88.5% vs 22.1%; blood: 85.2% vs 40%; renal biopsies: 77.8% vs 0%), and the AS and WW strains were only isolated from controls. Strain 128-1 was frequently associated with JC virus coinfection in both groups (PVAN: 78.3%; controls: 98%). Major WWT rearrangements were detected in 29.6% of the urine samples, 30.4% of the blood samples, and one renal biopsy from the PVAN cases, but in only one urine sample from the controls. Insertion of 8 base pairs (P block) was found in all 128-1 strains; WW and AS were archetypal in 78.9% and 57.7% of the samples, respectively. Although the study included only 8 PVAN cases, regulatory region sequence variations seem to be frequent and independent of the development of the disease, and the WWT strain seems more frequently related to the development of nephropathy than other strains.

Detection, distribution, and pathologic significance of BK virus strains isolated from patients with kidney transplants, with and without polyomavirus-associated nephropathy.

Abstract Context.—BK virus strains or regulatory region sequence variations may play a role in the pathogenesis of polyomavirus-associated nephropathy (PVAN), although no definite relationship has yet been demonstrated. Objective.—To investigate the pathologic significance of BK virus strains and regulatory region sequence variations. Design.—Eight (3.5%) of 226 patients with renal transplants developed PVAN; the remaining 218 cases were used as controls. From the patients who developed PVAN, 70 urine samples, 63 blood samples, and 17 renal biopsy samples were taken, and 682 urine samples, 677 blood samples, and 101 renal biopsy samples were taken from the control cases. Amplification and sequence analyses of regulatory region were obtained, and the sequences were analyzed using the Basic Local Alignment Search Tool program. Results.—The WWT strain was more frequently detected in PVAN cases than in the control cases (urine: 88.5% vs 22.1%; blood: 85.2% vs 40%; renal biopsies: 77.8% vs 0%), and the AS and ...

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

Motivation: Design a new computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects.Summary: SNPnexus database provides functional annotation for both novel and public SNPs. Possible effects on the transcriptome and proteome levels are characterized and reported from five major annotation systems providing the most extensive information on alternative splicing. Additional information on HapMap genotype and allele frequency, overlaps with potential regulatory elements or structural variations as well as related genetic diseases can be also retrieved. The SNPnexus database has a user-friendly web interface, providing single or batch query options using SNP identifiers from dbSNP as well as genomic location on clones, contigs or chromosomes. Therefore, SNPnexus is the only database currently providing a complete set of functional annotations of SNPs in public databases and newly detected from sequencing projects. Hence, we describe SNPnexus, provide details of the query options, the annotation categories as well as biological examples of use.Availability: The SNPnexus database is freely available at http://www.snp-nexus.org.Contact: claude.chelala@cancer.org.uk

Contribution of regulatory and structural variations in APOE to predicting dyslipidemia

The objective of this study was to evaluate 1) whether non single nucleotide polymorphisms-coding (non-cSNP) in the apolipoprotein E gene (APOE) identified by resequencing studies contribute to statistically explaining dyslipidemia if variations in the two cSNPs in exon 4 that define the 2, 3, and 4 alleles are ignored, and 2) whether the contribution of these additional SNPs persists when variations in the cSNPs are considered. We used an ecological, multiple-population, data-mining strategy to identify single-SNP and two-SNP genotypes that distinguish between high and low levels of plasma lipids in three training samples, European-Americans from Rochester, MN, African-Americans from Jackson, MS, and Europeans from North Karelia, Finland. We found that a pair of SNPs located in the 5' region define genotypes A560T832/A560T832, A560T832/A560G832, and A560T832/T560T832, which distinguish between high and low levels of HDL-cholesterol (HDL-C), triglycerides (TG), and/or total cholesterol (T-C). The A560T832/- genotypes predicted high TG and high T-C in both genders in a large independent test sample from Copenhagen, Denmark. Prediction of high T-C in the Danish females was dependent on genotypes defined by the cSNPs. Our study suggests that both regulatory and structural variations should be considered when evaluating the utility of APOE for predicting dyslipidemia in the population at large.