Interplay between DNA sequence and negative superhelicity drives R-loop structures.

R-loops are abundant three-stranded nucleic-acid structures that form in cis during transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms-junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription

LINE-1 Retrotransposition Activity in Human Genomes

SummaryHighly active (i.e., “hot”) long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel. Therefore, these results suggest that hot L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of interindividual genetic variation

Resolving the complexity of the human genome using single-molecule sequencing

The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome - 78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology

Diversity of human copy number variation and multicopy genes

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million singly unique nucleotide positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association

Bias correction and Bayesian analysis of aggregate counts in SAGE libraries

<p>Abstract</p> <p>Background</p> <p>Tag-based techniques, such as SAGE, are commonly used to sample the mRNA pool of an organism's transcriptome. Incomplete digestion during the tag formation process may allow for multiple tags to be generated from a given mRNA transcript. The probability of forming a tag varies with its relative location. As a result, the observed tag counts represent a biased sample of the actual transcript pool. In SAGE this bias can be avoided by ignoring all but the 3' most tag but will discard a large fraction of the observed data. Taking this bias into account should allow more of the available data to be used leading to increased statistical power.</p> <p>Results</p> <p>Three new hierarchical models, which directly embed a model for the variation in tag formation probability, are proposed and their associated Bayesian inference algorithms are developed. These models may be applied to libraries at both the tag and aggregate level. Simulation experiments and analysis of real data are used to contrast the accuracy of the various methods. The consequences of tag formation bias are discussed in the context of testing differential expression. A description is given as to how these algorithms can be applied in that context.</p> <p>Conclusions</p> <p>Several Bayesian inference algorithms that account for tag formation effects are compared with the DPB algorithm providing clear evidence of superior performance. The accuracy of inferences when using a particular non-informative prior is found to depend on the expression level of a given gene. The multivariate nature of the approach easily allows both univariate and joint tests of differential expression. Calculations demonstrate the potential for false positive and negative findings due to variation in tag formation probabilities across samples when testing for differential expression.</p

Phthalocyanine-nanocarbon ensembles: From discrete molecular and supramolecular systems to hybrid nanomaterials

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Accounts of Chemical Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ar5004384Conspectus Phthalocyanines (Pcs) are macrocyclic and aromatic compounds that present unique electronic features such as high molar absorption coefficients, rich redox chemistry, and photoinduced energy/electron transfer abilities that can be modulated as a function of the electronic character of their counterparts in donor-acceptor (D-A) ensembles. In this context, carbon nanostructures such as fullerenes, carbon nanotubes (CNTs), and, more recently, graphene are among the most suitable Pc companions. Pc-C60 ensembles have been for a long time the main actors in this field, due to the commercial availability of C60 and the ell-established synthetic methods for its functionalization. As a result, many Pc-C60 architectures have been prepared, featuring different connectivities (covalent or supramolecular), intermolecular interactions (self-organized or molecularly dispersed species), and Pc HOMO/LUMO levels. All these elements provide a versatile toolbox for tuning the photophysical properties in terms of the type of process (photoinduced energy/electron transfer), the nature of the interactions beteen the electroactive units (through bond or space), and the kinetics of the formation/decay of the photogenerated species. Some recent trends in this field include the preparation of stimuli-responsive multicomponent systems ith tunable photophysical properties and highly ordered nanoarchitectures and surface-supported systems shoing high charge mobilities. A breakthrough in the Pc-nanocarbon field as the appearance of CNTs and graphene, hich opened a ne avenue for the preparation of intriguing photoresponsive hybrid ensembles shoing light-stimulated charge separation. The scarce solubility of these 1-D and 2-D nanocarbons, together ith their loer reactivity ith respect to C60 stemming from their less strained sp2 carbon netorks, has not meant an unsurmountable limitation for the preparation of variety of Pc-based hybrids. These systems, hich sho improved solubility and dispersibility features, bring together the unique electronic transport properties of CNTs and graphene ith the excellent light-harvesting and tunable redox properties of Pcs. A singular and distinctive feature of these Pc-CNT/graphene (single- or fe-layers) hybrid materials is the control of the direction of the photoinduced charge transfer as a result of the band-like electronic structure of these carbon nanoforms and the adjustable electronic levels of Pcs. Moreover, these conjugates present intensified light-harvesting capabilities resulting from the grafting of several chromophores on the same nanocarbon platform.In this Account, recent progress in the construction of covalent and supramolecular Pc-nanocarbon ensembles is summarized, ith a particular emphasis on their photoinduced behavior. e believe that the high degree of control achieved in the preparation of Pc-carbon nanostructures, together ith the increasing knoledge of the factors governing their photophysics, ill allo for the design of next-generation light-fueled electroactive systems. Possible implementation of these Pc-nanocarbons in high performance devices is envisioned, finally turning into reality much of the expectations generated by these materialsFinancial support from the Spanish MICINN (CTQ2011-24187/BQU), the Comunidad de Madrid (S2013/MIT-2841 FOTOCARBON) and the EU (“SO2S” FP7-PEOPLE-2012-ITN, no.: 316975) is acknowledge

Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale - particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone- based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high- resolution sequence map of human structural variation - a standard for genotyping platforms and a prelude to future individual genome sequencing projects

Obesity prevention in child care: A review of U.S. state regulations

<p>ABSTRACT</p> <p>Objective</p> <p>To describe and contrast individual state nutrition and physical activity regulations related to childhood obesity for child care centers and family child care homes in the United States.</p> <p>Methods</p> <p>We conducted a review of regulations for child care facilities for all 50 states and the District of Columbia. We examined state regulations and recorded key nutrition and physical activity items that may contribute to childhood obesity. Items included in this review were: 1) Water is freely available; 2) Sugar-sweetened beverages are limited; 3) Foods of low nutritional value are limited; 4) Children are not forced to eat; 5) Food is not used as a reward; 6) Support is provided for breastfeeding and provision of breast milk; 7) Screen time is limited; and 8) Physical activity is required daily.</p> <p>Results</p> <p>Considerable variation exists among state nutrition and physical activity regulations related to obesity. Tennessee had six of the eight regulations for child care centers, and Delaware, Georgia, Indiana, and Nevada had five of the eight regulations. Conversely, the District of Columbia, Idaho, Nebraska and Washington had none of the eight regulations. For family child care homes, Georgia and Nevada had five of the eight regulations; Arizona, Mississippi, North Carolina, Oregon, Tennessee, Texas, Vermont, and West Virginia had four of the eight regulations. California, the District of Columbia, Idaho, Iowa, Kansas, and Nebraska did not have any of the regulations related to obesity for family child care homes.</p> <p>Conclusion</p> <p>Many states lack specific nutrition and physical activity regulations related to childhood obesity for child care facilities. If widely implemented, enhancing state regulations could help address the obesity epidemic in young children in the United States.</p