BackgroundMeasurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potential physiologically-relevant epigenetic changes. Illumina Infinium (Illumina, San Diego, CA, USA) is a commercially available microarray suite used to measure DNAm at many sites throughout the genome. However, it has been suggested that a subset of array probes may give misleading results due to issues related to probe design. To facilitate biologically significant data interpretation, we set out to enhance probe annotation of the newest Infinium array, the HumanMethylation450 BeadChip (450 k), with >485,000 probes covering 99% of Reference Sequence (RefSeq) genes (National Center for Biotechnology Information (NCBI), Bethesda, MD, USA). Annotation that was added or expanded on includes: 1) documented SNPs in the probe target, 2) probe binding specificity, 3) CpG classification of target sites and 4) gene feature classification of target sites.ResultsProbes with documented SNPs at the target CpG (4.3% of probes) were associated with increased within-tissue variation in DNAm. An example of a probe with a SNP at the target CpG demonstrated how sample genotype can confound the measurement of DNAm. Additionally, 8.6% of probes mapped to multiple locations in silico. Measurements from these non-specific probes likely represent a combination of DNAm from multiple genomic sites. The expanded biological annotation demonstrated that based on DNAm, grouping probes by an alternative high-density and intermediate-density CpG island classification provided a distinctive pattern of DNAm. Finally, variable enrichment for differentially methylated probes was noted across CpG classes and gene feature groups, dependant on the tissues that were compared.ConclusionDNAm arrays offer a high-throughput approach for which careful consideration of probe content should be utilized to better understand the biological processes affected. Probes containing SNPs and non-specific probes may affect the assessment of DNAm using the 450 k array. Additionally, probe classification by CpG enrichment classes and to a lesser extent gene feature groups resulted in distinct patterns of DNAm. Thus, we recommend that compromised probes be removed from analyses and that the genomic context of DNAm is considered in studies deciphering the biological meaning of Illumina 450 k array data.

Epigenetics is emerging as an attractive mechanism to explain the persistent genomic embedding of early-life experiences. Tightly linked to chromatin, which packages DNA into chromosomes, epigenetic marks primarily serve to regulate the activity of genes. DNA methylation is the most accessible and characterized component of the many chromatin marks that constitute the epigenome, making it an ideal target for epigenetic studies in human populations. Here, using peripheral blood mononuclear cells collected from a community-based cohort stratified for early-life socioeconomic status, we measured DNA methylation in the promoter regions of more than 14,000 human genes. Using this approach, we broadly assessed and characterized epigenetic variation, identified some of the factors that sculpt the epigenome, and determined its functional relation to gene expression. We found that the leukocyte composition of peripheral blood covaried with patterns of DNA methylation at many sites, as did demographic factors, such as sex, age, and ethnicity. Furthermore, psychosocial factors, such as perceived stress, and cortisol output were associated with DNA methylation, as was early-life socioeconomic status. Interestingly, we determined that DNA methylation was strongly correlated to the ex vivo inflammatory response of peripheral blood mononuclear cells to stimulation with microbial products that engage Toll-like receptors. In contrast, our work found limited effects of DNA methylation marks on the expression of associated genes across individuals, suggesting a more complex relationship than anticipated.population cohort | early-life environment | immune response

The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross-) regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules) with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a uniform set of criteria, permitting the definition of basic composition rules. The study demonstrates that computational methods are a powerful complement to experimental approaches in the analysis of transcription networks.

We present a theoretical study of electron transport through a molecule connected to two metallic nanocontacts. The system investigated is 1,4 benzenedithiolate (BDT) chemically bonded to two Au contacts. The surface chemistry is modeled by representing the tips of the Au contacts as two atomic clusters and treating the molecule-cluster complex as a single entity in an extended Hückel tight binding scheme. We model the tips using several different cluster geometries. An ideal lead is attached to each cluster, and the lead to lead transmission is calculated. The role of the molecule-cluster interaction in transport is analyzed by using single channel leads. We then extend the calculations to multi-channel leads that are a more realistic model of the tip's environment. Using the finite-voltage, finite temperature Landauer formula, we calculate the differential conductance for the different systems studied. The similarities and differences between the predictions of the present class of models and recent experimental work are discussed.

SUMMARY Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.

Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.Insulator elements participate in gene regulation by limiting potential interactions between promoters and regulatory elements. In transgene assays, an insulator can block enhancer-promoter interactions, but only when located between the enhancer and the promoter (21, 35). Similarly, insulators can block repression mediated by Polycomb group proteins (41). They can also protect bracketed transgenes from chromosomal position effects (36, 52). Because of these properties, insulators are thought to participate in genome organization and gene regulation by defining the boundaries of discrete regulatory domains (9,38,61,63). The mode of action of insulators is unclear but might involve acting as promoter decoys (20) or the formation of chromatin loops through interactions between insulators and perhaps also other nuclear substructures that remain to be biochemically defined (7,10,17,67).The scs and scsЈ elements from the 87A hsp70 heat shock locus were two of the first DNA sequences shown to have insulator activity (35,36,60). Two boundary element-associated factors (BEAFs), 32A and 32B, were identified based on their interaction with the scsЈ insulator element (but not the scs element) (29, 69). 32A and 32B are derived from the same gene and differ only by about 80 amino acids located at their amino termini. These unique regions harbor different atypical C 2 H 2 zinc finger DNA binding domains, termed BED fingers (3). BEAF binding sites are essential for scsЈ insulator activity (16), as is functional BEAF protein (22, 53). BEAF immunolocalizes to hundreds of sites on polytene chromosomes (69). Several of these genomic binding sites have been shown to have insulator activity (16), indicating that BEAF-dependen...

Ab-initio total energy calculations reveal benzene-dithiolate (BDT) molecules on a gold surface, contacted by a monoatomic gold STM tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity these Au/BDT/Au nanowires are shown to be electrically bi-stable switches, the smallest twoterminal molecular switches to date. Experiments with a conventional or novel self-assembled STM are proposed to test these predictions.Typeset using REVT E X 1

In this paper we address the topic of inelastic electron scattering in mesoscopic quantum transport. For systems where only elastic scattering is present, Landauer theory provides an adequate description of transport that relates the electronic current to single-particle transmission and reflection probabilities. A formalism proposed recently by Bonca and Trugman facilitates the calculation of the one-electron transmission and reflection probabilities for inelastic processes in mesoscopic conductors connected to onedimensional ideal leads. Building on their work, we have developed a selfconsistent procedure for the evaluation of the non-equilibrium electron distributions in ideal leads connecting such mesoscopic conductors to electron reservoirs at finite temperatures and voltages. We evaluate the net electronic current flowing through the mesoscopic device by utilizing these non-equilibrium distributions. Our approach is a generalization of Landauer theory that takes account of the Pauli exclusion principle for the various competing elastic and inelastic processes while satisfying the requirement of particle conservation.As an application we examine the influence of elastic and inelastic scattering on conduction through a two site molecular wire with longitudinal phonons using the Su-Schrieffer-Heeger model of electron-phonon coupling.