Sequence variation aware genome references and read mapping with the variation graph toolkit, bioRxiv, 2017-12-16
AbstractReference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual’s genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation, including large scale structural variation such as inversions and duplications.1 Equivalent structures are produced by de novo genome assemblers.2,3 Here we present vg, a toolkit of computational methods for creating, manipulating, and utilizing these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays,4 with improved accuracy over alignment to a linear reference, creating data structures to support downstream variant calling and genotyping. These capabilities make using variation graphs as reference structures for DNA sequencing practical at the scale of vertebrate genomes, or at the topological complexity of new species assemblies.
biorxiv genomics 200-500-users 2017Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis, bioRxiv, 2017-12-16
ABSTRACTLoss-of-function (LOF) methods, such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing, provide unparalleled power for studying the biological function of genes of interest. When coupled with transcriptomic analyses, LOF methods allow researchers to dissect networks of transcriptional regulation. However, a major concern is nonspecific targeting, which involves depletion of transcripts other than those intended. The off-target effects of each of these common LOF methods have yet to be compared at the whole-transcriptome level. Here, we systematically and experimentally compared non-specific activity of RNAi, antisense oligonucleotides and CRISPR interference (CRISPRi). All three methods yielded non-negligible offtarget effects in gene expression, with CRISPRi exhibiting clonal variation in the transcriptional profile. As an illustrative example, we evaluated the performance of each method for deciphering the role of a long noncoding RNA (lncRNA) with unknown function. Although all LOF methods reduced expression of the candidate lncRNA, each method yielded different sets of differentially expressed genes upon knockdown as well as a different cellular phenotype. Therefore, to definitively confirm the functional role of a transcriptional regulator, we recommend the simultaneous use of at least two different LOF methods and the inclusion of multiple, specifically designed negative controls.
biorxiv genomics 0-100-users 2017Stability, affinity and chromatic variants of the glutamate sensor iGluSnFR, bioRxiv, 2017-12-16
AbstractSingle-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of the glutamate sensor iGluSnFR that are functionally brighter; can detect sub-micromolar to millimolar concentrations of glutamate; and have blue, green or yellow emission profiles. These variants allow in vivo imaging where original-iGluSnFR was too dim, reveal glutamate transients at individual spine heads, and permit kilohertz imaging with inexpensive, powerful fiber lasers.
biorxiv neuroscience 0-100-users 2017Transcription organizes euchromatin similar to an active microemulsion, bioRxiv, 2017-12-16
Chromatin is organized into heterochromatin, which is transcriptionally inactive, and euchromatin, which can switch between transcriptionally active and inactive states. This switch in euchromatin activity is accompanied by changes in its spatial distribution. How euchromatin rearrangements are established is unknown. Here we use super-resolution and live-cell microscopy to show that transcriptionally inactive euchromatin moves away from transcriptionally active euchromatin. This movement is driven by the formation of RNA-enriched microenvironments that exclude inactive euchromatin. Using theory, we show that the segregation into RNA-enriched microenvironments and euchromatin domains can be considered an active microemulsion. The tethering of transcripts to chromatin via RNA polymerase II forms effective amphiphiles that intersperse the two segregated phases. Taken together with previous experiments, our data suggest that chromatin is organized in the following way heterochromatin segregates from euchromatin by phase separation, while transcription organizes euchromatin similar to an active microemulsion.
biorxiv cell-biology 100-200-users 2017Examining the genetic influences of educational attainment and the validity of value-added measures of progress, bioRxiv, 2017-12-15
AbstractIn this study, we estimate (i) the SNP heritability of educational attainment at three time points throughout the compulsory educational lifecourse; (ii) the SNP heritability of value-added measures of educational progress built from test data; and (iii) the extent to which value-added measures built from teacher rated ability may be biased due to measurement error. We utilise a genome wide approach using generalized restricted maximum likelihood (GCTA-GREML) to determine the total phenotypic variance in educational attainment and value-added measures that is attributable to common genetic variation across the genome within a sample of unrelated individuals from a UK birth cohort, the Avon Longitudinal Study of Parents and Children. Our findings suggest that the heritability of educational attainment measured using point score test data increases with age from 47% at age 11 to 61% at age 16. We also find that genetic variation does not contribute towards value-added measures created only from educational attainment point score data, but it does contribute a small amount to measures that additionally control for background characteristics (up to 20.09% [95%CI 6.06 to 35.71] from age 11 to 14). Finally, our results show that value-added measures built from teacher rated ability have higher heritability than those built from exam scores. Our findings suggest that the heritability of educational attainment increases through childhood and adolescence. Value-added measures based upon fine grain point scores may be less prone to between-individual genomic differences than measures that control for students’ backgrounds, or those built from more subjective measures such as teacher rated ability.
biorxiv genetics 0-100-users 2017Intrinsic neuronal dynamics predict distinct functional roles during working memory, bioRxiv, 2017-12-15
AbstractWorking memory (WM) is characterized by the ability to maintain stable representations over time; however, neural activity associated with WM maintenance can be highly dynamic. We explore whether complex population coding dynamics during WM relate to the intrinsic temporal properties of single neurons in lateral prefrontal cortex (lPFC), the frontal eye fields (FEF) and lateral intraparietal cortex (LIP) of two monkeys (Macaca mulatta). We found that cells with short timescales carried memory information relatively early during memory encoding in lPFC; whereas long timescale cells played a greater role later during processing, dominating coding in the delay period. We also observed a link between functional connectivity at rest and intrinsic timescale in FEF and LIP. Our results indicate that individual differences in the temporal processing capacity predicts complex neuronal dynamics during WM; ranging from rapid dynamic encoding of stimuli to slower, but stable, maintenance of mnemonic information.
biorxiv neuroscience 0-100-users 2017