Biology subjects

Juric, I.

Publications and source records attributed to Juric, I..

3 recordsLinked to original sources

bioRxiv2018

MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions centered on cohesin, CTCF and H3K4me3 associated regions in multiple cell types. MAPS is freely available at https://github.com/ijuric/MAPS.

bioinformatics↗

bioRxiv2018

Allele frequency dynamics in a pedigreed natural population

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes - variation in individual survival, reproductive success, and movement - are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

evolutionary biology↗

bioRxiv2018

Spatial photosynthesis modelling sets guidelines to constructing a viable single-cell cytoplasm-to-stroma C4 cycle

It has been proposed that introducing C4 photosynthesis into C3 crops would increase yield. The simplest scheme in- volves concentrating carbon originating from the cytosol in the chloroplast stroma of mesophyll cells without altering leaf or cell anatomy. Photosynthetic efficiency would then strongly depend on the chloroplast envelope permeability to CO2. We examine the performance of this C4 cycle with a spatial model of carbon assimilation in C3 mesophyll cell geometry, conducting a thorough exploration of parameter space relevant to C4 photosynthesis. For envelope perme- abilities below 300 {micro}m/s C4 photosynthesis has a higher quantum efficiency than C3. However, even when envelope permeability is above this threshold, the C4 pathway can provide a substantial boost to carbon assimilation with only a moderate decrease in efficiency. Depending on the available light-harvesting capacity of plastids, C4 photosynthesis could boost carbon assimilation anywhere from 20% to 100%. Gains are even more prominent under CO2 deprivation, and can be achieved in conjunction with lower investment in plastids if chloroplast surface coverage is also altered. A C4 pathway operating within individual mesophyll cells of C3 plants could hence lead to higher growth rates and better drought resistance in dry, high-sunlight climates.

plant biology↗