Biology subjects

Kidd, J. M.

Publications and source records attributed to Kidd, J. M..

18 recordsLinked to original sources

bioRxiv2026

Barking Up Inferred Trees: Detecting Signatures of Selection in Dog Genomes Using Ancestral Recombination Graphs

Identifying the molecular targets of selection is a major goal of evolutionary studies. Prior studies have employed summary statistics to identify genetic signals associated with the domestication of dogs (Canis lupus familiaris) from wolves. Recent computational advances enable new approaches based on Ancestral Recombination Graphs, which model the genealogical relationships of samples throughout the genome. Using Ancestral Recombination Graphs, we identified 285 outlier loci with an unusually recent mean time to the most recent common ancestor (TMRCA) in a geographically diverse set of 40 village dogs as compared to 41 wolves. Loci identified from prior studies are enriched in the tails of the observed TMRCA ratio distribution, indicating convergence among diverse approaches for identifying signals of selection in dogs. The outlier loci we identify are within 50 kb of many genes previously linked to domestication and include genes with functions in neurodevelopment and behavior. This study offers a refined set of candidate regions for future functional dissection of the precise molecular changes selected in the early evolution of dogs.

evolutionary biology↗

bioRxiv2026

Investigating the dynamics of proviral silencing in polyclonal HIV-1 infected Jurkat cell populations

Previous work demonstrated that individual HIV-1 provirus-containing Jurkat cell clones maintain stable bimodal expression patterns throughout 8 to 9 days of culture. However, within polyclonal infected cell pools, the overall proportion of cells displaying HIV-1 expression declines with time. Here, we examined the processes underlying population silencing in polyclonal pools comprised of hundreds of individual barcoded proviral clones throughout culturing periods of 22 and 90 days. Monitoring HIV-1 LTR activity via a GFP reporter confirmed that initially most clones exhibited bimodal expression, with mixtures of transcriptionally active and inactive cells. Over time, however, the overall fraction of LTR-active cells declined substantially. High-throughput clonal tracking showed that this decline was not driven by uniform transcriptional silencing. Instead, population silencing resulted from a combination of mechanisms: selective expansion of clones with low LTR activity, reductions in expression within certain clones, and long-term maintenance of stable bimodal expression in others. Notably, over half of clones retained stable bimodal expression patterns after 22 days, and approximately 17% of the clones retained stable bimodal expression even after 90 days in an independent second experiment, despite ongoing phenotypic switching at the single-cell level. These findings demonstrate that population-level HIV-1 silencing emerges from heterogeneous, clone-specific behaviors rather than uniform transcriptional repression. These observations confirm stability for a large subset of clones and provide insight into how integrants with diverse replication and expression properties can act together during HIV-1 polyclonal population silencing.

microbiology↗

bioRxiv2025

A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons

BackgroundDue to their history of domestication and breed formation, dogs are a powerful system for studying the phenotypic impact of genetic variation. Comparison of canine genome assemblies show that retrotransposons, mobile elements that mobilize via an RNA intermediate, are a major contributor to canine genetic diversity with an eightfold and 17-fold increase of LINE-1 and SINE differences, respectively, in dogs relative to that found among humans. The frequency of dimorphic retrotransposon insertions among dogs suggests these elements have mobilized at a high rate over recent canine evolution. However, the rate at which new insertions arise has yet to be determined. ResultsWe aligned a collection of genome assemblies derived from four breed dogs, a Dingo, and an American grey wolf to a Greenland grey wolf to identify dimorphic LINE-1 and SINEC insertions. Across our panel of seven canine assemblies, we identified and characterized 7,428 dimorphic LINE-1s and 51,572 dimorphic SINECs. Each assembly differs from the Greenland wolf genome by an average of 3,497 LINE-1s and 25,558 SINECs. Analysis of allele sharing among samples recapitulates known relationships and reveals substantial within-breed variation. Calibrating estimates using a previously estimated single nucleotide mutation rate of 4.5x10-9 per base pair per generation, we estimate that new LINE-1 and SINEC and insertions have occurred at a rate of 1/184 and 1/22 births over recent canine evolution. These estimates are largely consistent across assemblies and breeds. ConclusionsOur phylogenetic estimate of SINEC retrotransposition in canines is approximately twice as large as that estimated for Alu elements in humans, while the canine LINE-1 insertion rate is within the range of human estimates. These data suggest that although SINEC has been an outsized driver of canine genome evolution, the striking levels of canine LINE-1 and SINEC dimorphism mainly reflect high levels of long-standing genetic variation.

genomics↗

bioRxiv2025

Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination

BackgroundGenetic maps are a key resource for the analysis of genetic variation. Prior maps in dogs were based on the canFam3.1 genome assembly, which contains thousands of sequence gaps that include functional elements. Although long-read technologies have enabled the generation of updated reference assemblies, updated maps are required to take full advantage of these new resources. MethodsWe inferred fine-scale recombination maps that consider population demographic history for four populations of village dogs sequenced by the Dog10K Consortium. We compare properties among the newly generated and previously published maps and assess the effects of genetic map choice on genotype phasing accuracy. ResultsThe newly inferred maps are broadly consistent with previous studies of recombination in dogs. At small scales, stronger correlations are observed among maps inferred using linkage disequilibrium than with a pedigree-based map. The position of recombination hotspots showed significant overlap among inferred maps and were enriched for sequences that were gaps in a previous canine genome assembly. When using the Dog10K samples as a reference panel, a phase error rate of approximately 2% was found with the choice of genetic map having little effect. ConclusionsWe describe genetic maps based on the canFam4 assembly which will be useful for future studies of genetic variation that rely on updated dog genome references.

genomics↗

bioRxiv2025

Integrative genotyping and analysis of canine structural variation using long-read and short-read data

Structural variation makes an important contribution to canine evolution and phenotypic differences. Although recent advances in long-read sequencing have enabled the generation of multiple canine genome assemblies, most prior analyses of structural variation have relied on short read sequencing. To offer a more complete assessment of structural variation in canines, we performed an integrative analysis of structural variants present in 12 canine samples with available long-read and short-read sequencing data along with genome assemblies. Use of long-reads permits the discovery of heterozygous variation that is absent in existing haploid assembly representations while offering a marked increase in the ability to identify insertion variants relative to short-read approaches. Examination of the size spectrum of structural variants shows that dimorphic LINE-1 and SINE variants account for over 45% of all deletions and identified 1,410 LINE-1s with intact open reading frames that show presence-absence dimorphism. Using a graph-based approach, we genotype newly discovered structural variants in an existing collection of 1,879 resequenced dogs and wolves, generating a variant catalog containing a 56.5% increase in the number of deletions and 705% increase in the number of insertions previously found in the analyzed samples. Examination of allele frequencies across admixture components present across breed clades identified 283 structural variants evolving with a signature of selection. Significance statementExisting studies of structural variation have focused on genomes sequenced with short-read technology. In this study, we systematically combine short-read and long-read data sets to identify and genotype structural variation across canines, resulting in an expanded catalog of structural variants. Analysis of allele frequencies identified structural variants in genic regions that may have been evolving under selection across breed clades.

genomics↗

bioRxiv2024

Characterization of nuclear mitochondrial insertions in canine genome assemblies

BackgroundThe presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses of mitochondrial sequence variation and is a potential source of false positives in disease studies. To improve the analysis of mitochondrial variation in canines, we completed a systematic assessment of Numt content across genome assemblies, canine populations and the carnivore lineage. ResultsCentering our analysis on the UU_Cfam_GSD_1.0/canFam4/Mischka assembly, a commonly used reference in dog genetic variation studies, we find a total of 321 Numts, located throughout the nuclear genome and encompassing the entire sequence of the mitochondria. Comparison to 14 canine genome assemblies identified 63 Numts with presence-absence dimorphism among dogs, wolves, and a coyote. Further, a subset of Numts were maintained across carnivore evolutionary time (arctic fox, polar bear, cat), with 8 sequences likely more than 10 million years old, and shared with the domestic cat. On a population level, using structural variant data from the Dog10K Consortium for 1,879 dogs and wolves, we identified 11 Numts that are absent in at least one sample as well as 53 Numts that are absent from the Mischka assembly. ConclusionsWe highlight scenarios where the presence of Numts is a potentially confounding factor and provide an annotation of these sequences in canine genome assemblies. This resource will aid the identification and interpretation of polymorphisms in both somatic and germline mitochondrial studies in canines.

genomics↗

bioRxiv2024

A variant centric analysis of allele sharing in dogs and wolves

Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analysis of allele sharing among canine groups has been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We find that 22% of variants are common across wolves, village dogs, and breed dogs, that [~]16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.

genomics↗

bioRxiv2024

A map of canine sequence variation relative to a Greenland wolf outgroup

For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1,929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.

genomics↗

bioRxiv2024

Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes

Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1 or L1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing messenger RNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINE RNAs use strategies to hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.

molecular biology↗

bioRxiv2023

Duplications and retrogenes are numerous and widespread in modern canine genomic assemblies

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that approximately 8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with multiple metrics supporting the high-quality of the mCanLor1.2 wolf assembly constructed using PacBio HiFi reads. Comparison between the wolf and other canine assemblies found that approximately 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Together, our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies. SignificanceDuplications are highly influential on evolution, but are commonly misassembled, especially in lagging genomic groups like canines. We assessed nine canine assemblies for duplication presence, and found enrichment for acrocentric regions, misattribution of duplications to unplaced contigs, and the presence of short, high-recurrence duplications. Investigating further, we find high numbers of retrocopies retaining hallmarks present in the canine assemblies, and determine a rate of novel retrocopy insertion at 1 in 3,514 births.

genomics↗

bioRxiv2023

Mapping the Complex Genetic Landscape of Human Neurons

When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes.

neuroscience↗

bioRxiv2021

Vpr shapes the proviral landscape and polyclonal HIV-1 reactivation patterns in cultured cells

Cell culture models suggest that the HIV-1 viral protein R (Vpr) is dispensable for latency establishment. However, whether Vpr affects the persistent proviral landscape and responsiveness to latency reversing agents (LRAs) is unclear. Here, integration site landscape, clonal dynamics, and latency reversal effects of Vpr were studied by comparing barcoded vpr+ and vpr- populations arising after infection of Jurkat cells in vitro. The results showed that individual integrant clones differed in fractions of LTR-active daughter cells: some clones gave rise to few to no LTR-active cells while for others almost all daughter cells were LTR-active. Integrant clones with at least 60% LTR-active cells (high LTR-active clones) contained proviruses positioned closer to preexisting enhancers (H3K27ac) and promoters (H3K4me3) than clones with <30% LTR-active cells (low LTR-active clones). Comparing vpr+ and vpr- populations revealed that the vpr+ population was depleted of high LTR-active clones. Complementing vpr-defective proviruses by transduction with vpr 16 days after infection led to rapid loss of high LTR-active clones, indicating that the effect of Vpr on proviral populations occurs post-integration. Comparing vpr+ and vpr- integration sites revealed that predominant vpr+ proviruses were farther from enhancers and promoters. Correspondingly, distances to these marks among previously reported intact HIV proviruses in ART-suppressed patients were more similar to those in the vpr+ pool than to vpr- integrants. To compare latency reactivation agent (LRA) responsiveness, the LRAs prostratin and JQ1 were applied separately or in combination. vpr+ and vpr- population-wide trends were similar, but combination treatment reduced virion release in a subset of vpr- clones relative to when JQ1 was applied separately, an effect not observed in vpr+ pools. Together, these observations highlight the importance of Vpr to proviral population dynamics, integration site landscapes, and responsiveness to latency reversing agents. One Sentence Summary Expression properties and responsiveness to latency reactivation agents of individual HIV-1 proviral clones within polyclonal populations are masked by dominant clones and influenced by proviral proximity to certain epigenetic marks and by Vpr, a viral factor not previously known to affect latency and reactivation.

microbiology↗

bioRxiv2021

Dog10K_Boxer_Tasha_1.0: A long-read assembly of the dog reference genome

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named "Tasha" initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good quality draft, as with all assemblies produced at the time it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein coding genes. Here we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies, that increases sequence contiguity >100-fold, closes >23,000 gaps of the Canfam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.

genomics↗

bioRxiv2020

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3 end of LINE-1_Cfs (i.e., LINE-1_Cf 3-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

genomics↗

bioRxiv2019

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline -- TypeTE -- which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a gold standard set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.

bioinformatics↗

bioRxiv2019

Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis

HIV-1 gene expression is regulated by host and viral factors that interact with viral motifs and is influenced by proviral integration sites. Here, expression variation among integrants was followed for hundreds of individual proviral clones within polyclonal populations throughout successive rounds of virus and cultured cell replication. Initial findings in immortalized cells were validated using CD4+ cells from donor blood. Tracking clonal behavior by proviral \"zip codes\" indicated that mutational inactivation during reverse transcription was rare, while clonal expansion and proviral expression states varied widely. By sorting for provirus expression using a GFP reporter in the nef open reading frame, distinct clone-specific variation in on/off proportions were observed that spanned three orders of magnitude. Tracking GFP phenotypes over time revealed that as cells divided, their progeny alternated between HIV transcriptional activity and non-activity. Despite these phenotypic oscillations, the overall GFP+ population within each clone was remarkably stable, with clones maintaining clone-specific equilibrium mixtures of GFP+ and GFP-cells. Integration sites were analyzed for correlations between genomic features and the epigenetic phenomena described here. Integrants inserted in genes sense orientation were more frequently found to be GFP negative than those in the antisense orientation, and clones with high GFP+ proportions were more distal to repressive H3K9me3 peaks than low GFP+ clones. Clones with low frequencies of GFP positivity appeared to expand more rapidly than clones for which most cells were GFP+, even though the tested proviruses were Vpr-. Thus, much of the increase in the GFP-population in these polyclonal pools over time reflected differential clonal expansion. Together, these results underscore the temporal and quantitative variability in HIV-1 gene expression among proviral clones that are conferred in the absence of metabolic or cell-type dependent variability, and shed light on cell-intrinsic layers of regulation that affect HIV-1 population dynamics.\n\nSummaryVery few HIV-1 infected cells persist in patients for more than a couple days, but those that do pose life-long health risks. Strategies designed to eliminate these cells have been based on assumptions about what viral properties allow infected cell survival. However, such approaches for HIV-1 eradication have not yet shown therapeutic promise, possibly because much of the research underlying assumptions about virus persistence has been focused on a limited number of infected cell types, the averaged behavior of cells in diverse populations, or snapshot views. Here, we developed a high-throughput approach to study hundreds of distinct HIV-1 infected cells and their progeny over time in an unbiased way. This revealed that each virus established its own pattern of gene expression that, upon infected cell division, was stably transmitted to all progeny cells. Expression patterns consisted of alternating waves of activity and inactivity, with the extent of activity differing among infected cell families over a 1000-fold range. The dynamics and variability among infected cells and within complex populations that the work here revealed has not previously been evident, and may help establish more accurate correlates of persistent HIV-1 infection.

microbiology↗

bioRxiv2017

Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements

PurposeDNA methylation is a well characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of synthesizing a strand of RNA from DNA, or transcription, is controlled by proteins that regulate RNA polymerase activity by binding to specific gene regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell specific gene expression. While much is known about the functions and DNA binding specificity of CRX, less is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements.\n\nMethodsWe used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO, PDE6B, PAX6, and LINE. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences.\n\nResultsIn this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to our DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate that changes to the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX dependent transcription.\n\nConclusionCollectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.

molecular biology↗

bioRxiv2017

Selective sweep analysis using village dogs highlights the pivotal role of the neural crest in dog domestication

BackgroundDogs (Canis lupus familiaris) were domesticated from gray wolves between 10-40 kya in Eurasia, yet details surrounding the process of domestication remain unclear. The vast array of phenotypes exhibited by dogs mirror other domesticated animal species, a phenomenon known as the Domestication Syndrome. Here, we use signatures persisting in the dog genome to identify genes and pathways altered by the intensive selective pressures of domestication.\n\nResultsWe identified 246 candidate domestication regions containing 10.8Mb of genome sequence and 178 genes through whole-genome SNP analysis of 43 globally distributed village dogs and 10 wolves. Comparisons with ancient dog genomes suggest that these regions reflect signatures of domestication rather than breed formation. The strongest hit is located in the Retinoic Acid-Induced 1 (RAI1) gene, mutations of which cause Smith-Magenis syndrome. The identified regions contain a significant enrichment of genes linked to neural crest cell migration, differentiation and development. Read depth analysis suggests that copy number variation played a minor role in dog domestication.\n\nConclusionOur results indicate that phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development, are determined by genes which act early in embryogenesis. These differences are all phenotypes of the Domestication Syndrome, which can be explained by decreases in neural crest cells at these sites. We propose that initial selection during early dog domestication was for behavior, a trait also influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.

evolutionary biology↗