Browsing by Subject "Positive selection"
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Item Open Access Genome-wide Cross-species Analysis Linking Open Chromatin, Differential Expression and Positive Selection(2012) Shibata, YoichiroDeciphering the molecular mechanisms driving the phenotypic differences between humans and primates remains a daunting challenge. Mutations found in protein coding DNA alone has not been able to explain these phenotypic differences. The hypothesis that mutations in non-coding regulatory DNA are responsible for altered gene expression leading to these phenotypic changes has now been widely supported by differential gene expression experiments. Yet, comprehensive identification of all regulatory DNA elements across different species has not been performed. To identify the genetic source of regulatory change, genome-wide DNaseI hypersensitivity assays, marking all types of active gene regulatory element sites, were performed in human, chimpanzee, macaque, orangutan, and mouse. Many DNaseI hypersensitive (DHS) sites were conserved among all 5 species, but we also identified hundreds of novel human- and chimpanzee-specific DHS gains and losses that showed signatures of positive selection. Species-specific DHS gains were enriched in distal non-coding regions, associated with active histone modifications, and positively correlated with increased expression - indicating that these are likely to be functioning as enhancers. Comparison to mouse DHS data indicate that human or chimpanzee DHS gains are likely to have been a result of single events that occurred primarily on the human- or chimpanzee-specific branch, respectively. In contrast, DHS losses are associated with events that occurred on multiple branches. At least one mechanism contributing to DHS gains and losses are species-specific variants that lead to sequence changes at transcription factor binding motifs, affecting the binding of TFs such as AP1. These variants were functionally verified by DNase footprinting and ChIP-qPCR analyses.
Item Open Access Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.(BMC genomics, 2020-05-13) Berrio, Alejandro; Haygood, Ralph; Wray, Gregory ABACKGROUND:Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. RESULTS:We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We applied the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. Then, we evaluated the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity and specificity. We found that the length of the query alignment can vary between 150 bp and 1 kb without affecting the estimation of selection, while for the reference alignment, we found that a length of 3 kb is adequate for proper testing. We also simulated sequence alignments under different classes of evolution and validated our ability to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we re-confirmed that a quarter of all non-coding Human Accelerated Elements are evolving by positive selection. CONCLUSION:Here, we introduce a method we called adaptiPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome.Item Open Access Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function.(PeerJ, 2020-01) Berrio, Alejandro; Gartner, Valerie; Wray, Gregory ABackground:The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods:Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results:We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.Item Open Access Role of E-proteins in B Lymphocyte Commitment and Thymocyte Selection(2009) Jones, Mary ElizabethThe E-protein transcription factors E2A and HEB regulate various cell processes during the development of B and T lymphocytes, including cell differentiation, lineage commitment, recombination of immune receptor genes, proliferation, and survival. B cell development is dependent on E2A from the earliest stages whereas T cell development relies on the cooperative efforts of both E2A and HEB. Established work demonstrates that the timing and dosage of E-protein expression is critical for mediating these diverse functions. The goal of this dissertation is to develop and utilize new genetic tools to manipulate the timing and dosage of E2A and HEB expression in order to enhance our understanding of E-protein function. Here we develop two new mouse models to identify novel lineage and stage specific roles of E-proteins during B lineage commitment and thymocyte selection.
First, we have generated an E2A inducible mouse model to allow reversible regulation of E2A function and precise timing of induction at the protein level. This system was created by inserting a tamoxifen responsive region of the estrogen receptor ligand binding domain (ER) at the carboxyl end of the tcfe2a gene, encoding E2A, to generate E2AER fusion proteins. To our knowledge, the ER fusion system has not yet been tested from an endogenous locus in live animals. Using the E2AER system, we have demonstrated rapidly induced E2AER activity upon tamoxifen treatment that is capable of supporting B cell development in an ex vivo culture system. In addition to characterizing the kinetics and reversibility of this inducible system, we have utilized tamoxifen treatment of E2AER B cell progenitors to identify potential novel E2A target genes driving B lineage commitment.
Second, we have analyzed E-protein function during the double positive (DP) stage of alpha beta T cell development by using a Cre-loxp conditional deletion system. Here, E-protein dosage was manipulated by removal of both E2A and HEB, and the timing of deletion was controlled by using a CD4Cre transgene. During development, survival through the DP stage and initiation of differentiation to the subsequent single positive (SP) stage for generation mature alpha beta T cells is dependent on the production of a functional alpha beta T cell receptor (TCR). The mechanism that maintains cells at the DP stage prior to expression of a mature TCR remains unclear. In this study, we have shown that E2A and HEB together are required to maintain DP fate and regulate the transition to the SP stage. Loss of E2A and HEB in DP thymocytes was sufficient to trigger DP to SP differentiation, even in the absence of a TCR. Deletion of E2A and HEB allowed cells to bypass the requirement for a TCR-mediated positive selection signal. These findings identify E2A and HEB as key regulators enforcing thymocyte positive selection to ensure maturing T cells express a functional receptor.
Item Open Access Using Genomic Tools to Understand Speciation Dynamics in Madagascar's Mouse Lemurs (Order: Primates)(2019) Campbell, Christopher RyanMouse lemurs (genus Microcebus; Order Primates) are endemic to the island nation of Madagascar. These small, nocturnal primates offer a unique mammalian system ideally suited to study the patterns and processes of speciation, and the genomic revolution of the past decade has presented us with novel tools to test and understand these lineage-specific dynamics.
This thesis presents three independent projects on the speciation dynamics within mouse lemurs, interconnected by their utilization of the entire genome as a tool for reconstructing hidden evolutionary processes. Chapter 2 is an overview of the exploding field of speciation genomics and serves to ground these individual projects in evolutionary theory. In Chapter 3, we adopt a genome-wide approach to understand how the changing landscape of Madagascar has shaped the phylogeography of mouse lemurs while simultaneously leveraging the patterns derived from these species to discern clues about the ecology on the island in the distant past, and thus the impact of more recently arriving humans. The phylogenetic and population genetic patterns in a five-species clade of mouse lemurs suggest that longitudinal dispersal across the island occurred until approximately 500,000 ybp when a large ancestral population experienced rapid diversification, resulting in the present-day distributions of these species. However, the accuracy of the estimates of species ages from genetic data are limited primarily by our understanding of the mutation generation process in this non-model species. Thus, in Chapter 4, we improve these estimates by using high-coverage linked-read sequencing to estimate the generational de novo mutation rate within a family pedigree (n=8) of grey mouse lemurs (Microcebus murinus). We estimated a mutation rate of 1.64x10-8 mutations per basepair per generation, higher than nearly all mammals that have been previously characterized. Because estimates of these biological metrics critically affect estimates of divergence time we reanalyzed the results presented in the previous chapter and discover considerably more recent divergence times across the five-species clade. Finally, in Chapter 5, we utilize the knowledge of functional processes housed within genomic data to investigate the underlying causes of speciation in Microcebus. While many of the initial applications of genomic data in the genus have centered around understanding the phylogenetic relationships among the species rather than the mechanisms that underlie their diversification, we attempt to utilize genomic annotations to assess a putative mechanism driving speciation. We compared the rates of positive selection within sperm genes and a set of randomly drawn genes to look for the presence of positive selection. These comparisons reveal an elevated dN/dS, and thus evidence for positive selection, in sperm fertilization-related genes relative to sperm construction-related genes and a similarly-sized set of randomly-drawn genes. The results provide data that support our current knowledge of the behavior and natural history of these primates, highlighting what could be genomic mechanism of speciation among these highly speciose primates of Madagascar. In doing so we hope to have shown that detailed questions relating to both the extrinsic (e.g., inter- and intra- population and ecological interactions) and intrinsic (e.g., genome content and architecture) forces that drive speciation can be asked and answered, especially in non-model species.