Biology subjects

Callahan, C. M.

Publications and source records attributed to Callahan, C. M..

6 recordsLinked to original sources

bioRxiv2024

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

Genome-wide studies have identified significant allelic associations between genetic variants in or near the IKZF1 gene and multiple autoimmune disorders. IKZF1, encoding the transcription factor IKAROS, produces at least 10 distinct transcripts. To explore the impact of alternative splicing of IKZF1 on the function of mature T cells, we generated a panel of human T-cell clones with truncating mutations in IKZF1 exons 4, 6 or both. Differences in gene expression, chromatin accessibility, and protein abundance among clones were assessed by RNA-seq, ATAC-seq and immunoblotting. Clones with single targeting events clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKAROS family members. Our results suggest that even modest alterations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals. Author SummaryRNA sequencing has revealed an unexpectedly large population of alternative transcripts produced by most human genes, but the functional significance of such transcripts has been debated, with some authors arguing that they represent non-functional "noise" and others arguing that they are largely functional and greatly expand the potential human proteome. Here, we explore these issues for the transcription factor IKZF1, which produces numerous alternative transcripts in human T cells and is significantly associated with risk for type 1 diabetes and other autoimmune disorders. We introduce stop codons at multiple sites in alternatively spliced exons and evaluate transcript levels and chromatin accessibility in individually targeted clones, allowing us to assay the broad impact of alternative splicing of IKZF1 in human T cells. Our studies reveal that perturbation of IKZF1 splicing results in significant differences in gene expression, chromatin accessibility and protein production of other autoimmunity-associated genes and elicits compensatory expression changes in other IKAROS family members. Even modest alterations in IKZF1 splicing had significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals and suggesting that transcript isoforms produced by alternative splicing can and do have functional impacts.

genomics↗

bioRxiv2023

Molecular evolution of male reproduction across species with highly divergent sperm morphology in diverse murine rodents

It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass, presumably reflecting reduced sperm competition. Several sperm traits were associated with relative testes mass, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller relative testes mass due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction, and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.

evolutionary biology↗

bioRxiv2022

Genomic resolution of cryptic species diversity in chipmunks

Discovery of cryptic species is essential to understanding the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (T. amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.

evolutionary biology↗

bioRxiv2021

Human brain region-specific variably methylated regions (VMRs) are enriched for heritability of distinct neuropsychiatric traits

BACKGROUNDDNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focused on limited numbers of individuals and one to two brain regions. RESULTSUsing GTEx samples, we have generated a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12-23 donors. We identified differentially methylated regions between brain regions (DMRs) among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pair-wise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identified 2,295 unique CpG DMRs, many associated with ion transport. Consistent with prior studies, CpG DMRs were enriched in regulatory regions while non-CpG DMRs were enriched in intergenic regions. We also identified 81,130 regions of variably CpG methylated regions (VMRs), i.e. variable methylation among individuals in the same brain region, which were enriched in regulatory regions and in CpG DMRs. Many VMRs were unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. VMRs identified in the amygdala, anterior cingulate cortex, and hippocampus were enriched for heritability of schizophrenia. CONCLUSIONSThese data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.

genomics↗

bioRxiv2020

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and P. campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally-biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.

evolutionary biology↗

bioRxiv2020

The legacy of recurrent introgression during the radiation of hares

AO_SCPLOWBSTRACTC_SCPLOWHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

evolutionary biology↗