Biology subjects

Kramer, J. M.

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

7 recordsLinked to original sources

bioRxiv2026

Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome

Background Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies widely across species and sexes. This diversity makes saliva a powerful model to study evolution of gene expression. Here, we compared mouse and human salivary glands at the genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. Results We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. This contrasts the prevailing view that gene expression is largely conserved across tissues and highlights saliva as an unusually dynamic system of molecular evolution. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, 3.8 times higher than in the liver (p<0.001), a classic model of sex-biased expression. We also identified sex-specific expression of glycosylation genes associated with differential Muc19 sialylation. These results suggest that sexual dimorphism in mouse saliva arises from both transcriptional differences in secreted proteins and sex-specific post-translational modifications. Further, differentially expressed genes in submandibular gland cluster in genomic regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ~16.4% of male-biased submandibular gland expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Conclusions Together, our results reveal that lineage-specific genes disproportionately shape the mouse salivary transcriptome and that gene duplication and regulatory rewiring contribute to the rapid evolution of sex-biased expression in the submandibular gland. We describe a novel mechanism through which lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian saliva. Our findings support saliva as an evolutionarily dynamic system and are consistent with developmental systems drift, whereby similar phenotypes across species may be maintained despite substantial divergence in their underlying gene-regulatory programs.

evolutionary biology↗

bioRxiv2025

The SWI/SNF complex sub-unit Bap60 is required for training-induced gene transcription during long-term memory formation

Long-term memory (LTM) formation requires tightly regulated gene expression in response to neuronal activity. Chromatin remodeling is thought to play a role in enabling this transcriptional response, but the specific mechanisms remain unclear. In Drosophila, a transcriptional trace of courtship LTM training can be observed in the mushroom body (MB) during the memory consolidation phase after the end of training. Here, we investigated the role of Bap60, a core subunit of the Drosophila SWI/SNF chromatin remodeling complex, in the transcriptional trace of memory consolidation. Adult-specific knockdown of Bap60 in the MB selectively impaired LTM with short-term memory (STM) left intact. Transcriptome analysis of Bap60 knockdown MBs following courtship LTM training revealed near complete disruption of LTM training induced transcription in the MB. MB-specific CUT&RUN was used to map SWI/SNF binding sites and identify over 100 candidate direct Bap60-dependent training induced genes. Bap60 was not required for training induced activation of immediate early genes (IEGs), Hr38 and Sr, which are transcription factors that are critical for courtship LTM. This suggests that Bap60 may regulate LTM gene induction downstream of IEGs. Interestingly, we identified Sr binding sites at 30% of Bap60-dependent training induced genes. Many of these target genes were transcription factors, including Prospero (Pros), which we show is also required in the MB for LTM but not STM. Interestingly, Pros is induced in a subset of MB nuclei, suggesting Bap60 is involved in cell specific LTM training induced gene activation. Together, these findings reveal a critical role for Bap60, a core SWI/SNF subunit, as a key regulator of LTM training-induced transcription downstream of IEGs. Significance StatementAutosomal dominant mutations in SWI/SNF subunits are a leading cause of neurodevelopmental disorders (NDDs) including Autism and Intellectual Disability. Therefore, understanding their role in brain function can provide insight into the mechanisms underlying human disease. The SWI/SNF complex is an important chromatin remodeling complex that is conserved from yeast to mammals. This large protein complex is a transcriptional coactivator that uses energy from ATP to open up chromatin and create binding sites for transcription factors. Our knowledge about how SWI/SNF functions in different cell types of the brain is highly limited. In this study we investigate the Bap60 component of SWI/SNF in memory neurons of the fruit fly, Drosophila melanogaster. We find that Bap60 is required for activation of gene expression programs underlying long term memory consolidation. Dynamic gene expression, like that associated with LTM, is essential to build neural circuits during human cognitive development. It is therefore possible that this process is disrupted in people with SWI/SNF-related NDDs.

molecular biology↗

bioRxiv2023

Trithorax regulates long-term memory in Drosophila through epigenetic maintenance of mushroom body metabolic identity and translation capacity.

The role of epigenetics and chromatin in the maintenance of postmitotic neuronal cell identities is not well understood. Here, we show that the histone methyltransferase trithorax (trx) is required in postmitotic memory neurons of the Drosophila mushroom body (MB) to enable their capacity for long-term memory (LTM), but not short-term memory (STM). Using MB-specific RNA-, ChIP-, and ATAC-sequencing, we find that trx maintains expression of several non-canonical MB-enriched transcripts, including the orphan nuclear receptor Hr51, and the metabolic enzyme lactate dehydrogenase. Through these key targets, trx establishes a metabolic state characterized by high lactate levels in MB{gamma} neurons. This metabolic identity supports a high capacity for protein translation, a process that is essential for LTM, but not STM. These data suggest that trx, a classic regulator of cell type specification during development, has an alternative function in maintaining underappreciated aspects of postmitotic neuron identity, such as metabolic state. Our work supports a body of evidence suggesting that a high capacity for energy metabolism is an essential cell identity characteristic for neurons that mediate LTM.

molecular biology↗

bioRxiv2022

Mitochondrial ROS production by neutrophils is required for host antimicrobial function against Streptococcus pneumoniae and is controlled by A2B adenosine receptor signaling

Polymorphonuclear cells (PMNs) control Streptococcus pneumoniae (pneumococcus) infection through various antimicrobial activities. We previously found that reactive oxygen species (ROS) were required for optimal antibacterial function, however, the NADPH oxidase is known to be dispensable for the ability of PMNs to kill pneumococci. In this study, we explored the role of ROS produced by the mitochondria in PMN antimicrobial defense against pneumococci. We found that the mitochondria are an important source of overall intracellular ROS produced by murine PMNs in response to infection. We investigated the host and bacterial factors involved and found that mitochondrial ROS (MitROS) are produced independent of bacterial capsule or pneumolysin but presence of live bacteria that are in direct contact with PMNs enhanced the response. We further found that MyD88-/- PMNs failed to produce MitROS in response to pneumococcal infection suggesting that released bacterial products acting as TLR ligands are sufficient for inducing MitROS production in PMNs. To test the role of MitROS in PMN function, we used an opsonophagocytic killing assay and found that MitROS were required for the ability of PMNs to kill pneumococci. We then investigated the role of MitROS in host resistance and found that MitROS are produced by PMNs in response to pneumococcal infection. Importantly, treatment of mice with a MitROS scavenger prior to systemic challenge resulted in reduced survival of infected hosts. In exploring host pathways that control MitROS, we focused on extracellular adenosine, which is known to control PMN anti-pneumococcal activity, and found that signaling through the A2B adenosine receptor inhibits MitROS production by PMNs. A2BR-/- mice produced more MitROS and were significantly more resistant to infection. Finally, we verified the clinical relevance of our findings using human PMNs. In summary, we identified a novel pathway that controls MitROS production by PMNs, shaping host resistance against S. pneumoniae. Author summaryDespite the presence of antibiotics and vaccines, Streptococcus pneumoniae infections remain a serious cause of mortality and morbidity globally. Understanding protective host responses is key for designing improved therapies against infection. Neutrophils are innate immune cells that are crucial for control of S. pneumoniae infection. In this study we explored the mechanisms by which neutrophils kill S. pneumoniae. We found that the mitochondria, whose primary role is energy production, also produce reactive oxygen species (ROS) that are critical for the ability of neutrophils to kill S. pneumoniae. We explored the bacterial and host factors involved in mitochondrial ROS (MitROS) production by neutrophils. We found that recognition of bacterial products by neutrophils triggers this response and that the host A2B adenosine receptor regulates it. Importantly, MitROS were required for host resistance against S. pneumoniae. This study describes a novel pathway that controls anti-microbial responses and can be a future therapeutic target.

immunology↗

bioRxiv2019

Proteinase-Activated Receptor 4 (PAR4) Activation Triggers Cell Membrane Blebbing through RhoA and β-arrestin

Proteinase-Activated Receptors (PARs) are a four-member family of G-protein coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by serine proteinases such as thrombin, trypsin and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types including platelets, vascular smooth muscle cells and neuronal cells. In studying PAR4 signalling and trafficking, we observed dynamic changes in the cell membrane with spherical membrane protrusions that resemble plasma membrane blebbing. Since non-apoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release we sought to elucidate the signalling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/Cas9-mediated gene-editing approaches we establish that PAR4-dependent membrane blebbing occurs independently of the Gq/11 and Gi signalling pathways and is dependent on signalling via the {beta}-arrestin-1/-2 and RhoA signalling pathways. In order to gain a more comprehensive understanding of {beta}-arrestin-mediated signalling downstream of PAR4 and to guide future studies, we undertook RNA-seq analysis of PAR4 activated genes in control cells and in cells lacking {beta}-arrestin-1/-2. A list of differentially expressed genes was generated followed by Gene Ontology (GO) and enrichment analysis, revealing PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission-terms that relate back to known functions of PAR4 and are consistent with our finding of membrane blebbing triggered by PAR4 activation. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function.\n\nSignificance StatementWe find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA- and {beta}-arrestin-dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4. Finally through CRISPR/Cas9-mediated targeting and RNA-seq analysis we catalogue here PAR4-dependent transcription that is dependent on {beta}-arrestin.

pharmacology and toxicology↗

bioRxiv2018

Identification of SMARCD1 as a syndromic intellectual disability gene that is required for memory and context-dependent regulation of neuronal genes in Drosophila

Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause syndromic intellectual disability (ID). Here, we report on 5 individuals with mutations in the SMARCD1 gene, presenting with ID, developmental delay, hypotonia, feeding difficulties, and small extremities. The mutations were proven to be de novo in 4 of the 5 individuals. Mutations in other SWI/SNF components cause Coffin-Siris, Nicolaides-Baraitser, or other syndromic ID disorders. Although the individuals presented here have some clinical overlap with these disorders, they lack the typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog, Bap60, in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom body specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify SMARCD1 mutations as a novel cause of ID, and establish a role for the SMARCD1 ortholog Bap60 in regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development that is essential in establishing neuronal circuits that are required for learning and memory.

genetics↗

bioRxiv2018

Mushroom body specific transcriptome analysis reveals dynamic regulation of learning and memory genes after acquisition of long-term courtship memory in Drosophila

The formation and recall of long-term memory (LTM) requires neuron activity-induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Here, we performed transcriptome analysis in the Drosophila MB at two time points after the acquisition of LTM: 1 hour and 24 hours. The MB transcriptome was compared to biologically paired whole head (WH) transcriptomes. In both, we identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 302) than at 24 hours (WH = 23, MB = 20). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium-mediated neurotransmitter release and cAMP signalling. The neuron activity inducible genes hr38 and sr were also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory-related pathways after memory acquisition and provides a critical frame of reference for further investigation into the role of MB-specific gene regulation in memory.

genomics↗