Biology subjects

Swanson, M. S.

Publications and source records attributed to Swanson, M. S..

7 recordsLinked to original sources

bioRxiv2026

Molecular Basis of Histone H3 Reading and Writing by Legionella pneumophila SET Domain Lysine Methyltransferases

RomA and its highly conserved strain ortholog LegAS4 are SET and ankyrin domain-containing effector proteins of the intracellular bacterial pathogen Legionella pneumophila. These enzymes are secreted into host cells, where they translocate to the nucleus and methylate Lys14 in histone H3 (H3K14), a novel post-translation modification (PTM) that reprograms gene expression and promotes bacterial replication. To elucidate their H3K14 substrate specificity, we determined the crystal structures of LegAS4 and RomA bound to histone H3 peptides and characterized nucleosome binding and methylation by the enzymes. The results reveal a distinctive bipartite engagement of the histone H3 N-terminal tail by the enzymes SET and ankyrin domains. Further, the ankyrin domain distinguishes different PTMs at H3R2 and H3K4, which is crucial for nucleosome engagement and H3K14 methylation. Together, these studies yield new insights into histone H3 reading and writing by the L. pneumophila histone lysine methyltransferases during host cell infection.

biochemistry↗

bioRxiv2024

C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. Here, we show C9orf72Exp in pre-symptomatic and ALS-FTD patient cells and brains cause the folate- sensitive chromosomal fragile site, FRA9A. FRA9A centers on >33kb of C9orf72 as highly-compacted chromatin embedded in an 8.2Mb fragility zone spanning 9p21, encompassing 46 genes, making FRA9A one of the largest fragile sites. C9orf72Exp cells show chromosomal instability, heightened global- and Chr9p-enriched sister-chromatid exchanges, truncated-Chr9s, acentric-Chr9s and Chr9-containing micronuclei, providing endogenous sources of damaged and immunostimulatory DNA. Cells from one C9orf72Exp patient contained highly-rearranged FRA9A-expressing Chr9 with Chr9-wide dysregulated gene expression. Somatic C9orf72Exp repeat instability and chromosomal fragility are sensitive to folate-deficiency. Age-dependent repeat instability, chromosomal fragility, and chromosomal instability can be transferred to CNS and peripheral tissues of transgenic C9orf72Exp mice, implicating C9orf72Exp as the source. Our results highlight unappreciated effects of C9orf72 expansions that trigger vitamin-sensitive chromosome fragility, adding structural variations to the disease-enriched 9p21 locus, and likely elsewhere. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/620312v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@154b23borg.highwire.dtl.DTLVardef@1814a6dorg.highwire.dtl.DTLVardef@13d713eorg.highwire.dtl.DTLVardef@d5d994_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2019

Profilin 1 Controls the Assembly, Organization, and Dynamics of Leading Edge Actin Structures Through Internetwork Competition and Collaboration

How actin monomers are distributed to different networks remains poorly understood. One emerging concept is that the monomer pool is limited and heterogenous, causing biased assembly and internetwork competition. However, most knowledge regarding monomer distribution comes from studies where competing networks are discrete. In metazoans, many actin-based structures are complex, containing competing networks that overlap and are functionally interdependent. Addressing how monomers control the assembly and organization of these complex structures is critical to understanding how actin functions in cells. Here, we identify the monomer-binding protein profilin 1 (PFN1) as a major determinant of actin assembly, organization, and network homeostasis in mammalian cells. At the leading edge, PFN1 controls the localization and activity of the assembly factors Arp2/3 and Mena/VASP, with discrete stages of internetwork competition and collaboration occurring at different PFN1 concentrations. This causes substantial changes to leading edge actin architecture and the types of structures that form there.

cell biology↗

bioRxiv2019

A Two-Component System that Modulates Cyclic-di-GMP Metabolism Promotes Legionella pneumophila Differentiation and Viability in Low-Nutrient Conditions

During its life cycle, the environmental pathogen Legionella pneumophila alternates between a replicative and a transmissive cell type when cultured in broth, macrophages, or amoebae. Within a protozoan host, L. pneumophila further differentiates into the hardy cell type known as the Mature Infectious Form (MIF). The second messenger cyclic-di-GMP coordinates lifestyle changes in many bacterial species, but its role in the L. pneumophila life cycle is less understood. Using an in vitro broth culture model that approximates the intracellular transition from the replicative to transmissive form, here we investigate the contribution to L. pneumophila differentiation of a two-component system (TCS) that regulates cyclic-di-GMP metabolism. The TCS is encoded by lpg0278-lpg0277 and is co-transcribed with lpg0279, which encodes a protein upregulated in MIF cells. Using a gfp-reporter, we demonstrate that the promoter for this operon is RpoS-dependent and induced in nutrient-limiting conditions that do not support replication. The response regulator of the TCS (Lpg0277) is a bifunctional enzyme that both synthesizes and degrades cyclic-di-GMP. Using a panel of site-directed point mutants, we show that cyclic-di-GMP synthesis mediated by a conserved GGDEF domain promotes growth arrest of replicative L. pneumophila, production of pigment and poly-3-hydroxybutyrate storage granules, and viability in nutrient-limiting conditions. Genetic epistasis tests predict that the MIF protein Lpg0279 acts upstream of the TCS as a negative regulator. Thus, L. pneumophila is equipped with a regulatory network in which cyclic-di-GMP stimulates the switch from a replicative to a resilient state equipped to survive in low-nutrient environments.\n\nIMPORTANCEAlthough an intracellular pathogen, L. pneumophila has developed mechanisms to ensure long-term survival in low-nutrient aqueous conditions. Eradication of L. pneumophila from contaminated water supplies has proven challenging, as outbreaks have been traced to previously remediated systems. Understanding the genetic determinants that support L. pneumophila persistence in low-nutrient environments can inform design of remediation methods. Here we characterize a genetic locus that encodes a two-component signaling system (lpg0278-lpg0277) and a putative regulator protein (lpg0279) that modulates production of the messenger molecule cyclic-di-GMP. We show that this locus promotes both L. pneumophila cell differentiation and survival in nutrient-limiting conditions, thus advancing our understanding of the mechanisms that contribute to L. pneumophila environmental resilience.

microbiology↗

bioRxiv2018

Precise temporal regulation of alternative splicing during neural development

Alternative splicing (AS) is a crucial step of gene expression that must be tightly controlled, but the precise timing of dynamic splicing switches during neural development and the underlying regulatory mechanisms are poorly understood. Here we systematically analyzed the temporal regulation of AS in a large number of transcriptome profiles of developing mouse cortices, in vivo purified neuronal subtypes, and neurons differentiated in vitro. Our analysis revealed early- and late-switch exons in genes with distinct functions, and these switches accurately define neuronal maturation stages. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the \"immature\" splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome.

molecular biology↗

bioRxiv2017

Reversal of molecular pathology by RNA-targeting Cas9 in a myotonic dystrophy mouse model

The dominantly inherited, multi-systemic disease myotonic dystrophy type I (DM1) is caused by triplet repeat CTG expansions in the DMPK gene and is the most common form of adult-onset muscular dystrophy. Elimination of the toxic, repetitive CUG RNA constitutes a therapeutic for this disease. We report an RNA-targeting Cas9 (RCas9) system that supports efficient reversal of DM1 phenotypes via delivery to adult poly(CUG) DM1 mouse muscle using adeno-associated virus (AAV). We observe elimination of CUG RNA, restoration of CUG foci-associated Mbnl1 protein to wild-type subcellular localization, correction of DM1-type alternative splicing patterns in candidate genes including the voltage-gated chloride channel 1 (Clcn1) responsible for characteristic myotonia, recovery of Clcn1 staining, and reduction in centralized myonuclei. Our results establish RCas9 as a potential long-term in vivo therapeutic for DM1.\n\nOne Sentence SummaryA repurposed CRISPR system termed RNA-targeting Cas9 reverses the molecular pathology associated with the most common type of adult onset muscular dystrophy in adult mouse muscle.

molecular biology↗

bioRxiv2017

SFMetaDB: A Comprehensive Annotation of Mouse RNA Splicing Factor RNA-Seq Datasets

Although the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. Because of the importance of RNA splicing in diseases and biological processes, we constructed a database called SFMetaDB by curating datasets related with RNA splicing factors. Our effort focused on the RNA-Seq datasets in which splicing factors were knocked-down, knocked-out or over-expressed, leading to 75 datasets corresponding to 56 splicing factors. These datasets can be used in differential alternative splicing analysis for the identification of the potential targets of these splicing factors and other functional studies. Surprisingly, only [~]15% of all the splicing factors have been studied by loss- or gain-of-function experiments using RNA-Seq. In particular, splicing factors with domains from a few dominant Pfam domain families have not been studied. This suggests a significant gap that needs to be addressed to fully elucidate the splicing regulatory landscape. Indeed, there are already mouse models available for [~]20 of the unstudied splicing factors, and it can be a fruitful research direction to study these splicing factors in vitro and in vivo using RNA-Seq.\n\nDatabase URLhttp://sfmetadb.ece.tamu.edu/

bioinformatics↗