Biology subjects

Pearson, C. E.

Publications and source records attributed to Pearson, C. E..

4 recordsLinked to original sources

bioRxiv2024

Huntingtin is an RNA-binding protein and participates in NEAT1-mediated paraspeckles

AbstractHuntingtin protein, mutated in Huntington disease, is implicated in nucleic acid- mediated processes, yet evidence for direct huntingtin-nucleic acid interaction is limited. Here we show wildtype and mutant huntingtin co-purify with nucleic acids, primarily RNA, and interact directly with G-rich RNAs in in vitro assays. Huntingtin RNA immunoprecipitation sequencing from patient-derived fibroblasts and neuronal progenitor cells expressing wildtype and mutant huntingtin revealed NEAT1 as a significantly enriched transcript. Altered NEAT1 levels were evident in Huntingtons disease cells and postmortem brain tissues, and huntingtin knockdown decreased NEAT1 levels. Huntingtin co-localized with NEAT1 in paraspeckles, and we identified a high-affinity RNA motif preferred by huntingtin. This study highlights NEAT1 as a novel huntingtin interactor, demonstrating huntingtins involvement in RNA-mediated functions and paraspeckle regulation. One-Sentence SummaryHTT is an RNA-binding protein that interacts with G-rich sequences, including those in the paraspeckle lncRNA NEAT1.

cell biology↗

bioRxiv2022

Antagonistic roles of canonical and alternative RPA in tandem CAG repeat diseases

Tandem CAG repeat expansion mutations cause >15 neurodegenerative diseases, where ongoing expansions in patients brains are thought to drive disease onset and progression. Repeat length mutations will involve single-stranded DNAs prone to form mutagenic DNA structures. However, the involvement of single-stranded DNA binding proteins (SSBs) in the prevention or formation of repeat instability is poorly understood. Here, we assessed the role of two SSBs, canonical RPA (RPA1-RPA2-RPA3) and the related Alternative-RPA (Alt-RPA, RPA1-RPA4-RPA3), where the primate-specific RPA4 replaces RPA2. RPA is essential for all forms of DNA metabolism, while Alt-RPA has undefined functions. RPA and Alt-RPA are upregulated 2- and 10-fold, respectively, in brains of Huntington disease (HD) and spinocerebellar ataxia type 1 (SCA1) patients. Correct repair of slipped-CAG DNA structures, intermediates of expansion mutations, is enhanced by RPA, but blocked by Alt-RPA. Slipped-DNAs are bound and melted more efficiently by RPA than by Alt-RPA. Removal of excess slipped-DNAs by FAN1 nuclease is enhanced by RPA, but blocked by Alt-RPA. Protein-protein interactomes (BioID) reveal unique and shared partners of RPA and Alt-RPA, including proteins involved in CAG instability and known modifiers of HD and SCA1 disease. RPA overexpression inhibits rampant CAG expansions in SCA1 mouse brains, coinciding with improved neuron morphology and rescued motor phenotypes. Thus, SSBs are involved in repeat length mutations, where Alt-RPA antagonistically blocks RPA from suppressing CAG expansions and hence pathogenesis. The processing of repeat length mutations is one example by which an Alt-RPA{leftrightarrow}RPA antagonistic interaction can affect outcomes, illuminating questions as to which of the many processes mediated by canonical RPA may also be modulated by Alt-RPA.

genetics↗

bioRxiv2022

De Novo, Post-Zygotic, Inter-Tissue Mosaicism of Cell Autonomous ADNP Mutations in Autistic Individuals: Restricted Environmental Contribution

Many neurodevelopmental disorders, including autism, are caused by de novo mutations, that might arise as early as in the parental germline, during embryonic, fetal development, or as late as post-natal aging. Intra-tissue mutation-load variations could impact clinical presentation. One of the most common causes of autism is de novo mutations in ADNP. We developed an ultra-sensitive, highly-quantitative droplet digital PCR assay to determine ADNP mutation levels in patient tissues, including blood, teeth, hair, and 24 different tissues from a post-mortem de novo ADNP-mutated child ([~]6-years old), including a transplanted liver from a non-mutant donor (retained for 22 months). Striking variations of ADNP mosaicism arose between tissues of the same individual. Mutation load differences were evident between post-mortem tissues, but not in the transplanted liver -- supporting a cell autonomous genetic vulnerability to de novo mutations, arguing against a transferable environmentally-sensitive DNA damage/mutation predisposition. Variations between tissues suggest a developmental timing of the mutations. Most individuals showed at least one tissue with less than heterozygous mutations, where the presence of the homozygous non-mutant cells indicates that de novo ADNP mutations arose post-zygotically. Highly variable ADNP mosaicism between tissues, that within an individual can be less than heterozygous or approach homozygosity, indicate rapid ongoing post-zygotic, and possibly post-natal, somatic mutations, contributing to clinical variability.

genetics↗

bioRxiv2021

FAN1 nuclease processes and pauses on disease-associated slipped-DNA repeats: Mechanism against repeat expansions

FAN1 nuclease is a modifier of repeat expansion diseases, including Huntingtons disease (HD), fragile X syndrome, and autism. The age of HD onset correlates with ongoing inchworm-like repeat expansions (1-3 CAG units/event) in HD brains, and is regulated by three modifiers: The first two, repeat tract length and purity exert their effects by enhancing and slowing CAG expansions, respectively, by affecting the formation of slipped-DNAs -- mutagenic intermediates of instability; which are processed to expansions by the third modifiers, DNA repair proteins. FAN1 protects against hyper-expansions of repeats, by unknown mechanisms. We show FAN1, through iterative cycles bound, dimerized and cleaved slipped-DNAs, yielding striking patterns of distinct exo-nuclease pauses along slip-outs; 5'-C{downarrow}A{downarrow}GC{downarrow}A{downarrow}G-3' and 5'-C{downarrow}T{downarrow}G{downarrow}C{downarrow}T{downarrow}G-3'. The transcriptionally-displaced CAG strand was excised slower than its complementary CTG strand, required A*A and T*T mismatches, as fully-paired hairpins arrested excision progression, while disease-delaying CAA interruptions further slowed FAN1 excision. In contrast, endo-nucleolytic cleavage was insensitive to slip-outs. Rare FAN1 variants were found in autism individuals with CGG/CCG repeat expansions. Excision of CGG/CCG slip-outs were similarly excised, with CGG being slower than CCG. The slip-out specific ligand, Naphthyridine-Azaquinolone, shown to induce contractions of expanded repeats in cells, required FAN1 for its effect, and protected slip-outs from FAN1s exo- but not endo-nucleolytic digestion. FAN1s inchworm pausing of slip-out excision is suited to minimize incremental expansions and modulating disease onset.

genetics↗