Tip60's Novel RNA-Binding Function Modulates Alternative Splicing of Pre-mRNA Targets Implicated in Alzheimer's Disease

Abstract

The severity of Alzheimer’s Disease (AD) progression involves a complex interplay of genetics, age, and environmental factors orchestrated by histone acetyltransferase (HAT) mediated neuroepigenetic mechanisms. While disruption of Tip60 HAT action in neural gene control is implicated in AD, alternative mechanisms underlying Tip60 function remain unexplored. Here, we report a novel RNA binding function for Tip60 in addition to its HAT function. We show that Tip60 preferentially interacts with pre-mRNAs emanating from its chromatin neural gene targets in theDrosophilabrain and this RNA binding function is conserved in human hippocampus and disrupted inDrosophilabrains that model AD pathology and in AD patient hippocampus of either sex. Since RNA splicing occurs co-transcriptionally and alternative splicing (AS) defects are implicated in AD, we investigated whether Tip60-RNA targeting modulates splicing decisions and if this function is altered in AD. Replicate multivariate analysis of transcript splicing (rMATS) analysis of RNA-Seq data sets from wild-type and AD fly brains revealed a multitude of mammalian-like AS defects. Strikingly, over half of these altered RNAs identified as bona-fide Tip60-RNA targets that are enriched for in the AD-gene curated database, with some of these AS alterations prevented against by increasing Tip60 in the fly brain. Further, human orthologs of several Tip60-modulated splicing genes inDrosophilaare well characterized aberrantly spliced genes in human AD brains, implicating disruption of Tip60’s splicing function in AD pathogenesis. Our results support a novel RNA interaction and splicing regulatory function for Tip60 that may underly AS impairments that hallmark AD etiology.SIGNIFICANCE:Alzheimer’s Disease (AD) has recently emerged as a hotbed for RNA alternative splicing (AS) defects that alter protein function in the brain yet causes remain unclear. Although recent findings suggest convergence of epigenetics with co-transcriptional AS, whether epigenetic dysregulation in AD pathology underlies AS defects remains unknown. Here we identify a novel RNA interaction and splicing regulatory function for Tip60 histone acetyltransferase that is disrupted inDrosophilabrains modeling AD pathology and in human AD hippocampus. Importantly, mammalian orthologs of several Tip60-modulated splicing genes inDrosophilaare well characterized aberrantly spliced genes in human AD brain. We propose that Tip60 mediated AS modulation is a conserved critical post-transcriptional step that may underlie AS defects now characterized as hallmarks of AD.

Processivity and specificity of histone acetylation by the male-specific lethal complex

“…We conclude that the influence of RNA on the acetylation of the H4 N-terminus is a particular feature of the 4-MSL complex and not a property shared between the two MYST HAT family members, MOF and dTip60 ( 66 ).…”

“A CRISPR-dCas13 RNA-editing tool to study alternative splicing”

“…Furthermore, dCasRx not only efficiently shifts alternative splicing outcome into the correct splicing isoform, evidenced by amplicon sequencing of the edited transcripts, but it can do so to more than one alternatively spliced event by cotransfecting multiple gRNAs. This will significantly increase the phenotypic impact when correcting complex splicing-associated anomalies in which more than one splicing isoform is implicated, as in cancer or brain diseases (50)(51)(52). However, as a second caveat, we encountered some difficulties reaching functionally-relevant dCasRx expression levels in difficult-to-transfect cells.…”

Nurturing longevity through natural compounds: Where do we stand, and where do we go?

“…as a contributor to the development of myeloid malignancies, illustrating the importance of proper splicing regulation in maintaining cellular homeostasis (S. P. Palangat et al, 2019). Changes in alternative splicing patterns that occur with age are most significant in the brain; nevertheless, dysregulation of RNA homeostasis compromises cellular and tissue function, leading to age-related diseases (Adusumalli et al, 2019;Bhatnagar et al, 2023;Howe et al, 2022).…”

“…For instance, somatic mutations in splicing factors, such as U2 small nuclear RNA auxiliary factor 1, splicing factor 3b subunit 1 (SF3B1), and splicing factor 3b subunit 2 (SRSF2), have been identified as a contributor to the development of myeloid malignancies, illustrating the importance of proper splicing regulation in maintaining cellular homeostasis (S. P. Kim et al., 2021; Palangat et al., 2019). Changes in alternative splicing patterns that occur with age are most significant in the brain; nevertheless, dysregulation of RNA homeostasis compromises cellular and tissue function, leading to age‐related diseases (Adusumalli et al., 2019; Bhatnagar et al., 2023; Howe et al., 2022). Defects in the splicing of genes could contribute to the aging process through a feedback loop mechanism, further impairing RNA processing and translation.…”