The severity of Alzheimer’s Disease (AD) progression involves a complex interplay of genetics, ag... more 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...
Age-associated cognitive decline and neurodegenerative disorders such as Alzheimers disease (AD) ... more Age-associated cognitive decline and neurodegenerative disorders such as Alzheimers disease (AD) are associated with misregulation of synaptic plasticity linked genes; however the mechanisms underlying decline of such gene control during aging are unknown. Histone acetylation of chromatin promotes dynamic transcriptional responses in neurons that influence neuroplasticity critical for cognitive ability. Accordingly, aberrant changes to histone acetylation patterns in the aging brain epigenome are linked to memory loss. It is therefore critical to identify and study the histone acetyltransferases (HAT) that create such marks. One such promising candidate is Tip60, a HAT important for various cellular processes and also implicated in AD and shown by our laboratory to be critical in regulating neuronal processes linked to cognition. To explore a direct role for Tip60 in synaptic plasticity, here we explore the consequences of misregulating Tip60 HAT activity in the Drosophila neuromuscular junction (NMJ). The Drosophila NMJ is an extremely well characterized, highly tractable and valuable tool to study synaptic plasticity. In addition, many of the pathways present at the Drosophila NMJ are well conserved and homologous to the mammalian CNS. We show that the HAT dTip60 is concentrated both pre- and post-synaptically within the NMJ. Presynaptic targeted reduction of dTip60 HAT activity significantly increases synaptic bouton number that specifically affects type Is boutons while postsynaptic reduction results in significant loss of these boutons. The excess boutons demonstrate defects in neurotransmission function. Analysis using immunohistochemical staining to the MAP, futsch reveals a significant increase in the rearrangement of microtubule loop architecture that is required for bouton division. Our results are the first to demonstrate a causative role for the HAT dTip60 in the control of synaptic plasticity that is achieved, at least in part, via regulation of the synaptic microtubule cytoskeleton. We also show its post- synaptic role in the muscles and its function in retrograde signaling in addition to anterograde mechanisms. We show that postsynaptic loss of Tip60 HAT activity affects DLG localization, leads to decrease in GluRIIC subunit localization thus suggesting roles in activity dependent mechanisms. We also demonstrate its role in regulating genes involved in activity dependent synaptic plasticity and wingless pathway. Our ChIP-qPCR data suggests regulation of these genes via acetylation of learning and memory marks, H3K9, H4K12 and H4K16. We also report the functional interaction between HAT deficient Tip60 and hAPP at the NMJ, pre- and post-synaptically via the intracellular domain of APP (AICD), the molecule implicated in AD. Presynaptic expression of APP/Tip60 double mutants cause drastic increases in bouton numbers, and decrease in active zone synaptic function marker bruchpilot suggesting defects in neurotransmission. Conversely, postsynaptic expression…
Exploring the Alzheimer ’s disease neuroepigenome: recent advances and future trends: Alzheimer’s... more Exploring the Alzheimer ’s disease neuroepigenome: recent advances and future trends: Alzheimer’s disease (AD) is a chronic neurodegenerative disease and the most common cause of dementia. After decades of ongoing efforts by scientists, many hallmarks of AD, such as amyloid-β (Aβ) and tau pathologies, have finally been understood. But these milestone discoveries still failed to help us find a cure. In recent years, based on advances in genomics, researchers have discovered more than 20 AD-associated alleles. Three of these alleles can cause a u to s o m a l d o m i n a nt A D : a my l o i d precursor protein and presenilin 1/2 genes. The rest of these alleles can increase the risk to AD, such as the apolipoprotein E gene. These risk loci implicate Aβ, tau, immunity, and lipid processing, which have helped us accurately understand the complex changes in AD patients’ molecular networks.
Heritable and dynamic posttranslational modifications of histone proteins serve as the foundation... more Heritable and dynamic posttranslational modifications of histone proteins serve as the foundation for epigenetic mechanisms underlying gene transcriptional control in eukaryotes. Drosophila melanogaster has proven to be an invaluable model system for unraveling the fundamental role these marks play in various conserved biological processes. In this chapter we will discuss how studies utilizing Drosophila have provided important insights into the function of the generation and maintenance of specific epigenetic patterns in chromatin that govern processes unique to the fly, such as X-linked dosage compensation, and in processes conserved in humans, such as epigenetic mechanisms underlying gene control, position effect variegation, developmental programming, epigenetic inheritance, and neuronal plasticity guiding learning and memory. Finally, we will explore examples of how Drosophila represents a uniquely powerful tool for analyzing the detrimental consequences of aberrations in epige...
The Drosophila melanogaster HSC3 andHSC4 genes encode Hsc70 proteins homologous to the mammalian ... more The Drosophila melanogaster HSC3 andHSC4 genes encode Hsc70 proteins homologous to the mammalian endoplasmic reticulum (ER) protein BiP and the cytoplasmic clathrin uncoating ATPase, respectively. These proteins possess ATP binding/hydrolysis activities that mediate their ability to aid in protein folding by coordinating the sequential binding and release of misfolded proteins. To investigate the roles of HSC3(Hsc3p) and HSC4 (Hsc4p) proteins during development, GAL4-targeted gene expression was used to analyze the effects of producing dominant negatively acting Hsc3p (D231S, K97S) and Hsc4p (D206S, K71S) proteins, containing single amino acid substitutions in their ATP-binding domains, in specific tissues ofDrosophila throughout development. We show that the production of each mutant protein results in lethality over a range of developmental stages, depending on the levels of protein produced and which tissues are targeted. We demonstrate that the functions of both Hsc3p and Hsc4p ...
of expressing cells. The mechanisms of LCR action at different loci appear to be quite diverse (D... more of expressing cells. The mechanisms of LCR action at different loci appear to be quite diverse (Dean, 2006). Un-derstanding how these determinants activate gene ex-blocked a subset of downstream LCR transcripts and repressed hGH-N transcription. These changes oc-curred in the absence of appreciable alterations in his-tone acetylation within the hGH locus. These data lead us to conclude that the remote transcriptional domain plays a direct role in LCR-mediated, long-range gene
Background: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in di... more Background: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function; however, the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Methods and Findings: Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. Conclusions: We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for ner...
Background: Histone acetylation of chromatin plays a key role in promoting the dynamic transcript... more Background: Histone acetylation of chromatin plays a key role in promoting the dynamic transcriptional responses in neurons that influence the neuroplasticity linked to cognitive ability, yet the specific histone acetyltransferases (HATs) that create such epigenetic marks remain to be elucidated. Methods and Findings: Here we use the Drosophila neuromuscular junction (NMJ) as a well-characterized synapse model to identify HATs that control synaptic remodeling and structure. We show that the HAT dTip60 is concentrated both pre and post-synaptically within the NMJ. Presynaptic targeted reduction of dTip60 HAT activity causes a significant increase in synaptic bouton number that specifically affects type Is boutons. The excess boutons show a suppression of the active zone synaptic function marker bruchpilot, suggesting defects in neurotransmission function. Analysis of microtubule organization within these excess boutons using immunohistochemical staining to the microtubule associated ...
Disruption of histone acetylation-mediated gene control is a critical step in Alzheimer's Dis... more Disruption of histone acetylation-mediated gene control is a critical step in Alzheimer's Disease (AD), yet chromatin analysis of antagonistic histone acetyltransferases (HATs) and histone deacetylases (HDACs) causing these alterations remains uncharacterized. We report the first Tip60 HAT versus HDAC2 chromatin (ChIP-seq) and transcriptional (RNA-seq) profiling study in Drosophila melanogaster brains that model early human AD. We find Tip60 and HDAC2 predominantly recruited to identical neuronal genes. Moreover, AD brains exhibit robust genome-wide early alterations that include enhanced HDAC2 and reduced Tip60 binding and transcriptional dysregulation. Orthologous human genes to co-Tip60/HDAC2 D. melanogaster neural targets exhibit conserved disruption patterns in AD patient hippocampi. Notably, we discovered distinct transcription factor binding sites close or within Tip60/HDAC2 co-peaks in neuronal genes, implicating them in coenzyme recruitment. Increased Tip60 protects aga...
ABSTRACTAlzheimer’s disease (AD) is an age-related neurodegenerative disorder hallmarked by amylo... more ABSTRACTAlzheimer’s disease (AD) is an age-related neurodegenerative disorder hallmarked by amyloid-β (Aβ) plaque accumulation, neuronal cell death, and cognitive deficits that worsen during disease progression. Histone acetylation dysregulation, caused by an imbalance between reduced histone acetyltransferases (HAT) Tip60 and increased histone deacetylase 2 (HDAC2) levels, can directly contribute to AD pathology. However, whether such AD-associated neuroepigenetic alterations occur in response to Aβ peptide production and can be protected against by increasing Tip60 levels over the course of neurodegenerative progression remains unknown. Here we profile Tip60 HAT/HDAC2 dynamics and transcriptome-wide changes across early and late stage AD pathology in the Drosophila brain produced solely by human amyloid-β42. We show that early Aβ42 induction leads to disruption of Tip60 HAT/HDAC2 balance during early neurodegenerative stages preceding Aβ plaque accumulation that persists into late...
Epigenetic dysregulation is a common mechanism shared by molecularly and clinically heterogenous ... more Epigenetic dysregulation is a common mechanism shared by molecularly and clinically heterogenous neurodegenerative diseases (NDs). Histone acetylation homeostasis, maintained by the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs), is necessary for appropriate gene expression and neuronal function. Disruption of neural acetylation homeostasis has been implicated in multiple types of NDs including Alzheimer’s disease (AD), yet mechanisms underlying alterations remain unclear. We show that like AD, disruption of Tip60 HAT/HDAC2 balance with concomitant epigenetic repression of common Tip60 target neuroplasticity genes occurs early in multiple types of Drosophila ND models such as Parkinson’s Disease (PD), Huntington’s Disease (HD) and Amyotrophic Lateral Sclerosis (ALS). Repressed neuroplasticity genes show reduced enrichment of Tip60 and epigentic acetylation signatures at all gene loci examined with certain genes showing inappropriate HDAC2...
The severity of Alzheimer’s Disease (AD) progression involves a complex interplay of genetics, ag... more 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...
Age-associated cognitive decline and neurodegenerative disorders such as Alzheimers disease (AD) ... more Age-associated cognitive decline and neurodegenerative disorders such as Alzheimers disease (AD) are associated with misregulation of synaptic plasticity linked genes; however the mechanisms underlying decline of such gene control during aging are unknown. Histone acetylation of chromatin promotes dynamic transcriptional responses in neurons that influence neuroplasticity critical for cognitive ability. Accordingly, aberrant changes to histone acetylation patterns in the aging brain epigenome are linked to memory loss. It is therefore critical to identify and study the histone acetyltransferases (HAT) that create such marks. One such promising candidate is Tip60, a HAT important for various cellular processes and also implicated in AD and shown by our laboratory to be critical in regulating neuronal processes linked to cognition. To explore a direct role for Tip60 in synaptic plasticity, here we explore the consequences of misregulating Tip60 HAT activity in the Drosophila neuromuscular junction (NMJ). The Drosophila NMJ is an extremely well characterized, highly tractable and valuable tool to study synaptic plasticity. In addition, many of the pathways present at the Drosophila NMJ are well conserved and homologous to the mammalian CNS. We show that the HAT dTip60 is concentrated both pre- and post-synaptically within the NMJ. Presynaptic targeted reduction of dTip60 HAT activity significantly increases synaptic bouton number that specifically affects type Is boutons while postsynaptic reduction results in significant loss of these boutons. The excess boutons demonstrate defects in neurotransmission function. Analysis using immunohistochemical staining to the MAP, futsch reveals a significant increase in the rearrangement of microtubule loop architecture that is required for bouton division. Our results are the first to demonstrate a causative role for the HAT dTip60 in the control of synaptic plasticity that is achieved, at least in part, via regulation of the synaptic microtubule cytoskeleton. We also show its post- synaptic role in the muscles and its function in retrograde signaling in addition to anterograde mechanisms. We show that postsynaptic loss of Tip60 HAT activity affects DLG localization, leads to decrease in GluRIIC subunit localization thus suggesting roles in activity dependent mechanisms. We also demonstrate its role in regulating genes involved in activity dependent synaptic plasticity and wingless pathway. Our ChIP-qPCR data suggests regulation of these genes via acetylation of learning and memory marks, H3K9, H4K12 and H4K16. We also report the functional interaction between HAT deficient Tip60 and hAPP at the NMJ, pre- and post-synaptically via the intracellular domain of APP (AICD), the molecule implicated in AD. Presynaptic expression of APP/Tip60 double mutants cause drastic increases in bouton numbers, and decrease in active zone synaptic function marker bruchpilot suggesting defects in neurotransmission. Conversely, postsynaptic expression…
Exploring the Alzheimer ’s disease neuroepigenome: recent advances and future trends: Alzheimer’s... more Exploring the Alzheimer ’s disease neuroepigenome: recent advances and future trends: Alzheimer’s disease (AD) is a chronic neurodegenerative disease and the most common cause of dementia. After decades of ongoing efforts by scientists, many hallmarks of AD, such as amyloid-β (Aβ) and tau pathologies, have finally been understood. But these milestone discoveries still failed to help us find a cure. In recent years, based on advances in genomics, researchers have discovered more than 20 AD-associated alleles. Three of these alleles can cause a u to s o m a l d o m i n a nt A D : a my l o i d precursor protein and presenilin 1/2 genes. The rest of these alleles can increase the risk to AD, such as the apolipoprotein E gene. These risk loci implicate Aβ, tau, immunity, and lipid processing, which have helped us accurately understand the complex changes in AD patients’ molecular networks.
Heritable and dynamic posttranslational modifications of histone proteins serve as the foundation... more Heritable and dynamic posttranslational modifications of histone proteins serve as the foundation for epigenetic mechanisms underlying gene transcriptional control in eukaryotes. Drosophila melanogaster has proven to be an invaluable model system for unraveling the fundamental role these marks play in various conserved biological processes. In this chapter we will discuss how studies utilizing Drosophila have provided important insights into the function of the generation and maintenance of specific epigenetic patterns in chromatin that govern processes unique to the fly, such as X-linked dosage compensation, and in processes conserved in humans, such as epigenetic mechanisms underlying gene control, position effect variegation, developmental programming, epigenetic inheritance, and neuronal plasticity guiding learning and memory. Finally, we will explore examples of how Drosophila represents a uniquely powerful tool for analyzing the detrimental consequences of aberrations in epige...
The Drosophila melanogaster HSC3 andHSC4 genes encode Hsc70 proteins homologous to the mammalian ... more The Drosophila melanogaster HSC3 andHSC4 genes encode Hsc70 proteins homologous to the mammalian endoplasmic reticulum (ER) protein BiP and the cytoplasmic clathrin uncoating ATPase, respectively. These proteins possess ATP binding/hydrolysis activities that mediate their ability to aid in protein folding by coordinating the sequential binding and release of misfolded proteins. To investigate the roles of HSC3(Hsc3p) and HSC4 (Hsc4p) proteins during development, GAL4-targeted gene expression was used to analyze the effects of producing dominant negatively acting Hsc3p (D231S, K97S) and Hsc4p (D206S, K71S) proteins, containing single amino acid substitutions in their ATP-binding domains, in specific tissues ofDrosophila throughout development. We show that the production of each mutant protein results in lethality over a range of developmental stages, depending on the levels of protein produced and which tissues are targeted. We demonstrate that the functions of both Hsc3p and Hsc4p ...
of expressing cells. The mechanisms of LCR action at different loci appear to be quite diverse (D... more of expressing cells. The mechanisms of LCR action at different loci appear to be quite diverse (Dean, 2006). Un-derstanding how these determinants activate gene ex-blocked a subset of downstream LCR transcripts and repressed hGH-N transcription. These changes oc-curred in the absence of appreciable alterations in his-tone acetylation within the hGH locus. These data lead us to conclude that the remote transcriptional domain plays a direct role in LCR-mediated, long-range gene
Background: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in di... more Background: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function; however, the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Methods and Findings: Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. Conclusions: We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for ner...
Background: Histone acetylation of chromatin plays a key role in promoting the dynamic transcript... more Background: Histone acetylation of chromatin plays a key role in promoting the dynamic transcriptional responses in neurons that influence the neuroplasticity linked to cognitive ability, yet the specific histone acetyltransferases (HATs) that create such epigenetic marks remain to be elucidated. Methods and Findings: Here we use the Drosophila neuromuscular junction (NMJ) as a well-characterized synapse model to identify HATs that control synaptic remodeling and structure. We show that the HAT dTip60 is concentrated both pre and post-synaptically within the NMJ. Presynaptic targeted reduction of dTip60 HAT activity causes a significant increase in synaptic bouton number that specifically affects type Is boutons. The excess boutons show a suppression of the active zone synaptic function marker bruchpilot, suggesting defects in neurotransmission function. Analysis of microtubule organization within these excess boutons using immunohistochemical staining to the microtubule associated ...
Disruption of histone acetylation-mediated gene control is a critical step in Alzheimer's Dis... more Disruption of histone acetylation-mediated gene control is a critical step in Alzheimer's Disease (AD), yet chromatin analysis of antagonistic histone acetyltransferases (HATs) and histone deacetylases (HDACs) causing these alterations remains uncharacterized. We report the first Tip60 HAT versus HDAC2 chromatin (ChIP-seq) and transcriptional (RNA-seq) profiling study in Drosophila melanogaster brains that model early human AD. We find Tip60 and HDAC2 predominantly recruited to identical neuronal genes. Moreover, AD brains exhibit robust genome-wide early alterations that include enhanced HDAC2 and reduced Tip60 binding and transcriptional dysregulation. Orthologous human genes to co-Tip60/HDAC2 D. melanogaster neural targets exhibit conserved disruption patterns in AD patient hippocampi. Notably, we discovered distinct transcription factor binding sites close or within Tip60/HDAC2 co-peaks in neuronal genes, implicating them in coenzyme recruitment. Increased Tip60 protects aga...
ABSTRACTAlzheimer’s disease (AD) is an age-related neurodegenerative disorder hallmarked by amylo... more ABSTRACTAlzheimer’s disease (AD) is an age-related neurodegenerative disorder hallmarked by amyloid-β (Aβ) plaque accumulation, neuronal cell death, and cognitive deficits that worsen during disease progression. Histone acetylation dysregulation, caused by an imbalance between reduced histone acetyltransferases (HAT) Tip60 and increased histone deacetylase 2 (HDAC2) levels, can directly contribute to AD pathology. However, whether such AD-associated neuroepigenetic alterations occur in response to Aβ peptide production and can be protected against by increasing Tip60 levels over the course of neurodegenerative progression remains unknown. Here we profile Tip60 HAT/HDAC2 dynamics and transcriptome-wide changes across early and late stage AD pathology in the Drosophila brain produced solely by human amyloid-β42. We show that early Aβ42 induction leads to disruption of Tip60 HAT/HDAC2 balance during early neurodegenerative stages preceding Aβ plaque accumulation that persists into late...
Epigenetic dysregulation is a common mechanism shared by molecularly and clinically heterogenous ... more Epigenetic dysregulation is a common mechanism shared by molecularly and clinically heterogenous neurodegenerative diseases (NDs). Histone acetylation homeostasis, maintained by the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs), is necessary for appropriate gene expression and neuronal function. Disruption of neural acetylation homeostasis has been implicated in multiple types of NDs including Alzheimer’s disease (AD), yet mechanisms underlying alterations remain unclear. We show that like AD, disruption of Tip60 HAT/HDAC2 balance with concomitant epigenetic repression of common Tip60 target neuroplasticity genes occurs early in multiple types of Drosophila ND models such as Parkinson’s Disease (PD), Huntington’s Disease (HD) and Amyotrophic Lateral Sclerosis (ALS). Repressed neuroplasticity genes show reduced enrichment of Tip60 and epigentic acetylation signatures at all gene loci examined with certain genes showing inappropriate HDAC2...
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Papers by Felice Elefant