Shaghayegh Navabpour

All Publications

• Monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation LEARNING & MEMORY Navabpour, S., Farrell, K., Kincaid, S. E., Omar, N., Musaus, M., Lin, Y., Xie, H., Jarome, T. J. 2024; 31 (3)

  Abstract

  Posttranslational modification of histone proteins is critical for memory formation. Recently, we showed that monoubiquitination of histone H2B at lysine 120 (H2Bub) is critical for memory formation in the hippocampus. However, the transcriptome controlled by H2Bub remains unknown. Here, we found that fear conditioning in male rats increased or decreased the expression of 86 genes in the hippocampus but, surprisingly, siRNA-mediated knockdown of the H2Bub ligase, Rnf20, abolished changes in all but one of these genes. These findings suggest that monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation.

  View details for DOI 10.1101/lm.053912.123

  View details for Web of Science ID 001198573000001

  View details for PubMedID 38580378

  View details for PubMedCentralID PMC11000578

• Phosphorylation of RPT6 Controls Its Ability to Bind DNA and Regulate Gene Expression in the Hippocampus of Male Rats during Memory Formation. The Journal of neuroscience : the official journal of the Society for Neuroscience Farrell, K., Auerbach, A., Musaus, M., Navabpour, S., Liu, C., Lin, Y., Xie, H., Jarome, T. J. 2024; 44 (4)

  Abstract

  Memory formation requires coordinated control of gene expression, protein synthesis, and ubiquitin-proteasome system (UPS)-mediated protein degradation. The catalytic component of the UPS, the 26S proteasome, contains a 20S catalytic core surrounded by two 19S regulatory caps, and phosphorylation of the 19S cap regulatory subunit RPT6 at serine 120 (pRPT6-S120) has been widely implicated in controlling activity-dependent increases in proteasome activity. Recently, RPT6 was also shown to act outside the proteasome where it has a transcription factor-like role in the hippocampus during memory formation. However, little is known about the proteasome-independent function of "free" RPT6 in the brain or during memory formation and whether phosphorylation of S120 is required for this transcriptional control function. Here, we used RNA-sequencing along with novel genetic approaches and biochemical, molecular, and behavioral assays to test the hypothesis that pRPT6-S120 functions independently of the proteasome to bind DNA and regulate gene expression during memory formation. RNA-sequencing following siRNA-mediated knockdown of free RPT6 revealed 46 gene targets in the dorsal hippocampus of male rats following fear conditioning, where RPT6 was involved in transcriptional activation and repression. Through CRISPR-dCas9-mediated artificial placement of RPT6 at a target gene, we found that RPT6 DNA binding alone may be important for altering gene expression following learning. Further, CRISPR-dCas13-mediated conversion of S120 to glycine on RPT6 revealed that phosphorylation at S120 is necessary for RPT6 to bind DNA and properly regulate transcription during memory formation. Together, we reveal a novel function for phosphorylation of RPT6 in controlling gene transcription during memory formation.

  View details for DOI 10.1523/JNEUROSCI.1453-23.2023

  View details for PubMedID 38124005

  View details for PubMedCentralID PMC10860611

• Proteasome-independent K63 polyubiquitination selectively regulates ATP levels and proteasome activity during fear memory formation in the female amygdala. Molecular psychiatry Farrell, K., Musaus, M., Auerbach, A., Navabpour, S., Ray, W. K., Helm, R. F., Jarome, T. J. 2023; 28 (6): 2594-2605

  Abstract

  Females are more likely than males to develop post-traumatic stress disorder (PTSD). However, the neurobiological mechanisms responsible for these sex differences remain elusive. The ubiquitin proteasome system (UPS) is involved in fear memory formation and implicated in PTSD development. Despite this, proteasome-independent functions of the UPS have rarely been studied in the brain. Here, using a combination of molecular, biochemical, proteomic, behavioral, and novel genetic approaches, we investigated the role of proteasome-independent lysine-63 (K63)-polyubiquitination, the second most abundant ubiquitin modification in cells, in the amygdala during fear memory formation in male and female rats. Only females had increased levels of K63-polyubiquitination targeting in the amygdala following fear conditioning, which targeted proteins involved in ATP synthesis and proteasome function. CRISPR-dCas13b-mediated knockdown of K63-polyubiquitination in the amygdala via editing of the K63 codon in the major ubiquitin gene, Ubc, impaired fear memory in females, but not males, and caused a reduction in learning-related increases in ATP levels and proteasome activity in the female amygdala. These results suggest that proteasome-independent K63-polyubiquitination is selectively involved in fear memory formation in the female amygdala, where it is involved in the regulation of ATP synthesis and proteasome activity following learning. This indicates the first link between proteasome-independent and proteasome-dependent UPS functions in the brain during fear memory formation. Importantly, these data are congruent with reported sex differences in PTSD development and may contribute to our understanding of why females are more likely to develop PTSD than males.

  View details for DOI 10.1038/s41380-023-02112-0

  View details for PubMedID 37198264

  View details for PubMedCentralID PMC10615704

• Epigenetic Mechanisms in Memory and Cognitive Decline Associated with Aging and Alzheimer's Disease INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Maity, S., Farrell, K., Navabpour, S., Narayanan, S., Jarome, T. J. 2021; 22 (22)

  Abstract

  Epigenetic mechanisms, which include DNA methylation, a variety of post-translational modifications of histone proteins (acetylation, phosphorylation, methylation, ubiquitination, sumoylation, serotonylation, dopaminylation), chromatin remodeling enzymes, and long non-coding RNAs, are robust regulators of activity-dependent changes in gene transcription. In the brain, many of these epigenetic modifications have been widely implicated in synaptic plasticity and memory formation. Dysregulation of epigenetic mechanisms has been reported in the aged brain and is associated with or contributes to memory decline across the lifespan. Furthermore, alterations in the epigenome have been reported in neurodegenerative disorders, including Alzheimer's disease. Here, we review the diverse types of epigenetic modifications and their role in activity- and learning-dependent synaptic plasticity. We then discuss how these mechanisms become dysregulated across the lifespan and contribute to memory loss with age and in Alzheimer's disease. Collectively, the evidence reviewed here strongly supports a role for diverse epigenetic mechanisms in memory formation, aging, and neurodegeneration in the brain.

  View details for DOI 10.3390/ijms222212280

  View details for Web of Science ID 000733707700001

  View details for PubMedID 34830163

  View details for PubMedCentralID PMC8618067

• Activation of VTA/CeA/mPFC cannabinoid CB1 receptors induced conditioned drug effects via interacting with hippocampal CAMKII-CREB-BDNF signaling pathway in rats EUROPEAN JOURNAL OF PHARMACOLOGY Navabpour, S., Rezayof, A., Ghasemzadeh, Z. 2021; 909: 174417

  Abstract

  The present study intended to investigate whether the activation of cannabinoid CB1 receptors of the ventral tegmental area (VTA), the central amygdala (CeA) and the medial prefrontal cortex (mPFC) could induce conditioned place preference or aversion (CPP or CPA) in adult male Wistar rats. The involvement of hippocampal signaling pathway of Ca2+/calmodulin-dependent protein kinase II (CaMKII)/cAMP response element-binding protein (CREB)/brain-derived neurotrophic factor (BDNF) was also examined following a 3-day schedule of conditioning with the injection of arachidonylcyclopropylamide (ACPA; a selective cannabinoid CB1 receptors agonist) into the targeted sites. The results showed that intra-VTA injection of the higher dose of ACPA (5 ng/rat) caused a significant CPP associating with the increased hippocampal level of the phosphorylated (p)-CAMKII/CAMKII. Intra-mPFC injection of ACPA at 3 ng/rat caused a significant CPA associating with the decreased p-CAMKII and p-CREB levels and the increased BDNF level in the hippocampus. Moreover, intra-CeA injection of the ACPA (5 ng/rat) induced a significant CPP which was associated with the increased hippocampal levels of p-CAMKII/total (t) CAMKII, p-CREB/tCREB, and BDNF. Exposing the animals to the CPP apparatus after receiving intra-cerebral vehicle injection increased the hippocampal CAMKII/CREB/BDNF signaling pathway, confirming that CPP is an associative learning task. In all experiments, the conditioning treatment with the different doses of ACPA did not affect locomotor activity in the testing phase. Taken together, it can be concluded that cannabinoid CB1 receptors of the VTA, the CeA, and the mPFC are involved in rewarding/aversion effects through the changes in the hippocampal signaling pathways.

  View details for DOI 10.1016/j.ejphar.2021.174417

  View details for Web of Science ID 000712276300006

  View details for PubMedID 34389313

• Ubiquitination of Histone H2B by Proteasome Subunit RPT6 Controls Histone Methylation Chromatin Dynamics During Memory Formation BIOLOGICAL PSYCHIATRY Jarome, T. J., Perez, G. A., Webb, W. M., Hatch, K. M., Navabpour, S., Musaus, M., Farrell, K., Hauser, R. M., McFadden, T., Martin, K., Butler, A. A., Wang, J., Lubin, F. D. 2021; 89 (12): 1176-1187

  Abstract

  Posttranslational histone modifications play a critical role in the regulation of gene transcription underlying synaptic plasticity and memory formation. One such epigenetic change is histone ubiquitination, a process that is mediated by the ubiquitin-proteasome system in a manner similar to that by which proteins are normally targeted for degradation. However, histone ubiquitination mechanisms are poorly understood in the brain and in learning. In this article, we describe a new role for the ubiquitin-proteasome system in histone crosstalk, showing that learning-induced monoubiquitination of histone H2B (H2Bubi) is required for increases in the transcriptionally active H3 lysine 4 trimethylation (H3K4me3) mark at learning-related genes in the hippocampus.Using a series of molecular, biochemical, electrophysiological, and behavioral experiments, we interrogated the effects of short interfering RNA-mediated knockdown and CRISPR (clustered regularly interspaced short palindromic repeats)-mediated upregulation of ubiquitin ligases, deubiquitinating enzymes and histone methyltransferases in the rat dorsal hippocampus during memory consolidation.We show that H2Bubi recruits H3K4me3 through a process that is dependent on the 19S proteasome subunit RPT6 and that a loss of H2Bubi in the hippocampus prevents learning-induced increases in H3K4me3, gene transcription, synaptic plasticity, and memory formation. Furthermore, we show that CRISPR-dCas9-mediated increases in H2Bubi promote H3K4me3 and memory formation under weak training conditions and that promoting histone methylation does not rescue memory impairments resulting from loss of H2Bubi.These results suggest that H2B ubiquitination regulates histone crosstalk in learning by way of nonproteolytic proteasome function, demonstrating a novel mechanism by which histone modifications are coordinated in response to learning.

  View details for DOI 10.1016/j.biopsych.2020.12.029

  View details for Web of Science ID 000656919800013

  View details for PubMedID 33934885

  View details for PubMedCentralID PMC8178164

• Males and females differ in the regulation and engagement of, but not requirement for, protein degradation in the amygdala during fear memory formation NEUROBIOLOGY OF LEARNING AND MEMORY Devulapalli, R., Jones, N., Farrell, K., Musaus, M., Kugler, H., McFadden, T., Orsi, S. A., Martin, K., Nelsen, J., Navabpour, S., O'Donnell, M., McCoig, E., Jarome, T. J. 2021; 180: 107404

  Abstract

  Over the last decade, strong evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system is critical for fear memory formation in the amygdala. However, this work has been done primarily in males, leaving unanswered questions about whether females also require protein degradation during fear memory formation. Here, we found that male and female rats differed in their engagement and regulation of, but not need for, protein degradation in the amygdala during fear memory formation. Male, but not female, rats had increased protein degradation in the nuclei of amygdala cells after fear conditioning. Conversely, females had elevated baseline levels of overall ubiquitin-proteasome activity in amygdala nuclei. Gene expression and DNA methylation analyses identified that females had increased baseline expression of the ubiquitin coding gene Uba52, which had increased DNA 5-hydroxymethylation (5hmc) in its promoter region, indicating a euchromatin state necessary for increased levels of ubiquitin in females. Consistent with this, persistent CRISPR-dCas9 mediated silencing of Uba52 and proteasome subunit Psmd14 in the amygdala reduced baseline protein degradation levels and impaired fear memory in male and female rats, while enhancing baseline protein degradation in the amygdala of both sexes promoted fear memory formation. These results suggest that while both males and females require protein degradation in the amygdala for fear memory formation, they differ in their baseline regulation and engagement of this process following learning. These results have important implications for understanding the etiology of sex-related differences in fear memory formation.

  View details for DOI 10.1016/j.nlm.2021.107404

  View details for Web of Science ID 000642482000006

  View details for PubMedID 33609735

  View details for PubMedCentralID PMC8076082

• DNA Double-Strand Breaks Are a Critical Regulator of Fear Memory Reconsolidation INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Navabpour, S., Rogers, J., McFadden, T., Jarome, T. J. 2020; 21 (23)

  Abstract

  Numerous studies have shown that following retrieval, a previously consolidated memory requires increased transcriptional regulation in order to be reconsolidated. Previously, it was reported that histone H3 lysine-4 trimethylation (H3K4me3), a marker of active transcription, is increased in the hippocampus after the retrieval of contextual fear memory. However, it is currently unknown how this epigenetic mark is regulated during the reconsolidation process. Furthermore, though recent evidence suggests that neuronal activity triggers DNA double-strand breaks (DSBs) in some early-response genes, it is currently unknown if DSBs contribute to the reconsolidation of a memory following retrieval. Here, using chromatin immunoprecipitation (ChIP) analyses, we report a significant overlap between DSBs and H3K4me3 in area CA1 of the hippocampus during the reconsolidation process. We found an increase in phosphorylation of histone H2A.X at serine 139 (H2A.XpS139), a marker of DSB, in the Npas4, but not c-fos, promoter region 5 min after retrieval, which correlated with increased H3K4me3 levels, suggesting that the two epigenetic marks may work in concert during the reconsolidation process. Consistent with this, in vivo siRNA-mediated knockdown of topoisomerase II β, the enzyme responsible for DSB, prior to retrieval, reduced Npas4 promoter-specific H2A.XpS139 and H3K4me3 levels and impaired long-term memory, indicating an indispensable role of DSBs in the memory reconsolidation process. Collectively, our data propose a novel mechanism for memory reconsolidation through increases in epigenetic-mediated transcriptional control via DNA double-strand breaks.

  View details for DOI 10.3390/ijms21238995

  View details for Web of Science ID 000597558600001

  View details for PubMedID 33256213

  View details for PubMedCentralID PMC7730899

• The diversity of linkage-specific polyubiquitin chains and their role in synaptic plasticity and memory formation NEUROBIOLOGY OF LEARNING AND MEMORY Musaus, M., Navabpour, S., Jarome, T. J. 2020; 174: 107286

  Abstract

  Over the last 20 years, a number of studies have provided strong support for protein degradation mediated by the ubiquitin-proteasome system in synaptic plasticity and memory formation. In this system, target substrates become covalently modified by the small protein ubiquitin through a series of enzymatic reactions involving hundreds of different ligases. While some substrates will acquire only a single ubiquitin, most will be marked by multiple ubiquitin modifications, which link together at specific lysine sites or the N-terminal methionine on the previous ubiquitin to form a polyubiquitin chain. There are at least eight known linkage-specific polyubiquitin chains a target protein can acquire, many of which are independent of the proteasome, and these chains can be homogenous, mixed, or branched in nature, all of which result in different functional outcomes and fates for the target substrate. However, as the focus has remained on protein degradation, much remains unknown about the role of these diverse ubiquitin chains in the brain, particularly during activity- and learning-dependent synaptic plasticity. Here, we review the different types and functions of ubiquitin chains and summarize evidence suggesting a role for these diverse ubiquitin modifications in synaptic plasticity and memory formation. We conclude by discussing how technological limitations have limited our ability to identify and elucidate the role of different ubiquitin chains in the brain and speculate on the future directions and implications of understanding linkage-specific ubiquitin modifications in activity- and learning-dependent synaptic plasticity.

  View details for DOI 10.1016/j.nlm.2020.107286

  View details for Web of Science ID 000569898500008

  View details for PubMedID 32745599

  View details for PubMedCentralID PMC7484030

• AVPR1A variation is linked to gray matter covariation in the social brain network of chimpanzees GENES BRAIN AND BEHAVIOR Mulholland, M. M., Navabpour, S., Mareno, M. C., Schapiro, S. J., Young, L. J., Hopkins, W. D. 2020; 19 (4): e12631

  Abstract

  The vasopressin system has been implicated in the regulation of social behavior and cognition in humans, nonhuman primates and other social mammals. In chimpanzees, polymorphisms in the vasopressin V1a receptor gene (AVPR1A) have been associated with social dimensions of personality, as well as to responses to sociocommunicative cues and mirror self-recognition. Despite evidence of this association with social cognition and behavior, there is little research on the neuroanatomical correlates of AVPR1A variation. In the current study, we tested the association between AVPR1A polymorphisms in the RS3 promotor region and gray matter covariation in chimpanzees using magnetic resonance imaging and source-based morphometry. The analysis identified 13 independent brain components, three of which differed significantly in covariation between the two AVPR1A genotypes (DupB-/- and DupB+/-; P < .05). DupB+/- chimpanzees showed greater covariation in gray matter in the premotor and prefrontal cortex, basal forebrain, lunate and cingulate cortex, and lesser gray matter covariation in the superior temporal sulcus and postcentral sulcus. Some of these regions were previously found to differ in vasopressin and oxytocin neural fibers between nonhuman primates, and in AVPR1A gene expression in humans with different RS3 alleles. This is the first report of an association between AVPR1A and gray matter covariation in nonhuman primates, and specifically links an AVPR1A polymorphism to structural variation in the social brain network. These results further affirm the value of chimpanzees as a model species for investigating the relationship between genetic variation, brain structure and social cognition with relevance to psychiatric disorders, including autism.

  View details for DOI 10.1111/gbb.12631

  View details for Web of Science ID 000524525100008

  View details for PubMedID 31894656

  View details for PubMedCentralID PMC7141960

• A neuroscientist's guide to transgenic mice and other genetic tools NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS Navabpour, S., Kwapis, J. L., Jarome, T. J. 2020; 108: 732-748

  Abstract

  The past decade has produced an explosion in the number and variety of genetic tools available to neuroscientists, resulting in an unprecedented ability to precisely manipulate the genome and epigenome in behaving animals. However, no single resource exists that describes all of the tools available to neuroscientists. Here, we review the genetic, transgenic, and viral techniques that are currently available to probe the complex relationship between genes and cognition. Topics covered include types of traditional transgenic mouse models (knockout, knock-in, reporter lines), inducible systems (Cre-loxP, Tet-On, Tet-Off) and cell- and circuit-specific systems (TetTag, TRAP, DIO-DREADD). Additionally, we provide details on virus-mediated and siRNA/shRNA approaches, as well as a comprehensive discussion of the myriad manipulations that can be made using the CRISPR-Cas9 system, including single base pair editing and spatially- and temporally-regulated gene-specific transcriptional control. Collectively, this review will serve as a guide to assist neuroscientists in identifying and choosing the appropriate genetic tools available to study the complex relationship between the brain and behavior.

  View details for DOI 10.1016/j.neubiorev.2019.12.013

  View details for Web of Science ID 000505535400048

  View details for PubMedID 31843544

  View details for PubMedCentralID PMC8049509

• Males and Females Differ in the Subcellular and Brain Region Dependent Regulation of Proteasome Activity by CaMKII and Protein Kinase A NEUROSCIENCE Devulapalli, R. K., Nelsen, J. L., Orsi, S. A., McFadden, T., Navabpour, S., Jones, N., Martin, K., O'Donnell, M., McCoig, E. L., Jarome, T. J. 2019; 418: 1-14

  Abstract

  The ubiquitin-proteasome system (UPS) controls the degradation of ~90% of short-lived proteins in cells and is involved in activity- and learning-dependent synaptic plasticity in the brain. Calcium/calmodulin dependent protein kinase II (CaMKII) and Protein Kinase A (PKA) can regulate activity of the proteasome. However, there have been a number of conflicting reports regarding under what conditions CaMKII and PKA regulate proteasome activity in the brain. Furthermore, this work has been done exclusively in males, leaving questions about whether these kinases also regulate the proteasome in females. Here, using subcellular fractionation protocols in combination with in vitro pharmacology and proteasome activity assays, we investigated the conditions under which CaMKII and PKA regulate proteasome activity in the brains of male and female rats. In males, nuclear proteasome chymotrypsin activity was regulated by PKA in the amygdala but CaMKII in the hippocampus. Conversely, in females CaMKII regulated nuclear chymotrypsin activity in the amygdala, but not hippocampus. Additionally, in males CaMKII and PKA regulated proteasome trypsin activity in the cytoplasm of hippocampal, but not amygdala cells, while in females both CaMKII and PKA could regulate this activity in the nucleus of cells in both regions. Proteasome peptidylglutamyl activity was regulated by CaMKII and PKA activity in the nuclei of amygdala and hippocampus cells in males. However, in females PKA regulated nuclear peptidylglutamyl activity in the amygdala, but not hippocampus. Collectively, these results suggest that CaMKII- and PKA-dependent regulation of proteasome activity in the brain varies significantly across subcellular compartments and between males and females.

  View details for DOI 10.1016/j.neuroscience.2019.08.031

  View details for Web of Science ID 000498389600001

  View details for PubMedID 31449987