Check out the lab’s publication on the feed below! Click post title to be redirected to PubMed for more info.

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  • Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues
    by Allen Yen on September 27, 2023

    Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next-generation sequencing. Compared with other genomic assays, readouts of which provide a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to...

  • Relationship between sex biases in gene expression and sex biases in autism and Alzheimer's disease
    by Stuart B Fass on September 11, 2023

    Sex differences in the brain may play an important role in sex-differential prevalence of neuropsychiatric conditions. In order to understand the transcriptional basis of sex differences, we analyzed multiple, large-scale, human postmortem brain RNA-seq datasets using both within-region and pan-regional frameworks. We find evidence of sex-biased transcription in many autosomal genes, some of which provide evidence for pathways and cell population differences between chromosomally male and female...

  • A comprehensive assay of social motivation reveals sex-specific roles of autism-associated genes and oxytocin
    by Susan E Maloney on July 10, 2023

    Social motivation is critical to the development of typical social functioning. Social motivation, specifically one or more of its components (e.g., social reward seeking or social orienting), could be relevant for understanding phenotypes related to autism. We developed a social operant conditioning task to quantify effort to access a social partner and concurrent social orienting in mice. We established that mice will work for access to a social partner, identified sex differences, and...

  • Extensive characterization of a Williams syndrome murine model shows Gtf2ird1-mediated rescue of select sensorimotor tasks, but no effect on enhanced social behavior
    by Kayla R Nygaard on June 28, 2023

    Williams syndrome is a rare neurodevelopmental disorder exhibiting cognitive and behavioral abnormalities, including increased social motivation, risk of anxiety and specific phobias along with perturbed motor function. Williams syndrome is caused by a microdeletion of 26-28 genes on chromosome 7, including GTF2IRD1, which encodes a transcription factor suggested to play a role in the behavioral profile of Williams syndrome. Duplications of the full region also lead to frequent autism diagnosis,...

  • Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues
    by Allen Yen on June 19, 2023

    Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next generation sequencing. Compared to other genomic assays, whose readout provides a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert...

  • Local translation in microglial processes is required for efficient phagocytosis
    by Michael J Vasek on June 5, 2023

    Neurons, astrocytes and oligodendrocytes locally regulate protein translation within distal processes. Here, we tested whether there is regulated local translation within peripheral microglial processes (PeMPs) from mouse brain. We show that PeMPs contain ribosomes that engage in de novo protein synthesis, and these are associated with transcripts involved in pathogen defense, motility and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the...

  • MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
    by Jiayang Chen on April 26, 2023

    In vitro studies indicate the neurodevelopmental disorder gene myelin transcription factor 1-like (MYT1L) suppresses non-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio of DL/UL neurons in the adult mouse cortex. To define potential...

  • Mecp2 deletion results in profound alterations of developmental and adult functional connectivity
    by Rachel M Rahn on March 10, 2023

    As a regressive neurodevelopmental disorder with a well-established genetic cause, Rett syndrome and its Mecp2 loss-of-function mouse model provide an excellent opportunity to define potentially translatable functional signatures of disease progression, as well as offer insight into the role of Mecp2 in functional circuit development. Thus, we applied widefield optical fluorescence imaging to assess mesoscale calcium functional connectivity (FC) in the Mecp2 cortex both at postnatal day (P)35 in...

  • Cnih3 Deletion Dysregulates Dorsal Hippocampal Transcription across the Estrous Cycle
    by Bernard Mulvey on February 27, 2023

    In females, the hippocampus, a critical brain region for coordination of learning, memory, and behavior, displays altered physiology and behavioral output across the estrous or menstrual cycle. However, the molecular effectors and cell types underlying these observed cyclic changes have only been partially characterized to date. Recently, profiling of mice null for the AMPA receptor trafficking gene Cnih3 have demonstrated estrous-dependent phenotypes in dorsal hippocampal synaptic plasticity,...

  • Sex Significantly Impacts the Function of Major Depression-Linked Variants In Vivo
    by Bernard Mulvey on February 21, 2023

    CONCLUSIONS: Our study provides novel insights into the influence of age, biological sex, and cell type on regulatory variant function and provides a framework for in vivo parallel assays to functionally define interactions between organismal variables such as sex and regulatory variation. Moreover, we experimentally demonstrate that a portion of the sex differences seen in MDD occurrence may be a product of sex-differentiated effects at associated regulatory variants.

  • Extensive characterization of a Williams Syndrome murine model shows Gtf2ird1 -mediated rescue of select sensorimotor tasks, but no effect on enhanced social behavior
    by Kayla R Nygaard on January 30, 2023

    Williams Syndrome is a rare neurodevelopmental disorder exhibiting cognitive and behavioral abnormalities, including increased social motivation, risk of anxiety and specific phobias along with perturbed motor function. Williams Syndrome is caused by a microdeletion of 26-28 genes on chromosome 7, including GTF2IRD1 , which encodes a transcription factor suggested to play a role in the behavioral profile of Williams Syndrome. Duplications of the full region also lead to frequent autism...

  • Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process
    by Darshan Sapkota on October 19, 2022

    Within eukaryotic cells, translation is regulated independent of transcription, enabling nuanced, localized, and rapid responses to stimuli. Neurons respond transcriptionally and translationally to synaptic activity. Although transcriptional responses are documented in astrocytes, here we test whether astrocytes have programmed translational responses. We show that seizure activity rapidly changes the transcripts on astrocyte ribosomes, some predicted to be downstream of BDNF signaling. In acute...

  • Aqp4 stop codon readthrough facilitates amyloid-β clearance from the brain
    by Darshan Sapkota on August 24, 2022

    Alzheimer's disease is initiated by the toxic aggregation of amyloid-β. Immunotherapeutics aimed at reducing amyloid beta are in clinical trials but with very limited success to date. Identification of orthogonal approaches for clearing amyloid beta may complement these approaches for treating Alzheimer's disease. In the brain, the astrocytic water channel Aquaporin 4 is involved in clearance of amyloid beta, and the fraction of Aquaporin 4 found perivascularly is decreased in Alzheimer's...

  • MYT1L in the making: emerging insights on functions of a neurodevelopmental disorder gene
    by Jiayang Chen on July 22, 2022

    Large scale human genetic studies have shown that loss of function (LoF) mutations in MYT1L are implicated in neurodevelopmental disorders (NDDs). Here, we provide an overview of the growing number of published MYT1L patient cases, and summarize prior studies in cells, zebrafish, and mice, both to understand MYT1L's molecular and cellular role during brain development and consider how its dysfunction can lead to NDDs. We integrate the conclusions from these studies and highlight conflicting...

  • Fluoxetine exposure throughout neurodevelopment differentially influences basilar dendritic morphology in the motor and prefrontal cortices
    by Susan E Maloney on May 9, 2022

    The significance of serotonin (5HT) in mental health is underscored by the serotonergic action of many classes of psychiatric medication. 5HT is known to have a significant role in neurodevelopment, thus 5HT disruption during development may have a long term impact on brain structure and circuits. We previously generated a model of 5HT alteration throughout neurodevelopment by maternal administration of the selective serotonin reuptake inhibitor fluoxetine. We found resulting social behavior...

  • A Proposed Role for Interactions between Argonautes, miRISC, and RNA Binding Proteins in the Regulation of Local Translation in Neurons and Glia
    by Sarah K Koester on April 21, 2022

    The first evidence of local translation in the CNS appeared nearly 40 years ago, when electron microscopic studies showed polyribosomes localized to the base of dendritic spines. Since then, local translation has been established as an important regulatory mechanism for gene expression in polarized or functionally compartmentalized cells. While much attention has been placed on characterizing the local transcriptome and regulatory "grammar" directing mRNA localization in neurons and glia, less...

  • A MYT1L syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation
    by Jiayang Chen on October 6, 2021

    Human genetics have defined a new neurodevelopmental syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes intellectual disability, autism, ADHD, obesity, and brain anomalies is unknown. Here, we developed a Myt1l haploinsufficient mouse model that develops obesity, white-matter thinning, and microcephaly, mimicking common clinical phenotypes. During brain development we discovered...

  • utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation
    by Yating Liu on September 3, 2021

    SUMMARY: Whole genome sequencing of patient populations is identifying thousands of new variants in untranslated regions (UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are some known features of UTRs that modulate their function. utr.annotation is an R package that can be used to annotate potential deleterious variants in the UTR regions for both human and mouse species. Given a CSV or VCF format variant file,...

  • Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays
    by Bernard Mulvey on July 23, 2021

    Family and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters) based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are...

  • Oxytocin receptor activation does not mediate associative fear deficits in a Williams Syndrome model
    by Kayla R Nygaard on May 12, 2021

    Williams Syndrome results in distinct behavioral phenotypes, which include learning deficits, anxiety, increased phobias and hypersociability. While the underlying mechanisms driving this subset of phenotypes is unknown, oxytocin (OT) dysregulation is hypothesized to be involved as some studies have shown elevated blood OT and altered OT receptor expression in patients. A "Complete Deletion" (CD) mouse, modeling the hemizygous deletion in Williams Syndrome, recapitulates many of the phenotypes...

  • Loss of Quaking RNA binding protein disrupts the expression of genes associated with astrocyte maturation in mouse brain
    by Kristina Sakers on March 22, 2021

    Quaking RNA binding protein (QKI) is essential for oligodendrocyte development as myelination requires myelin basic protein mRNA regulation and localization by the cytoplasmic isoforms (e.g., QKI-6). QKI-6 is also highly expressed in astrocytes, which were recently demonstrated to have regulated mRNA localization. Here, we define the targets of QKI in the mouse brain via CLIPseq and we show that QKI-6 binds 3'UTRs of a subset of astrocytic mRNAs. Binding is also enriched near stop codons,...

  • CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements
    by Michael A Rieger on December 28, 2020

    CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3' UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6...

  • Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts
    by Bernard Mulvey on August 27, 2020

    Neuropsychiatric phenotypes have long been known to be influenced by heritable risk factors, directly confirmed by the past decade of genetic studies that have revealed specific genetic variants enriched in disease cohorts. However, the initial hope that a small set of genes would be responsible for a given disorder proved false. The more complex reality is that a given disorder may be influenced by myriad small-effect noncoding variants and/or by rare but severe coding variants, many de novo....

  • Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA binding and long-term behavioral consequences
    by Nathan D Kopp on April 22, 2020

    Gtf2ird1 and Gtf2i are two transcription factors (TFs) among the 28 genes deleted in Williams syndrome, and prior mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain and test for additive effects of their mutation on transcription and behavior. GTF2IRD1 binding targets were enriched for transcriptional and chromatin regulators and mediators of ubiquitination. GTF2I targets were enriched for signal transduction proteins,...

  • A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues
    by Alexander J Cammack on April 18, 2020

    Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer...

  • An inducible Cre mouse line to sparsely target nervous system cells, including Remak Schwann cells
    by Darshan Sapkota on February 22, 2020

    Nerves of the peripheral nervous system contain two classes of Schwann cells: myelinating Schwann cells that ensheath large caliber axons and generate the myelin sheath, and Remak Schwann cells that surround smaller axons and do not myelinate. While tools exist for genetic targeting of Schwann cell precursors and myelinating Schwann cells, such reagents have been challenging to generate specifically for the Remak population, in part because many of the genes that mark this population in maturity...

  • Gtf2i and Gtf2ird1 mutation do not account for the full phenotypic effect of the Williams syndrome critical region in mouse models
    by Nathan Kopp on August 17, 2019

    Williams syndrome (WS) is a neurodevelopmental disorder caused by a 1.5-1.8 Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of WS include cardiovascular problems, craniofacial dysmorphology, deficits in visual-spatial cognition and a characteristic hypersocial personality. There are still no genes in the region that have been consistently linked to the cognitive and behavioral phenotypes, although human studies and mouse models have led to the current...

  • Loss of CELF6 RNA binding protein impairs cocaine conditioned place preference and contextual fear conditioning
    by Susan E Maloney on June 20, 2019

    In addition to gene expression differences in distinct cell types, there is substantial post-transcriptional regulation driven in part by RNA binding proteins (RBPs). Loss-of-function RBP mutations have been associated with neurodevelopmental disorders, such as Fragile-X syndrome and syndromic autism. Work performed in animal models to elucidate the influence of neurodevelopmental disorder-associated RBPs on distinct behaviors has showed a connection between normal post-transcriptional...

  • Erroneous inference based on a lack of preference within one group: Autism, mice, and the social approach task
    by Kayla R Nygaard on June 13, 2019

    The Social Approach Task is commonly used to identify sociability deficits when modeling liability factors for autism spectrum disorder (ASD) in mice. It was developed to expand upon existing assays to examine distinct aspects of social behavior in rodents and has become a standard component of mouse ASD-relevant phenotyping pipelines. However, there is variability in the statistical analysis and interpretation of results from this task. A common analytical approach is to conduct within-group...

  • The Differences in Local Translatome across Distinct Neuron Types Is Mediated by Both Baseline Cellular Differences and Post-transcriptional Mechanisms
    by Rebecca Ouwenga on February 7, 2019

    Local translation in neurites is a phenomenon that enhances the spatial segregation of proteins and their functions away from the cell body, yet it is unclear how local translation varies across neuronal cell types. Further, it is unclear whether differences in local translation across cell types simply reflect differences in transcription or whether there is also a cell type-specific post-transcriptional regulation of the location and translation of specific mRNAs. Most of the mRNAs discovered...

  • Cell-Type-Specific Profiling of Alternative Translation Identifies Regulated Protein Isoform Variation in the Mouse Brain
    by Darshan Sapkota on January 17, 2019

    Alternative translation initiation and stop codon readthrough in a few well-studied cases have been shown to allow the same transcript to generate multiple protein variants. Because the brain shows a particularly abundant use of alternative splicing, we sought to study alternative translation in CNS cells. We show that alternative translation is widespread and regulated across brain transcripts. In neural cultures, we identify alternative initiation on hundreds of transcripts, confirm several...

  • Examining the Reversibility of Long-Term Behavioral Disruptions in Progeny of Maternal SSRI Exposure
    by Susan E Maloney on August 4, 2018

    Serotonergic dysregulation is implicated in numerous psychiatric disorders. Serotonin plays widespread trophic roles during neurodevelopment; thus perturbations to this system during development may increase risk for neurodevelopmental disorders. Epidemiological studies have examined association between selective serotonin reuptake inhibitor (SSRI) treatment during pregnancy and increased autism spectrum disorder (ASD) risk in offspring. It is unclear from these studies whether ASD...

  • Molecular and Functional Sex Differences of Noradrenergic Neurons in the Mouse Locus Coeruleus
    by Bernard Mulvey on May 24, 2018

    Preclinical work has long focused on male animals, though biological sex clearly influences risk for certain diseases, including many psychiatric disorders. Such disorders are often treated by drugs targeting the CNS norepinephrine system. Despite roles for noradrenergic neurons in behavior and neuropsychiatric disease models, their molecular characterization has lagged. We profiled mouse noradrenergic neurons in vivo, defining over 3,000 high-confidence transcripts expressed therein, including...

  • Weaving New Insights for the Genetic Regulation of Human Cognitive Phenotypes
    by Bernard Mulvey on January 13, 2018

    Psychiatric genetic studies have drawn associations between human cognitive traits and noncoding genomic variants. However, the mechanistic effects of these variants are unclear. By weaving in strands of genomic data from developing human brains, de la Torre-Ubieta et al. tie disease-associated loci to functional enhancers, target genes, and putatively affected cell types.

  • The Expanding Toolkit of Translating Ribosome Affinity Purification
    by Joseph D Dougherty on December 15, 2017

    Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances...

  • Characterization of early communicative behavior in mouse models of neurofibromatosis type 1
    by Susan E Maloney on August 27, 2017

    Neurofibromatosis type 1 (NF1) is a monogenic neurodevelopmental disease caused by germline loss-of-function mutations in the NF1 tumor suppressor gene. Cognitive impairments are observed in approximately 80% of children with this disease, with 45-60% exhibiting autism spectrum disorder (ASD) symptomatology. In light of the high comorbidity rate between ASD and NF1, we assessed early communicative behavior by maternal-separation induced pup ultrasonic vocalizations (USV) and developmental...

  • Transcriptomic Analysis of Ribosome-Bound mRNA in Cortical Neurites In Vivo
    by Rebecca Ouwenga on August 20, 2017

    Localized translation in neurites helps regulate synaptic strength and development. Dysregulation of local translation is associated with many neurological disorders. However, due to technical limitations, study of this phenomenon has largely been limited to brain regions with laminar organization of dendrites such as the hippocampus or cerebellum. It has not been examined in the cortex, a region of importance for most neurological disorders, where dendrites of each neuronal population are...

  • Generation and characterization of a mouse line for monitoring translation in dopaminergic neurons
    by Joseph D Dougherty on August 16, 2017

    We developed a mouse line targeting midbrain dopamine neurons for Translating Ribosome Affinity Purification(TRAP). Here, we briefly report on the basic characterization of this mouse line including confirmation of expression of the transgene in midbrain dopamine neurons and validation of its effectiveness in capturing mRNA from these cells. We also report a translational profile of these neurons which may be of use to investigators studying the gene expression of these cells. Finally, we have...

  • Astrocytes locally translate transcripts in their peripheral processes
    by Kristina Sakers on April 26, 2017

    Local translation in neuronal processes is key to the alteration of synaptic strength necessary for long-term potentiation, learning, and memory. Here, we present evidence that regulated de novo protein synthesis occurs within distal, perisynaptic astrocyte processes. Astrocyte ribosomal proteins are found adjacent to synapses in vivo, and immunofluorescent detection of peptide elongation in acute slices demonstrates robust translation in distal processes. We have also developed a biochemical...

  • Quantitative Nucleotide Level Analysis of Regulation of Translation in Response to Depolarization of Cultured Neural Cells
    by Jasbir S Dalal on February 14, 2017

    Studies on regulation of gene expression have contributed substantially to understanding mechanisms for the long-term activity-dependent alterations in neural connectivity that are thought to mediate learning and memory. Most of these studies, however, have focused on the regulation of mRNA transcription. Here, we utilized high-throughput sequencing coupled with ribosome footprinting to globally characterize the regulation of translation in primary mixed neuronal-glial cultures in response to...