@article {47, title = {Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons.}, journal = {Genome Biol}, volume = {19}, year = {2018}, month = {2018 08 15}, pages = {117}, abstract = {

BACKGROUND: Alternative RNA processing plays an essential role in shaping cell identity and connectivity in the central nervous system. This is believed to involve differential regulation of RNA processing in various cell types. However, in vivo study of cell type-specific post-transcriptional regulation has been a challenge. Here, we describe a sensitive and stringent method combining genetics and CLIP (crosslinking and immunoprecipitation) to globally identify regulatory interactions between NOVA and RNA in the mouse spinal cord motoneurons.

RESULTS: We developed a means of undertaking motoneuron-specific CLIP to explore motoneuron-specific protein-RNA interactions relative to studies of the whole spinal cord in mouse. This allowed us to pinpoint differential RNA regulation specific to motoneurons, revealing a major role for NOVA in regulating cytoskeleton interactions in motoneurons. In particular, NOVA specifically promotes the palmitoylated isoform of the cytoskeleton protein Septin 8 in motoneurons, which enhances dendritic arborization.

CONCLUSIONS: Our study demonstrates that cell type-specific RNA regulation is important for fine tuning motoneuron physiology and highlights the value of defining RNA processing regulation at single cell type resolution.

}, keywords = {Alternative Splicing, Amino Acid Sequence, Animals, Cercopithecus aethiops, Chromosomes, Artificial, Bacterial, COS Cells, Cross-Linking Reagents, Cytoskeleton, Dendrites, Exons, Immunoprecipitation, Lipoylation, Mice, Mice, Transgenic, Motor Neurons, Nerve Tissue Proteins, NIH 3T3 Cells, Pseudopodia, RNA, RNA-Binding Proteins, Septins, Transcriptome}, issn = {1474-760X}, doi = {10.1186/s13059-018-1493-2}, author = {Yuan, Yuan and Xie, Shirley and Darnell, Jennifer C and Darnell, Andrew J and Saito, Yuhki and Phatnani, Hemali and Murphy, Elisabeth A and Zhang, Chaolin and Maniatis, Tom and Darnell, Robert B} } @article {24, title = {cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation.}, journal = {Neuron}, volume = {95}, year = {2017}, month = {2017 Sep 13}, pages = {1334-1349.e5}, abstract = {

Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP,~that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes~and microglia, regulated in part by neuron-specific~RNA-binding proteins NOVA2 and PTBP2. We further~identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell types and cellular states within the brain.

}, keywords = {Animals, Antigens, Neoplasm, Astrocytes, Brain, Cells, Cultured, Female, Humans, Male, Mice, Microglia, Nerve Tissue Proteins, Neuro-Oncological Ventral Antigen, Neurons, Organ Specificity, Polyadenylation, Polypyrimidine Tract-Binding Protein, Protein Isoforms, Protein Serine-Threonine Kinases, RNA-Binding Proteins}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.08.024}, author = {Hwang, Hun-Way and Saito, Yuhki and Park, Christopher Y and Blach{\`e}re, Nathalie E and Tajima, Yoko and Fak, John J and Zucker-Scharff, Ilana and Darnell, Robert B} } @article {14, title = {Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans.}, journal = {Nat Genet}, volume = {49}, year = {2017}, month = {2017 Apr}, pages = {527-536}, abstract = {

Gain-of-function mutations in some genes underlie neurodegenerative conditions, whereas loss-of-function mutations in the same genes have distinct phenotypes. This appears to be the case with the protein ataxin 1 (ATXN1), which forms a transcriptional repressor complex with capicua (CIC). Gain of function of the complex leads to neurodegeneration, but ATXN1-CIC is also essential for survival. We set out to understand the functions of the ATXN1-CIC complex in the developing forebrain and found that losing this complex results in hyperactivity, impaired learning and memory, and abnormal maturation and maintenance of upper-layer cortical neurons. We also found that CIC activity in the hypothalamus and medial amygdala modulates social interactions. Informed by these neurobehavioral features in mouse mutants, we identified five individuals with de novo heterozygous truncating mutations in CIC who share similar clinical features, including intellectual disability, attention deficit/hyperactivity disorder (ADHD), and autism spectrum disorder. Our study demonstrates that loss of ATXN1-CIC complexes causes a spectrum of neurobehavioral phenotypes.

}, keywords = {Animals, Ataxin-1, Autism Spectrum Disorder, Cerebellum, Female, Humans, Intellectual Disability, Interpersonal Relations, Male, Mice, Nerve Tissue Proteins, Neurodegenerative Diseases, Nuclear Proteins, Phenotype, Repressor Proteins}, issn = {1546-1718}, doi = {10.1038/ng.3808}, author = {Lu, Hsiang-Chih and Tan, Qiumin and Rousseaux, Maxime W C and Wang, Wei and Kim, Ji-Yoen and Richman, Ronald and Wan, Ying-Wooi and Yeh, Szu-Ying and Patel, Jay M and Liu, Xiuyun and Lin, Tao and Lee, Yoontae and Fryer, John D and Han, Jing and Chahrour, Maria and Finnell, Richard H and Lei, Yunping and Zurita-Jimenez, Maria E and Ahimaz, Priyanka and Anyane-Yeboa, Kwame and Van Maldergem, Lionel and Lehalle, Daphne and Jean-Marcais, Nolwenn and Mosca-Boidron, Anne-Laure and Thevenon, Julien and Cousin, Margot A and Bro, Della E and Lanpher, Brendan C and Klee, Eric W and Alexander, Nora and Bainbridge, Matthew N and Orr, Harry T and Sillitoe, Roy V and Ljungberg, M Cecilia and Liu, Zhandong and Schaaf, Christian P and Zoghbi, Huda Y} } @article {23, title = {Genomic Patterns of De Novo Mutation in Simplex Autism.}, journal = {Cell}, volume = {171}, year = {2017}, month = {2017 Oct 19}, pages = {710-722.e12}, abstract = {

To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of \~{}1.5~{\texttimes} 10 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe~missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p~= 1.8~{\texttimes} 10, OR~= 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p~= 3~{\texttimes} 10), suggesting a path forward for genetically characterizing more complex cases of autism.

}, keywords = {Animals, Autistic Disorder, DNA Copy Number Variations, DNA Mutational Analysis, Female, Genome-Wide Association Study, Humans, INDEL Mutation, Male, Mice, Polymorphism, Single Nucleotide}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.08.047}, author = {Turner, Tychele N and Coe, Bradley P and Dickel, Diane E and Hoekzema, Kendra and Nelson, Bradley J and Zody, Michael C and Kronenberg, Zev N and Hormozdiari, Fereydoun and Raja, Archana and Pennacchio, Len A and Darnell, Robert B and Eichler, Evan E} }