Splicing Regulation in Neurologic Disease

Neurodegenerative Tauopathies

Lee, V. M.-Y., Goedert, M., & Trojanowski, J. Q. (2001) · Annual Review of Neuroscience · doi:10.1146/annurev.neuro.24.1.1121 · Cited by 2,480

Listening to silence and understanding nonsense: exonic mutations that affect splicing

Cartegni, L., Chew, S. L., & Krainer, A. R. (2002) · Nature Reviews Genetics · doi:10.1038/nrg775 · Cited by 2,209

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120

A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration

Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabó, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.03.032 · Cited by 789

HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and sex-lethal

Szabo, A., Dalmau, J., Manley, G., Rosenfeld, M., Wong, E., Henson, J., Posner, J. B., & Furneaux, H. M. (1991) · Cell · doi:10.1016/0092-8674(91)90184-z · Cited by 553

Nova regulates brain-specific splicing to shape the synapse

Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.-S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1610 · Cited by 509

Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2

Young, J. I., Hong, E. P., Castle, J. C., Crespo-Barreto, J., Bowman, A. B., Rose, M. F., Kang, D., Richman, R., Johnson, J. M., Berget, S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507856102 · Cited by 484

Tau gene alternative splicing: expression patterns, regulation and modulation of function in normal brain and neurodegenerative diseases

Andreadis, A. (2005) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2004.08.010 · Cited by 311

The de novo chromosome 16 translocations of two patients with abnormal phenotypes (mental retardation and epilepsy) disrupt the A2BP1 gene

Bhalla, K., Phillips, H. A., Crawford, J., McKenzie, O. L. D., Mulley, J. C., Eyre, H., Gardner, A. E., Kremmidiotis, G., & Callen, D. F. (2004) · Journal of Human Genetics · doi:10.1007/s10038-004-0145-4 · Cited by 146

ELAV inhibits 3′-end processing to promote neural splicing of ewg pre-mRNA

Soller, M., & White, K. (2003) · Genes & Development · doi:10.1101/gad.1106703 · Cited by 89

Spatio-temporal transcriptome of the human brain

Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., et al. (2011) · Nature · doi:10.1038/nature10523 · Cited by 2,084

The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing

Makeyev, E. V., Zhang, J., Carrasco, M. A., & Maniatis, T. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.015 · Cited by 1,395

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

Johnson, M. B., Kawasawa, Y. I., Mason, C. E., Krsnik, Ž., Coppola, G., Bogdanović, D., Geschwind, D. H., Mane, S. M., State, M. W., & Šestan, N. (2009) · Neuron · doi:10.1016/j.neuron.2009.03.027 · Cited by 603

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

Raj, B., & Blencowe, B. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.004 · Cited by 475

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

Darnell, R. B. (2010) · WIREs RNA · doi:10.1002/wrna.31 · Cited by 382

Neuronal regulation of alternative pre-mRNA splicing

Li, Q., Lee, J.-A., & Black, D. L. (2007) · Nature Reviews Neuroscience · doi:10.1038/nrn2237 · Cited by 376

The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain

Gehman, L. T., Stoilov, P., Maguire, J., Damianov, A., Lin, C.-H., Shiue, L., Ares, M., Mody, I., & Black, D. L. (2011) · Nature Genetics · doi:10.1038/ng.841 · Cited by 331

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

Zhang, C., Frias, M. A., Mele, A., Ruggiu, M., Eom, T., Marney, C. B., Wang, H., Licatalosi, D. D., Fak, J. J., & Darnell, R. B. (2010) · Science · doi:10.1126/science.1191150 · Cited by 294

The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function

Gehman, L. T., Meera, P., Stoilov, P., Shiue, L., O'Brien, J. E., Meisler, M. H., Ares, M., Otis, T. S., & Black, D. L. (2012) · Genes & Development · doi:10.1101/gad.182477.111 · Cited by 213

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

Feng, J., Wilkinson, M., Liu, X., Purushothaman, I., Ferguson, D., Vialou, V., Maze, I., Shao, N., Kennedy, P., Koo, J., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-4-r65 · Cited by 198

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

Licatalosi, D. D., Yano, M., Fak, J. J., Mele, A., Grabinski, S. E., Zhang, C., & Darnell, R. B. (2012) · Genes & Development · doi:10.1101/gad.191338.112 · Cited by 193

Nova2 Regulates Neuronal Migration through an RNA Switch in Disabled-1 Signaling

Yano, M., Hayakawa-Yano, Y., Mele, A., & Darnell, R. B. (2010) · Neuron · doi:10.1016/j.neuron.2010.05.007 · Cited by 176

RNA Protein Interaction in Neurons

Darnell, R. B. (2013) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-062912-114322 · Cited by 181

The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

Li, Q., Zheng, S., Han, A., Lin, C.-H., Stoilov, P., Fu, X.-D., & Black, D. L. (2014) · eLife · doi:10.7554/elife.01201 · Cited by 174

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q., & Zhang, C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt216 · Cited by 123

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Scheckel, C., Drapeau, E., Frias, M. A., Park, C. Y., Fak, J., Zucker-Scharff, I., Kou, Y., Haroutunian, V., Ma'ayan, A., Buxbaum, J. D., et al. (2016) · eLife · doi:10.7554/elife.10421 · Cited by 139

NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure

Eom, T., Zhang, C., Wang, H., Lay, K., Fak, J., Noebels, J. L., & Darnell, R. B. (2013) · eLife · doi:10.7554/elife.00178 · Cited by 118

Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration

Jia, Y., Mu, J. C., & Ackerman, S. L. (2012) · Cell · doi:10.1016/j.cell.2011.11.057 · Cited by 114

Rescuing Z + agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing

Ruggiu, M., Herbst, R., Kim, N., Jevsek, M., Fak, J. J., Mann, M. A., Fischbach, G., Burden, S. J., & Darnell, R. B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813112106 · Cited by 113

Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1

Vuong, C. K., Wei, W., Lee, J.-A., Lin, C.-H., Damianov, A., de la Torre-Ubieta, L., Halabi, R., Otis, K. O., Martin, K. C., O’Dell, T. J., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.03.008 · Cited by 102

Developments in RNA Splicing and Disease

Poulos, M. G., Batra, R., Charizanis, K., & Swanson, M. S. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000778 · Cited by 98

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

Schor, I. E., Fiszbein, A., Petrillo, E., & Kornblihtt, A. R. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.167 · Cited by 90

Genes, behavior and next‐generation RNA sequencing

Hitzemann, R., Bottomly, D., Darakjian, P., Walter, N., Iancu, O., Searles, R., Wilmot, B., & McWeeney, S. (2013) · Genes, Brain and Behavior · doi:10.1111/gbb.12007 · Cited by 88

Misregulation of alternative splicing in a mouse model of Rett syndrome

Li, R., Dong, Q., Yuan, X., Zeng, X., Gao, Y., Chiao, C., Li, H., Zhao, X., Keles, S., Wang, Z., et al. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006129 · Cited by 67

Motor coordination defects in mice deficient for the Sam68 RNA-binding protein

Lukong, K. E., & Richard, S. (2008) · Behavioural Brain Research · doi:10.1016/j.bbr.2008.01.010 · Cited by 48

HnRNP L and hnRNP LL antagonistically modulate PTB-mediated splicing suppression of CHRNA1 pre-mRNA

Rahman, M. A., Masuda, A., Ohe, K., Ito, M., Hutchinson, D. O., Mayeda, A., Engel, A. G., & Ohno, K. (2013) · Scientific Reports · doi:10.1038/srep02931 · Cited by 44

DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype-phenotype prediction

Chandrashekar, P. B., Alatkar, S., Wang, J., Hoffman, G. E., He, C., Jin, T., Khullar, S., Bendl, J., Fullard, J. F., Roussos, P., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01248-6 · Cited by 37

Identification and characterization of a neuron-specific isoform of protrudin

Ohnishi, T., Shirane, M., Hashimoto, Y., Saita, S., & Nakayama, K. I. (2014) · Genes to Cells · doi:10.1111/gtc.12109 · Cited by 33

Introduction to Sequencing the Brain Transcriptome

Hitzemann, R., Darakjian, P., Walter, N., Dan Iancu, O., Searles, R., & McWeeney, S. (2014) · International Review of Neurobiology · doi:10.1016/b978-0-12-801105-8.00001-1 · Cited by 20

A Flanking Gene Problem Leads to the Discovery of a Gprc5b Splice Variant Predominantly Expressed in C57Bl/6J Mouse Brain and in Maturing Neurons

Cool, B. H., Chan, G. C.-K., Lee, L., Oshima, J., Martin, G. M., & Hu, Q. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010351 · Cited by 18