FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns.

Dominant mutations and mislocalization or aggregation of Fused in Sarcoma (FUS), an RNA-binding protein (RBP), cause neuronal degeneration in Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD), two incurable neurological diseases. However, the function of FUS in neurons is not well understood. To uncover the impact of FUS in the neuronal transcriptome, we used high-throughput sequencing of immunoprecipitated and cross-linked RNA (HITS-CLIP) of FUS in human brains and mouse neurons differentiated from embryonic stem cells, coupled with RNA-seq and FUS knockdowns. We report conserved neuronal RNA targets and networks that are regulated by FUS. We find that FUS regulates splicing of genes coding for RBPs by binding to their highly conserved introns. Our findings have important implications for understanding the impact of FUS in neurodegenerative diseases and suggest that perturbations of FUS can impact the neuronal transcriptome via perturbations of RBP transcripts.

[1]  Stephanie C Huelga,et al.  Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs , 2012, Nature Neuroscience.

[2]  Nejc Haberman,et al.  Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain , 2012, Scientific Reports.

[3]  C. van Broeckhoven,et al.  The genetics and neuropathology of frontotemporal lobar degeneration , 2012, Acta Neuropathologica.

[4]  Kinji Ohno,et al.  Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions , 2012, Scientific Reports.

[5]  Larry N. Singh,et al.  U1 snRNP Determines mRNA Length and Regulates Isoform Expression , 2012, Cell.

[6]  P. Alexiou,et al.  Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis , 2012, Nature Structural &Molecular Biology.

[7]  I. Mackenzie,et al.  FET proteins in frontotemporal dementia and amyotrophic lateral sclerosis , 2012, Brain Research.

[8]  Oliver D. King,et al.  The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease , 2012, Brain Research.

[9]  S. Prusiner,et al.  A Unifying Role for Prions in Neurodegenerative Diseases , 2012, Science.

[10]  Michael T. McManus,et al.  Precursor microRNA-programmed silencing complex assembly pathways in mammals. , 2012, Molecular cell.

[11]  Jimin Pei,et al.  Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels , 2012, Cell.

[12]  H. Bussemaker,et al.  TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements , 2012, Proceedings of the National Academy of Sciences.

[13]  H. Hakonarson,et al.  Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis. , 2012, Human molecular genetics.

[14]  L. Maquat,et al.  Regulation of cytoplasmic mRNA decay , 2012, Nature Reviews Genetics.

[15]  Z. Mourelatos,et al.  RNA dysregulation in diseases of motor neurons. , 2012, Annual review of pathology.

[16]  Gene W. Yeo,et al.  Integrative genome‐wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins , 2012, Cell reports.

[17]  J. Trojanowski,et al.  Gains or losses: molecular mechanisms of TDP43-mediated neurodegeneration , 2011, Nature Reviews Neuroscience.

[18]  J. Trojanowski,et al.  A yeast functional screen predicts new candidate ALS disease genes , 2011, Proceedings of the National Academy of Sciences.

[19]  Chris Sander,et al.  RNA targets of wild-type and mutant FET family proteins , 2011, Nature Structural &Molecular Biology.

[20]  K. Nishida,et al.  Mechanisms and consequences of alternative polyadenylation. , 2011, Molecules and Cells.

[21]  Olaf Ansorge,et al.  FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations. , 2011, Brain : a journal of neurology.

[22]  N. Proudfoot.  Ending the message: poly(A) signals then and now. , 2011, Genes & development.

[23]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[24]  A. Krainer,et al.  Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly , 2011, Proceedings of the National Academy of Sciences.

[25]  Charles D. Smith,et al.  Hippocampal sclerosis in advanced age: clinical and pathological features. , 2011, Brain : a journal of neurology.

[26]  Robert H. Brown,et al.  Mutational analysis reveals the FUS homolog TAF15 as a candidate gene for familial amyotrophic lateral sclerosis , 2011, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[27]  J. Ule,et al.  Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. , 2011, Nature neuroscience.

[28]  Gene W. Yeo,et al.  Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43 , 2011, Nature Neuroscience.

[29]  Fatih Ozsolak,et al.  RNA sequencing: advances, challenges and opportunities , 2011, Nature Reviews Genetics.

[30]  H. Kovar.  Dr. Jekyll and Mr. Hyde: The Two Faces of the FUS/EWS/TAF15 Protein Family , 2010, Sarcoma.

[31]  I. Mackenzie,et al.  ALS‐associated fused in sarcoma (FUS) mutations disrupt Transportin‐mediated nuclear import , 2010, The EMBO journal.

[32]  D. Cleveland,et al.  TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. , 2010, Human molecular genetics.

[33]  O. King,et al.  Prion-like disorders: blurring the divide between transmissibility and infectivity , 2010, Journal of Cell Science.

[34]  R. Chitta,et al.  Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery. , 2010, Journal of proteome research.

[35]  D. Black,et al.  Autoregulation of Fox protein expression to produce dominant negative splicing factors. , 2010, RNA.

[36]  Lawrence Rajendran,et al.  The Transcellular Spread of Cytosolic Amyloids, Prions, and Prionoids , 2009, Neuron.

[37]  J. Manley,et al.  TLS Inhibits RNA Polymerase III Transcription , 2009, Molecular and Cellular Biology.

[38]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[39]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[40]  K. Khabar,et al.  Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation , 2009, Nucleic acids research.

[41]  J L Haines,et al.  Supporting Online Material Materials and Methods Figs. S1 to S7 Tables S1 to S4 References Mutations in the Fus/tls Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis , 2022 .

[42]  Xun Hu,et al.  Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6 , 2009, Science.

[43]  H. Wichterle,et al.  Xenotransplantation of embryonic stem cell-derived motor neurons into the developing chick spinal cord. , 2009, Methods in molecular biology.

[44]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[45]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[46]  C. Glass,et al.  Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription , 2008, Nature.

[47]  B. McConkey,et al.  TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis , 2008, Nature Genetics.

[48]  Murray Grossman,et al.  TARDBP mutations in amyotrophic lateral sclerosis with TDP-43 neuropathology: a genetic and histopathological analysis , 2008, The Lancet Neurology.

[49]  B. Blencowe,et al.  Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay , 2008, Molecular and Cellular Biology.

[50]  Xun Hu,et al.  TDP-43 Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis , 2008, Science.

[51]  Tyson A. Clark,et al.  Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. , 2007, Genes & development.

[52]  H. Akiyama,et al.  TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. , 2006, Biochemical and biophysical research communications.

[53]  Bruce L. Miller,et al.  Ubiquitinated TDP-43 in Frontotemporal Lobar Degeneration and Amyotrophic Lateral Sclerosis , 2006, Science.

[54]  David Haussler,et al.  Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays , 2005, PLoS Comput. Biol..

[55]  Bin Tian,et al.  A large-scale analysis of mRNA polyadenylation of human and mouse genes , 2005, Nucleic acids research.

[56]  T. Takumi,et al.  Domain Architectures and Characterization of an RNA-binding Protein, TLS* , 2004, Journal of Biological Chemistry.

[57]  Rainer Breitling,et al.  Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.

[58]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[59]  R. Sorek,et al.  Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. , 2003, Genome research.

[60]  Steven P. Gygi,et al.  Comprehensive proteomic analysis of the human spliceosome , 2002, Nature.

[61]  M. Mann,et al.  Large-scale Proteomic Analysis of the Human Spliceosome References , 2006 .

[62]  G. Dreyfuss,et al.  Messenger-RNA-binding proteins and the messages they carry , 2002, Nature Reviews Molecular Cell Biology.

[63]  J. Castresana.  Estimation of genetic distances from human and mouse introns , 2002, Genome Biology.

[64]  C. Orvain,et al.  Identification of an RNA Binding Specificity for the Potential Splicing Factor TLS* , 2001, The Journal of Biological Chemistry.

[65]  M. Garcia-Blanco,et al.  Protein–protein interactions and 5'-splice-site recognition in mammalian mRNA precursors , 1994, Nature.