The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila

Significance How gene regulation orchestrates brain activities that lead to cognition and behavior remains a challenging question in biology. Alternative pre-mRNA splicing (AS) is a crucial mechanism that is extensively used in the brain to generate diverse and functionally distinct protein products from a limited number of eukaryotic genes, and can thereby switch neuron functions and rewire neural circuits for different behaviors. Here, we elucidate the function of an essential AS regulatory protein, P-element somatic inhibitor (PSI), in coordinating male courtship behavior in the fruit fly Drosophila melanogaster. We show that PSI fine-tunes the AS patterns of a dynamic network of neural gene transcripts and exerts precise control of male mating behavior. Our results provide important information into mechanisms for behavior control in animals. Alternative pre-mRNA splicing (AS) is a critical regulatory mechanism that operates extensively in the nervous system to produce diverse protein isoforms. Fruitless AS isoforms have been shown to influence male courtship behavior, but the underlying mechanisms are unknown. Using genome-wide approaches and quantitative behavioral assays, we show that the P-element somatic inhibitor (PSI) and its interaction with the U1 small nuclear ribonucleoprotein complex (snRNP) control male courtship behavior. PSI mutants lacking the U1 snRNP-interacting domain (PSIΔAB mutant) exhibit extended but futile mating attempts. The PSIΔAB mutant results in significant changes in the AS patterns of ∼1,200 genes in the Drosophila brain, many of which have been implicated in the regulation of male courtship behavior. PSI directly regulates the AS of at least one-third of these transcripts, suggesting that PSI–U1 snRNP interactions coordinate the behavioral network underlying courtship behavior. Importantly, one of these direct targets is fruitless, the master regulator of courtship. Thus, PSI imposes a specific mode of regulatory control within the neuronal circuit controlling courtship, even though it is broadly expressed in the fly nervous system. This study reinforces the importance of AS in the control of gene activity in neurons and integrated neuronal circuits, and provides a surprising link between a pleiotropic pre-mRNA splicing pathway and the precise control of successful male mating behavior.

[1]  Michael Q. Zhang,et al.  HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. , 2014, Cell reports.

[2]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[3]  W. Huber,et al.  Detecting differential usage of exons from RNA-seq data , 2012, Genome research.

[4]  T. Nilsen,et al.  Dynamic Regulation of Alternative Splicing by Silencers that Modulate 5′ Splice Site Competition , 2008, Cell.

[5]  M. Adams,et al.  An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element. , 2001, RNA.

[6]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[7]  Christopher R. Sibley,et al.  iCLIP: Protein–RNA interactions at nucleotide resolution , 2014, Methods.

[8]  M. Koganezawa,et al.  Genes and circuits of courtship behaviour in Drosophila males , 2013, Nature Reviews Neuroscience.

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

[10]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[11]  C. Will,et al.  The Spliceosome: Design Principles of a Dynamic RNP Machine , 2009, Cell.

[12]  D. Rio,et al.  Mechanisms and Regulation of Alternative Pre-mRNA Splicing. , 2015, Annual review of biochemistry.

[13]  M. Adams,et al.  The KH-type RNA-binding protein PSI is required for Drosophila viability, male fertility, and cellular mRNA processing. , 2002, Genes & development.

[14]  Larry N. Singh,et al.  U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation , 2010, Nature.

[15]  Benjamin J. Blencowe,et al.  Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles , 2015, Neuron.

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

[17]  D. Rio,et al.  The mechanism of somatic inhibition of Drosophila P-element pre-mRNA splicing: multiprotein complexes at an exon pseudo-5' splice site control U1 snRNP binding. , 1992, Genes & development.

[18]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[19]  Mark D. Robinson,et al.  Moderated statistical tests for assessing differences in tag abundance , 2007, Bioinform..

[20]  Anne C. von Philipsborn,et al.  Cellular and Behavioral Functions of fruitless Isoforms in Drosophila Courtship , 2014, Current Biology.

[21]  Marco Blanchette,et al.  SR proteins control a complex network of RNA-processing events , 2015, RNA.

[22]  A. Mele,et al.  Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis , 2014, Nature Protocols.

[23]  P. Emery RNA extraction from Drosophila heads. , 2007, Methods in molecular biology.

[24]  Mohsen Khorshid,et al.  PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins , 2010, Journal of visualized experiments : JoVE.

[25]  D. Baralle,et al.  Novel roles of U1 snRNP in alternative splicing regulation , 2010, RNA biology.

[26]  D. Rio,et al.  Regulation of tissue-specific P-element pre-mRNA splicing requires the RNA-binding protein PSI. , 1994, Genes & development.

[27]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[28]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[29]  J. Valcárcel,et al.  The splicing regulator TIA‐1 interacts with U1‐C to promote U1 snRNP recruitment to 5′ splice sites , 2002, The EMBO journal.

[30]  D. Rio,et al.  Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. , 1995, Genes & development.

[31]  William Bialek,et al.  Mapping the stereotyped behaviour of freely moving fruit flies , 2013, Journal of The Royal Society Interface.

[32]  M. Adams,et al.  Modulation of P-element pre-mRNA splicing by a direct interaction between PSI and U1 snRNP 70K protein. , 2001, Molecular cell.

[33]  J. Manley,et al.  Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches , 2009, Nature Reviews Molecular Cell Biology.

[34]  Douglas L. Black,et al.  Neuronal regulation of alternative pre-mRNA splicing , 2007, Nature Reviews Neuroscience.

[35]  Li Yang,et al.  Conservation of an RNA regulatory map between Drosophila and mammals. , 2011, Genome research.

[36]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

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

[38]  P. Silver,et al.  PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. , 2013, Genes & development.

[39]  Robert Castelo,et al.  Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. , 2005, Molecular cell.

[40]  Barry J. Dickson,et al.  fruitless Splicing Specifies Male Courtship Behavior in Drosophila , 2005, Cell.