An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element

Amarasinghe, Asoka K.; MacDiarmid, Robin M.; Adams, Melissa D.; Rio, Donald C.

doi:10.1017/s1355838201010603

Cited by 29 publications

(28 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4B, red arrows). Furthermore, motif analysis in the vicinity of the identified PSI binding sites revealed significant enrichment for two major sequence motif categories: the A/CUU binding motif of PSI that had been previously identified by SELEX (23) and, remarkably, the 5′SS-like sequences (CAG/GTAAGT) that are known to be putative U1 snRNP binding sites (3,8) (Fig. 4C).…”

Section: Targeting Of Psi To Key Courtship Behavior Regulatory Gene Tmentioning

confidence: 81%

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

Wang

Taliaferro

Klibaite

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

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.PSI | U1 snRNP | alternative pre-mRNA splicing | male courtship behavior H ow gene regulation modulates neuronal activities leading to cognition and behavior is an important question in biology. Although many behavior-associated genes and neuronal cell types have been identified, a detailed understanding that links the molecular events of gene regulation to specific behaviors is still lacking. Alternative pre-mRNA splicing (AS) is a crucial gene regulatory mechanism that enables a single gene to generate functionally distinct messenger RNA transcripts (mRNAs) and protein products (1). The nervous system makes extensive use of AS to generate diverse and complex neural mRNA expression patterns that determine numerous neuronal cell types and functions (2). AS is regulated by the small nuclear ribonucleoprotein complexes (snRNPs) that compose the spliceosome for intron recognition and removal, as well as a large repertoire of non-snRNP RNA-binding proteins that affect decisions on splice site use (3). This dynamic and complex AS regulatory network modulates diverse neuronal functions, like synaptic transmission and signal processing, hence further impacting higher brain functions, such as cognition and behavioral control (4).The Drosophila KH-domain RNA binding splicing factor P-element somatic inhibitor (PSI) is best known for regulating tissue-specific AS of the Drosophila P-element transposon transcripts to restrict transposition activity to germ-line tissues (5, 6). PSI directly interacts with the U1 snRNP through a 70-aa tandem direct ...

show abstract

Section: Targeting Of Psi To Key Courtship Behavior Regulatory Gene Tmentioning

confidence: 81%

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

Wang

Taliaferro

Klibaite

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Putative SREs have previously been identified with in vitro SELEX experiments, as well as in vivo functional selection of minigene reporter libraries (Shi et al 1997;Liu et al 1998;Amarasinghe et al 2001;Wang et al 2004;Smith et al 2006;Blanchette et al 2009). Previous computational approaches have also been successful at identifying SREs.…”

Section: Introductionmentioning

confidence: 99%

Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans

Brooks

Aspden²,

Podgornaia³

et al. 2011

RNA

Self Cite

View full text Add to dashboard Cite

RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 59 and 39 splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58% %) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% % of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes.

show abstract

“…In many cases, these elements have been shown to bind hnRNP proteins, in particular hnRNP A1 (Chabot et al 2003) or PTB (Wagner and Garcia-Blanco 2001). Iterative functional selections have not yet been applied toward a functional definition of ISE or ISS elements, although they have been used to define the binding sites of specific splicing inhibitory factors, e.g., PSI, PTB, and hnRNP A1 (Burd and Dreyfuss 1994;Singh et al 1995;Amarasinghe et al 2001). Iterative selections have been used to define functional polypyrimidine tracts and BP sequences (Buvoli et al 1997;Lund et al 2000).…”

mentioning

confidence: 99%

Dichotomous splicing signals in exon flanks

Zhang

Leslie

Chasin³

2005

Genome Res.

View full text Add to dashboard Cite

Intronic elements flanking the splice-site consensus sequences are thought to play a role in pre-mRNA splicing. However, the generality of this role, the catalog of effective sequences, and the mechanisms involved are still lacking. Using molecular genetic tests, we first showed that the ∼50-nt intronic flanking sequences of exons beyond the splice-site consensus are generally important for splicing. We then went on to characterize exon flank sequences on a genomic scale. The G+C content of flanks displayed a bimodal distribution reflecting an exaggeration of this base composition in flanks relative to the gene as a whole. We divided all exons into two classes according to their flank G+C content and used computational and statistical methods to define pentamers of high relative abundance and phylogenetic conservation in exon flanks. Upstream pentamers were often common to the two classes, whereas downstream pentamers were totally different. Upstream and downstream pentamers were often identical around low G+C exons, and in contrast, were often complementary around high G+C exons. In agreement with this complementarity, predicted base pairing was more frequent between the flanks of high G+C exons. Pseudo exons did not exhibit this behavior, but rather tended to form base pairs between flanks and exon bodies. We conclude that most exons require signals in their immediate flanks for efficient splicing. G+C content is a sequence feature correlated with many genetic and genomic attributes. We speculate that there may be different mechanisms for splice site recognition depending on G+C content.[Supplemental material is available online at www.genome.org.]Pre-mRNA splicing is a fundamental step in gene expression. During this process, splice sites must be recognized within large introns before subsequent steps occur. How the splicing machinery manages to recognize splice sites remains a central problem in the study of splicing and its regulation. Three conserved sequence motifs, the 5Ј splice site, the 3Ј splice site and the branchpoint (BP), are known to be necessary for the two sequential transesterification reactions by which introns are removed and exons are joined (Adams et al. 1996;Jurica and Moore 2003). However, these sequences are quite degenerate; one can find about two orders of magnitude more intronic sequences that match either splice-site consensus, as well as or better than the sites that are actually used (Sun and Chasin 2000;Zhang et al. 2003). The BP consensus is even more degenerate Senapathy et al. 1990).There is strong genetic and biochemical evidence for the idea that the exon is the unit of initial recognition, and that there is coupling between the recognition of 5Ј and 3Ј splice sites across the exon (Robberson et al. 1990;Carothers et al. 1993;Berget 1995). However, even if pairing of 3' and 5' splice site-like sequences is stipulated and the distance between them constrained to a range typical for real exons, these "pseudo exons" still outnumber the real exons by at least an order of magnitu...

show abstract

An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element

Cited by 29 publications

References 36 publications

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

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

Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans

Dichotomous splicing signals in exon flanks

Contact Info

Product

Resources

About