SR proteins control a complex network of RNA-processing events

Bradley, Todd; Cook, Malcolm; Blanchette, Marco

doi:10.1261/rna.043893.113

Cited by 125 publications

(152 citation statements)

References 60 publications

(69 reference statements)

Supporting

Mentioning

136

Contrasting

Order By: Relevance

“…However, we unexpectedly found that both SRSF1 and SRSF2 increase CD44 exon v5 exclusion in a concentration-dependent manner, suggesting that SRSF1 is not always specific for exon inclusion but may also be involved in exon exclusion. In agreement with this, a recent genome-wide analysis has revealed that SR proteins (SRSF1-4) cause similar numbers of exon inclusion and exon inclusion events (31)(32)(33). This finding suggests that the combinational contents of the splicing machinery complex are more important for alternative splicing than the specific mRNA interaction tendency of a single SR protein.…”

Section: Discussionsupporting

confidence: 60%

Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity

Kim

Choi

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Nuclear speckles are subnuclear storage sites containing pre-mRNA splicing machinery. Proteins assembled in nuclear speckles are known to modulate transcription and pre-mRNA processing. We have previously identified nuclear speckle-related protein 70 (NSrp70) as a novel serine/arginine (SR)-related protein that co-localizes with classical SR proteins such as serine/arginine-rich splicing factor 1 (SRSF1 or ASF/SF2) and SRSF2 (SC35). NSrp70 mediates alternative splice site selection, targeting several pre-mRNAs, including CD44 exon v5. Here we demonstrated that NSrp70 interacts physically with two SR proteins, SRSF1 and SRSF2, and reverses their splicing activity in terms of CD44 exon v5 as exon exclusion. The NSrp70 RS-like region was subdivided into three areas. Deletion of the first arginine/serine-rich-like region (RS1) completely abrogated binding to the SR proteins and to target mRNA and also failed to induce splicing of CD44 exon v5, suggesting that RS1 is critical for NSrp70 functioning. Interestingly, RS1 deletion also resulted in the loss of NSrp70 and SR protein speckle positioning, implying a potential scaffolding role for NSrp70 in nuclear speckles. NSrp70 contains an N-terminal coiled-coil domain that is critical not only for self-oligomerization but also for splicing activity. Consistently, deletion of the coiled-coil domain resulted in indefinite formation of nuclear speckles. Collectively, these results demonstrate that NSrp70 acts as a new molecular counterpart for alternative splicing of target RNA, counteracting SRSF1 and SRSF2 splicing activity.The mammalian cell nucleus contains non-membranous subnuclear bodies such as the nucleolus, Cajal bodies, promyelocytic leukemia bodies, and nuclear speckles. These bodies are generally classified by the presence of a distinct group of proteins and RNAs within them (1, 2). Nuclear speckles are irregular, punctuate structures that vary in size and shape at the immunofluorescence microscope level and are located in interchromatin regions of the nucleoplasm of mammalian cells (3,4). Several reports have demonstrated that nuclear speckles serve as storage/assembly sites for pre-mRNA splicing machinery and, therefore, elaborately regulate gene expression (2). Nuclear speckles are known to be functional centers that spatially organize transcriptional and posttranscriptional mechanisms of gene regulation. RNA-binding proteins involved in transcription and pre-mRNA processing, such as small nuclear ribonucleoprotein and arginine/serine-rich family factors (SR protein, SR-related protein), are associated with nuclear speckles (5, 6). Remarkably, two classical SR proteins, SRSF1 and SRSF2, are well known components of nuclear speckles. These SR proteins modulate both constitutive and alternative splicing by assembly of the mature spliceosome (7,8).In a previous report, we identified a novel SR-related protein, nuclear speckle-related protein 70 (NSrp70), that modulates alternative splicing site selection of several mRNAs in vivo, including Tra2␤1 v2, Fas v6, and...

show abstract

Section: Discussionsupporting

confidence: 60%

Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity

Kim

Choi

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…This allows the MSL complex to first be recruited to a small number of HASs and then explore nearby chromatin through reversibly interacting with roX RNAs. of total events in the uvCLAP background control and were also detected for MLE and MSL2 iCLIP (3% and 31% of total crosslinking events, respectively) and iCLIP experiments of eight different SR proteins (SC35, SF2, SRp54, XL6, Rbp1, B52, Rsf1, and Rbp1L) (Bradley et al 2015). The large fraction of CR41602 events in the uvCLAP background control and its independent detection by iCLIP experiments for at least 10 different proteins indicate that CR41602 constitutes an unspecific background.…”

Section: Quantitative Investigation Of Mle Point Mutantsmentioning

confidence: 86%

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

et al. 2017

View full text Add to dashboard Cite

The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX long noncoding RNAs (lncRNAs) harbor several redundant domains to interact with the ubiquitin ligase male-specific lethal 2 (MSL2) and the RNA helicase Maleless (MLE) for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By using the uvCLAP (UV cross-linking and affinity purification) methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild-type and various MLE mutant derivatives, including a catalytically inactive MLE derivative, MLE GET , we show that the minimal roX RNA contains two mutually exclusive stem-loops that exist in a peculiar structural arrangement: When one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation, as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.[Keywords: dosage compensation; H4K16ac; MLE; X chromosome; acetylation; roX RNA] Supplemental material is available for this article. RNA helicases are a large family of proteins that have important roles in many aspects of RNA biology. Although the name "helicase" suggests that the main function of these proteins is to destabilize and remove RNA secondary structures, there are several RNA helicases, especially of the DEAD-box subfamily, that use their helicase domains to simply interact with RNA (such as eIF4A3) and not for remodeling. On the other hand, a closely related RNA helicase, eIF4A1, can unwind RNA structures but only when they are relatively weak and short (Rogers et al. 2001). At the other extreme, several helicases are proposed to act as annealers that facilitate the formation of structured RNA rather than the other way around (Jankowsky 2011).Thus, although the helicase family is quite large, specific functions assigned to helicases that involve the actual removal of secondary structures in vivo are rather sparse. Maleless (MLE), known primarily for its role in Drosophila dosage compensation, is an RNA helicase of the DExH family, which is composed of relatively large multidomain helicases that (unlike the DEAD-box family) are thought to work as processive RNA helicases.

show abstract

Section: Methodsmentioning

confidence: 99%

“…Nuclear extracts from Drosophila Schneider Line-2 (S2) cells were prepared from UV-irradiated S2 cells, as described previously (20,30). Standard iCLIP assays were performed as previously described (20,30). UV-cross-linked nuclear extracts were subjected to immunoprecipitation with anti-PSI rabbit antibodies (31,32) and processed for iCLIP exactly as described previously (22), except that the cDNA was electroeluted from the gel slices as described for PAR-CLIP (33).…”

Section: Methodsmentioning

confidence: 99%

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

Wang

Taliaferro

Klibaite

et al. 2016

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

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

SR proteins control a complex network of RNA-processing events

Cited by 125 publications

References 60 publications

Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity

Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

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

Contact Info

Product

Resources

About