scholarly journals The Disease-Associated ProteinsDrosophilaNab2 and Ataxin-2 Interact with Shared RNAs and Coregulate Neuronal Morphology

2021 ◽  
Author(s):  
J. Christopher Rounds ◽  
Edwin B. Corgiat ◽  
Changtian Ye ◽  
Joseph A. Behnke ◽  
Seth M. Kelly ◽  
...  
Keyword(s):  
Rna Binding ◽  
Target Selection ◽  
Tail Length ◽  
High Specificity ◽  
Neuronal Morphology ◽  
Functional Protein ◽  
Specific Subset ◽  
Rna Immunoprecipitation ◽  
Ataxin 2

ABSTRACTNab2encodes a conserved polyadenosine RNA-binding protein (RBP) with broad roles in post-transcriptional regulation, including in poly(A) RNA export, poly(A) tail length control, transcription termination, and mRNA splicing. Mutation of theNab2human orthologZC3H14gives rise to an autosomal recessive intellectual disability, but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships likely remain unidentified. Here we present evidence thatDrosophila melanogasterNab2 interacts with the RBP Ataxin-2 (Atx2), a neuronal translational regulator, and implicate these proteins in coordinate regulation of neuronal morphology and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs inDrosophilabrain neurons using an RNA immunoprecipitation-sequencing (RIP-Seq) approach. Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neuronsin vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g.drk,me31B,stai) and of transcripts specific to Nab2 or Atx2 (e.g.Arpc2,tea, respectively) promise insight into neuronal functions of and interactions between each RBP. Significantly, Nab2-associated RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. Taken together, these data demonstrate that Nab2 opposingly regulates neuronal morphology and shares associated neuronal RNAs with Atx2, and thatDrosophilaNab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.

scholarly journals The Disease-Associated Proteins Drosophila Nab2 and Ataxin-2 Interact with Shared RNAs and Coregulate Neuronal Morphology

Genetics ◽  
2021 ◽  
Author(s):  
J Christopher Rounds ◽  
Edwin B Corgiat ◽  
Changtian Ye ◽  
Joseph A Behnke ◽  
Seth M Kelly ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Target Selection ◽  
High Specificity ◽  
Neuronal Morphology ◽  
Functional Protein ◽  
Specific Subset ◽  
Drosophila Brain ◽  
Ataxin 2

Abstract Nab2 encodes the Drosophila melanogaster member of a conserved family of zinc finger polyadenosine RNA-binding proteins (RBPs) linked to multiple steps in post-transcriptional regulation. Mutation of the Nab2 human ortholog ZC3H14 gives rise to an autosomal recessive intellectual disability but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships remain unidentified. Here, we present evidence that Nab2 genetically interacts with Ataxin-2 (Atx2), which encodes a neuronal translational regulator, and that these factors coordinately regulate neuronal morphology, circadian behavior, and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs in Drosophila brain neurons using RNA immunoprecipitation-sequencing (RIP-Seq). Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g., drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g., Arpc2 and tea) promise insight into neuronal functions of, and genetic interactions between, each RBP. Consistent with prior biochemical studies, Nab2-associated neuronal RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. These data support a model where Nab2 functionally opposes Atx2 in neurons, demonstrate Nab2 shares associated neuronal RNAs with Atx2, and reveal Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.

scholarly journals Target selection by natural and redesigned PUF proteins

2015 ◽  
Vol 112 (52) ◽  
pp. 15868-15873 ◽  
Author(s):  
Douglas F. Porter ◽  
Yvonne Y. Koh ◽  
Brett VanVeller ◽  
Ronald T. Raines ◽  
Marvin Wickens
Keyword(s):  
Rna Binding ◽  
Target Selection ◽  
Mutant Protein ◽  
Sequence Specificity ◽  
Wild Type ◽  
Rna Recognition Motifs ◽  
Puf Proteins ◽  
Binding Domains ◽  
Recognition Motifs

Pumilio/fem-3 mRNA binding factor (PUF) proteins bind RNA with sequence specificity and modularity, and have become exemplary scaffolds in the reengineering of new RNA specificities. Here, we report the in vivo RNA binding sites of wild-type (WT) and reengineered forms of the PUF protein Saccharomyces cerevisiae Puf2p across the transcriptome. Puf2p defines an ancient protein family present throughout fungi, with divergent and distinctive PUF RNA binding domains, RNA-recognition motifs (RRMs), and prion regions. We identify sites in RNA bound to Puf2p in vivo by using two forms of UV cross-linking followed by immunopurification. The protein specifically binds more than 1,000 mRNAs, which contain multiple iterations of UAAU-binding elements. Regions outside the PUF domain, including the RRM, enhance discrimination among targets. Compensatory mutants reveal that one Puf2p molecule binds one UAAU sequence, and align the protein with the RNA site. Based on this architecture, we redesign Puf2p to bind UAAG and identify the targets of this reengineered PUF in vivo. The mutant protein finds its target site in 1,800 RNAs and yields a novel RNA network with a dramatic redistribution of binding elements. The mutant protein exhibits even greater RNA specificity than wild type. The redesigned protein decreases the abundance of RNAs in its redesigned network. These results suggest that reengineering using the PUF scaffold redirects and can even enhance specificity in vivo.

scholarly journals The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity

2018 ◽  
Vol 1 (5) ◽  
pp. e201800187 ◽  
Author(s):  
Daniela Lazzaretti ◽  
Lina Bandholz-Cajamarca ◽  
Christiane Emmerich ◽  
Kristina Schaaf ◽  
Claire Basquin ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Structural Information ◽  
Target Selection ◽  
Mrna Localization ◽  
In Vitro Binding ◽  
Vitro Binding

During mRNA localization, RNA-binding proteins interact with specific structured mRNA localization motifs. Although several such motifs have been identified, we have limited structural information on how these interact with RNA-binding proteins. Staufen proteins bind structured mRNA motifs through dsRNA-binding domains (dsRBD) and are involved in mRNA localization in Drosophila and mammals. We solved the structure of two dsRBDs of human Staufen1 in complex with a physiological dsRNA sequence. We identified interactions between the dsRBDs and the RNA sugar–phosphate backbone and direct contacts of conserved Staufen residues to RNA bases. Mutating residues mediating nonspecific backbone interactions only affected Staufen function in Drosophila when in vitro binding was severely reduced. Conversely, residues involved in base-directed interactions were required in vivo even when they minimally affected in vitro binding. Our work revealed that Staufen can read sequence features in the minor groove of dsRNA and suggests that these influence target selection in vivo.

scholarly journals A novel essential RNA-binding protein complex in Trypanosoma brucei

2020 ◽  
Author(s):  
Kathrin Bajak ◽  
Kevin Leiss ◽  
Christine Clayton ◽  
Esteban Erben
Keyword(s):  
Ribosomal Proteins ◽  
Rna Binding ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Gtpase Domain ◽  
Gtp Hydrolysis ◽  
Coding Regions ◽  
Rna Immunoprecipitation ◽  
Reading Frames

AbstractZC3H5 is an essential cytoplasmic trypanosome protein with a single Cx7Cx5Cx3H zinc finger domain. We here show that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500 and Tb927.7.3040. ZC3H5 interacts directly with Tb927.11.4900, which in turn interacts with Tb927.7.3040. Tb927.11.4900 has a circularly permuted GTPase domain, which is required for the Tb927.7.3040 interaction. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5’-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). Tethering of ZC3H5, or other complex components, to a reporter repressed its expression. However, depletion of ZC3H5 in vivo did not increase the abundance of ZC3H5-bound mRNAs: instead, counter-intuitively, there were very minor decreases in a few targets, and marked increases in the abundances of very stable mRNAs encoding ribosomal proteins. Depletion also resulted in an increase in monosomes at the expense of large polysomes, and appearance of “halfmer” disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of sub-optimal open reading frames; complex assembly might be regulated by GTP hydrolysis and GTP-GDP exchange.

scholarly journals Temporal-specific roles of fragile X mental retardation protein in the development of the hindbrain auditory circuit

Development ◽  
2020 ◽  
Vol 147 (21) ◽  
pp. dev188797
Author(s):  
Xiaoyu Wang ◽  
Ayelet Kohl ◽  
Xiaoyan Yu ◽  
Diego A. R. Zorio ◽  
Avihu Klar ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Rna Binding ◽  
Fragile X ◽  
Neuronal Cell ◽  
High Specificity ◽  
Fragile X Mental Retardation ◽  
Midline Crossing ◽  
Mental Retardation Protein ◽  
Axonal Targeting

ABSTRACTFragile X mental retardation protein (FMRP) is an RNA-binding protein abundant in the nervous system. Functional loss of FMRP leads to sensory dysfunction and severe intellectual disabilities. In the auditory system, FMRP deficiency alters neuronal function and synaptic connectivity and results in perturbed processing of sound information. Nevertheless, roles of FMRP in embryonic development of the auditory hindbrain have not been identified. Here, we developed high-specificity approaches to genetically track and manipulate throughout development of the Atoh1+ neuronal cell type, which is highly conserved in vertebrates, in the cochlear nucleus of chicken embryos. We identified distinct FMRP-containing granules in the growing axons of Atoh1+ neurons and post-migrating NM cells. FMRP downregulation induced by CRISPR/Cas9 and shRNA techniques resulted in perturbed axonal pathfinding, delay in midline crossing, excess branching of neurites, and axonal targeting errors during the period of circuit development. Together, these results provide the first in vivo identification of FMRP localization and actions in developing axons of auditory neurons, and demonstrate the importance of investigating early embryonic alterations toward understanding the pathogenesis of neurodevelopmental disorders.

scholarly journals Xenopus LSm Proteins Bind U8 snoRNA via an Internal Evolutionarily Conserved Octamer Sequence

2002 ◽  
Vol 22 (12) ◽  
pp. 4101-4112 ◽  
Author(s):  
Nenad Tomasevic ◽  
Brenda A. Peculis
Keyword(s):  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Ribosomal Subunit ◽  
High Specificity ◽  
Sm Proteins ◽  
U6 Snrna ◽  
Evolutionarily Conserved

ABSTRACT U8 snoRNA plays a unique role in ribosome biogenesis: it is the only snoRNA essential for maturation of the large ribosomal subunit RNAs, 5.8S and 28S. To learn the mechanisms behind the in vivo role of U8 snoRNA, we have purified to near homogeneity and characterized a set of proteins responsible for the formation of a specific U8 RNA-binding complex. This 75-kDa complex is stable in the absence of added RNA and binds U8 with high specificity, requiring the conserved octamer sequence present in all U8 homologues. At least two proteins in this complex can be cross-linked directly to U8 RNA. We have identified the proteins as Xenopus homologues of the LSm (like Sm) proteins, which were previously reported to be involved in cytoplasmic degradation of mRNA and nuclear stabilization of U6 snRNA. We have identified LSm2, -3, -4, -6, -7, and -8 in our purified complex and found that this complex associates with U8 RNA in vivo. This purified complex can bind U6 snRNA in vitro but does not bind U3 or U14 snoRNA in vitro, demonstrating that the LSm complex specifically recognizes U8 RNA.

scholarly journals A transgenic DND1GFP fusion allele reports in vivo expression and RNA binding targets in undifferentiated mouse germ cells

2021 ◽  
Author(s):  
Victor A Ruthig ◽  
Tetsuhiro Yokonishi ◽  
Matthew B Friedersdorf ◽  
Sofia Batchvarova ◽  
Josiah Hardy ◽  
...  
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Rna Binding ◽  
Cell Transformation ◽  
Primordial Germ Cell ◽  
Fetal Life ◽  
Mouse Line ◽  
Transgenic Mouse Line ◽  
Rna Immunoprecipitation

Abstract In vertebrates, the RNA binding protein (RBP) Dead End 1 (DND1) is essential for primordial germ cell (PGC) survival and maintenance of cell identity. In multiple species, Dnd1 loss or mutation leads to severe PGC loss soon after specification or, in some species, germ cell transformation to somatic lineages. Our investigations into the role of DND1 in PGC specification and differentiation have been limited by the absence of an available antibody. To address this problem, we used CRISPR/Cas9 gene editing to establish a transgenic mouse line carrying a DND1GFP fusion allele. We present imaging analysis of DND1GFP expression showing that DND1GFP expression is heterogeneous among male germ cells (MGCs) and female germ cells (FGCs). DND1GFP was detected in MGCs throughout fetal life but lost from FGCs at meiotic entry. In postnatal and adult testes, DND1GFP expression correlated with classic markers for the pre-meiotic spermatogonial population. Utilizing the GFP-tag for RNA immunoprecipitation (RIP) analysis in MGCs validated this transgenic as a tool for identifying in vivo transcript targets of DND1. The DND1GFP mouse line is a novel tool for isolation and analysis of embryonic and fetal germ cells, and the spermatogonial population of the postnatal and adult testis.

scholarly journals Loss of KHSRP Increases Neuronal Growth and Synaptic Transmission and Alters Memory Consolidation Through RNA Stabilization

2020 ◽  
Author(s):  
Sarah L. Olguin ◽  
Priyanka Patel ◽  
Michela Dell’Orco ◽  
Amy S. Gardiner ◽  
Robert Cole ◽  
...  
Keyword(s):  
Memory Consolidation ◽  
Rna Binding ◽  
Regulatory Protein ◽  
Axon Growth ◽  
Neurite Growth ◽  
Neuronal Morphology ◽  
Long Term Memory ◽  
Neuronal Cultures ◽  
Spine Density

ABSTRACTThe KH-type splicing regulatory protein (KHSRP) is an RNA-binding protein linked to decay of AU-rich element containing mRNAs. We have previously shown that KHSRP destabilizes the mRNA encoding the growth-associated protein GAP-43 and decreases neurite growth in cultured embryonic neurons. In contrast, loss of KHSRP stabilizes Gap43 mRNA and increases neurite growth. Here, we have tested functions of neural KHSRP in vivo. We find upregulation of 1460 mRNAs in the neocortex of adult Khsrp−/− mice, of which 527 bind to KHSRP with high specificity. These KHSRP targets are involved in pathways for neuronal morphology, axon guidance, neurotransmission and long-term memory. Neocortical neurons show increased axon growth and dendritic spine density in Khsrp−/− mice. Analyses of neuronal cultures from embryonic Khsrp−/− mice point to a neuron-intrinsic alteration in axonal and dendritic growth and elevations in KHSRP-target mRNAs, including subcellularly localized mRNAs. Hippocampus and infralimbic cortex of Khsrp−/− mice show presynaptic elevations in neurotransmission. The Khsrp−/− mice have significant deficits in both trace conditioning and attention set-shifting tasks compared Khsrp+/+ mice, indicating impaired prefrontal- and hippocampal-dependent memory consolidation with loss of KHSRP. Overall, our results indicate that prenatal deletion of KHSRP impairs neuronal development resulting in alterations in neuronal morphology and function by changing post-transcriptional control of neuronal gene expression.

scholarly journals Circular RNA circDLC1 Inhibits MMP1-Mediated Liver Cancer Progression via Interaction with HuR

2020 ◽  
Author(s):  
Hailing Liu ◽  
Tian Lan ◽  
Hui Li ◽  
Lin Xu ◽  
Xing Chen ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Rna Binding ◽  
Circular Rna ◽  
Hepatoma Cells ◽  
Circular Rnas ◽  
Rna Seq ◽  
Downstream Target ◽  
Rna Immunoprecipitation

Abstract Background: N6-methyladenosine (m6A) modification has been demonstrated to be closely related to cancer progression. KIAA1429, a key component of the m6A methyltransferase complex, has recently been reported to promote hepatocellular carcinoma (HCC) progression by regulating the m6A methylation. However, the involvement of circular RNAs (circRNAs) in KIAA1429-mediated HCC progression is still unknown.Methods: RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (m6A-seq) were utilized to identify KIAA1429-regulated circRNAs. The effects of circDLC1 on proliferation and metastasis of hepatoma cells were examined in vitro and in vivo. RT-qPCR was used to measure the expression of circDLC1 in HCC tissues and hepatoma cells. RNA FISH, RIP assays and biotin-labeled RNA pull-down were used to investigate the downstream effector of circDLC1. The downstream targets of circDLC1 were identified using RNA-seq.Results: Our data demonstrated that circDLC1 was downregulated in HCC tissues and closely relevant to favorable prognosis. Overexpression of circDLC1 inhibited the proliferation and motility of hepatoma cells in vitro and in vivo, while silencing of circDLC1 played the opposite role. Mechanistic investigations revealed that circDLC1 could bind to RNA-binding protein HuR, which subsequently reduced the interaction between HuR and MMP1 mRNAs, thus inhibited the expression of MMP1, finally contributed to inhibition of HCC progression.Conclusion: Our work suggests that circDLC1, a downstream target of KIAA1429, is a promising prognostic marker for HCC patients, and the circDLC1-HuR-MMP1 axis may serve as a potential therapeutic target for HCC treatment.

scholarly journals FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo

2020 ◽  
Author(s):  
Yongwoo Na ◽  
Hyunjoon Kim ◽  
Yeon Choi ◽  
Sanghee Shin ◽  
Jae Hun Jung ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
High Specificity ◽  
Xenopus Laevis Oocytes ◽  
Tissue Samples ◽  
Rnp Complex ◽  
Multicellular Organisms

Abstract RNA–protein interaction is central to post-transcriptional gene regulation. Identification of RNA-binding proteins relies mainly on UV-induced crosslinking (UVX) followed by the enrichment of RNA–protein conjugates and LC-MS/MS analysis. However, UVX has limited applicability in tissues of multicellular organisms due to its low penetration depth. Here, we introduce formaldehyde crosslinking (FAX) as an alternative chemical crosslinking for RNA interactome capture (RIC). Mild FAX captures RNA–protein interaction with high specificity and efficiency in cell culture. Unlike UVX-RIC, FAX-RIC robustly detects proteins that bind to structured RNAs or uracil-poor RNAs (e.g. AGO1, STAU1, UPF1, NCBP2, EIF4E, YTHDF proteins and PABP), broadening the coverage. Applied to Xenopus laevis oocytes and embryos, FAX-RIC provided comprehensive and unbiased RNA interactome, revealing dynamic remodeling of RNA–protein complexes. Notably, translation machinery changes during oocyte-to-embryo transition, for instance, from canonical eIF4E to noncanonical eIF4E3. Furthermore, using Mus musculus liver, we demonstrate that FAX-RIC is applicable to mammalian tissue samples. Taken together, we report that FAX can extend the RNA interactome profiling into multicellular organisms.

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