Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns

Alpert, Tara; Straube, Korinna; Oesterreich, Fernando Carrillo; Herzel, Lydia; Neugebauer, Karla M.

doi:10.1016/j.celrep.2020.108324

Cited by 26 publications

(13 citation statements)

References 67 publications

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“…This opposing role possibility aligns with some of the known functions of each protein. Namely, in S. cerevisiae Nab2 contributes to proper nuclear processing events including protection from enzymatic degradation, poly(A) tail length control, splicing, and transcriptional termination while also facilitating poly(A) RNA export from the nucleus (Green et al 2002;Hector et al 2002;Kelly et al 2010;Schmid et al 2015;Soucek et al 2016;Alpert et al 2020). If Drosophila Nab2 also performs some or all of these nuclear processing roles on its associated RNAs, then Nab2 binding should contribute to transcript stability, nuclear export, and ultimately protein expression.…”

Section: A Model Of Opposing Regulatory Roles For Nab2 and Atx2mentioning

confidence: 99%

“…While the precise molecular function of Drosophila Nab2 on its associated transcripts is unknown, informed hypotheses may be drawn by synthesizing research on Drosophila Nab2 and orthologs murine ZC3H14, human ZC3H14, and S. cerevisiae Nab2, the most well-studied Nab2/ZC3H14 ortholog (reviewed in Fasken et al 2019). In S. cerevisiae, Nab2 functions pervasively across many RNAs in transcript stability and transcription termination, and it likely acts similarly broadly in poly(A) tail length control and poly(A) RNA export (Schmid et al 2015;Fasken et al 2019;Alpert et al 2020). Mutation of S. cerevisiae Nab2 induces dramatic increases in bulk poly(A) tail length and disrupts bulk poly(A) export from the nucleus (Green et al 2002;Kelly et al 2010).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Rounds¹,

Corgiat²,

Ye³

et al. 2021

Preprint

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Drosophila encodes 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 the Drosophila 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 likely remain unidentified. Here we present evidence that Drosophila melanogaster Nab2 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 in Drosophila brain 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 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, 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 that Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.

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Section: A Model Of Opposing Regulatory Roles For Nab2 and Atx2mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Rounds¹,

Corgiat²,

Ye³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Nab2 has been identified as a component of cytoplasmic ribonucleoprotein particles (RNPs) linked to mRNA trafficking and translation (20, 23, 25), and as a nuclear component of post-transcriptional complexes (20, 21) that control mRNA splicing (22, 27, 28), transcription termination (30), and polyadenylation (16). To explore how Drosophila Nab2 affects the mRNA-derived proteome in the developing pupal brain, global label-free LC-MS/MS was performed on dissected 24hr APF brains of control (C155>Gal4, w 1118 ), mutant Nab2 ex3 (C155>Gal4;;Nab2 ex3 ), and neuronal specific Nab2 overexpression ( Nab2 oe ) ( C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) animals as illustrated in Figure 2 .…”

Section: Resultsmentioning

confidence: 99%

“…A small pool of Nab2 is detected in the axonal and dendritic cytoplasm of neurons (15–17, 20, 21) raising the possibility that Nab2 has both nuclear and cytoplasmic roles in neurons. Multiple studies in a variety of model organisms have defined key roles for Nab2 in pre-mRNA processing events within the nucleus, including regulation of splicing events, transcript termination, and control of poly(A) tail length (19, 27–30). Additional studies localize Nab2 within cytoplasmic mRNA ribonucleoprotein particles and imply roles in translational repression, likely mediated in part through interactions with FMRP (20–23, 28).…”

Section: Introductionmentioning

confidence: 99%

The RNA binding protein Nab2 regulates the proteome of the developingDrosophilabrain

Corgiat

List

Rounds

et al. 2020

Preprint

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The human ZC3H14 gene, which encodes a ubiquitously expressed polyadenosine zinc finger RNA binding protein, is mutated in an inherited form of autosomal recessive, non-syndromic intellectual disability. To gain insight into ZC3H14 neurological functions, we previously developed a Drosophila melanogaster model of ZC3H14 loss by deleting the fly ortholog, Nab2. Studies in this invertebrate model reveal that Nab2 controls final patterns of neuron projection within fully developed adult brains. Here, we examine earlier pupal stages and define roles for Nab2 in controlling the dynamic growth of axons into the developing brain mushroom bodies (MBs), which support olfactory learning and memory, and in regulating abundance of a small fraction of the total brain proteome, a portion of which is rescued by overexpression of Nab2 specifically in brain neurons. The group of Nab2-regulated brain proteins, identified by quantitative proteomic analysis, includes the microtubule binding protein Futsch, the neuronal Ig-family transmembrane protein Turtle, the glial:neuron adhesion protein Contactin, the RacGAP Tumbleweed, and the planar cell polarity factor Van Gogh, which collectively link Nab2 to a the processes of brain morphogenesis, neuroblast proliferation, circadian sleep/wake cycles, and synaptic development. Overall, these data indicate that Nab2 controls abundance of a subset of brain proteins during the active process of wiring the pupal brain mushroom body, and thus provide a window into potentially conserved functions of the Nab2/ZC3H14 RNA binding proteins in neurodevelopment and function.

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“…It is also possible that in the absence of Npl3, defects in splicing are more widespread due to a disruption to nuclear homeostasis (e.g. sequestration of the spliceosome and other proteins on a subset of transcripts) ( 100 , 101 ). These system-wide defects may differentiate the meiotic splicing phenotypes that are observed in npl3Δ versus a Npl3 methylation mutant.…”

Section: Discussionmentioning

confidence: 99%

The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae

Sandhu

Sinha

Montpetit

2021

Nucleic Acids Research

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The meiotic gene expression program in Saccharomyces cerevisiae involves regulated splicing of meiosis-specific genes via multiple splicing activators (e.g. Mer1, Nam8, Tgs1). Here, we show that the SR protein Npl3 is required for meiotic splicing regulation and is essential for proper execution of the meiotic cell cycle. The loss of Npl3, though not required for viability in mitosis, caused intron retention in meiosis-specific transcripts, inefficient meiotic double strand break processing and an arrest of the meiotic cell cycle. The targets of Npl3 overlapped in some cases with other splicing regulators, while also having unique target transcripts that were not shared. In the absence of Npl3, splicing defects for three transcripts (MER2, HOP2 and SAE3) were rescued by conversion of non-consensus splice sites to the consensus sequence. Methylation of Npl3 was further found to be required for splicing Mer1-dependent transcripts, indicating transcript-specific mechanisms by which Npl3 supports splicing. Together these data identify an essential function for the budding yeast SR protein Npl3 in meiosis as part of the meiotic splicing regulatory network.

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Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns

Cited by 26 publications

References 67 publications

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

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

The RNA binding protein Nab2 regulates the proteome of the developingDrosophilabrain

The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae

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