The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

McCann, Kathleen L.; Teramoto, Takamasa; Zhang, Jun; Hall, Traci M. Tanaka; Baserga, Susan J.

doi:10.7554/elife.16381

Cited by 11 publications

(19 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, because many RBPs contain two or more RRMs, a single missense mutation may not abolish RNA binding or intramolecular contacts completely and may still be compatible with life. Unlike RRM1, tested UHM substitutions in PD invariably reduced PUF60 expression (Figure 7I ), possibly through impaired folding, as shown for a RRM3 substitution in RBM28 in the ANE syndrome ( 119 ). Tested residues mutated in PD lack known post-translation modifications and all (except for E181) had a predicted accessible surface area below 30% ( http://www.phosphosite.org ; http://dbptm.mbc.ntcu.edu ).…”

Section: Discussionmentioning

confidence: 64%

PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

Královičová

Sevcikova

Stejskalová

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.

show abstract

Section: Discussionmentioning

confidence: 64%

PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

Královičová

Sevcikova

Stejskalová

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…However, yeast has no known equivalent of p53 and is therefore well-suited for investigating the interaction between ribosome formation and cell cycle progression in the absence of p53. Indeed, the mechanisms for several ribosomopathies have recently been modeled in yeast by mutating yeast equivalents of human ribosomopathy genes [ 32 – 34 ] supporting the competency of yeast as a disease model for ribosomopathies.…”

Section: Introductionmentioning

confidence: 99%

Analysis of cell cycle parameters during the transition from unhindered growth to ribosomal and translational stress conditions

et al. 2017

View full text Add to dashboard Cite

Abrogation of ribosome synthesis (ribosomal stress) leads to cell cycle arrest. However, the immediate cell response to cessation of ribosome formation and the transition from normal cell proliferation to cell cycle arrest have not been characterized. Furthermore, there are conflicting conclusions about whether cells are arrested in G2/M or G1, and whether the cause is dismantling ribosomal assembly per se, or the ensuing decreased number of translating ribosomes. To address these questions, we have compared the time kinetics of key cell cycle parameters after inhibiting ribosome formation or function in Saccharomyces cerevisiae. Within one-to-two hours of repressing genes for individual ribosomal proteins or Translation Elongation factor 3, configurations of spindles, spindle pole bodies began changing. Actin began depolarizing within 4 hours. Thus the loss of ribosome formation and function is sensed immediately. After several hours no spindles or mitotic actin rings were visible, but membrane ingression was completed in most cells and Ace2 was localized to daughter cell nuclei demonstrating that the G1 stage was reached. Thus cell division was completed without the help of a contractile actin ring. Moreover, cell wall material held mother and daughter cells together resulting in delayed cell separation, suggesting that expression or function of daughter gluconases and chitinases is inhibited. Moreover, cell development changes in very similar ways in response to inhibition of ribosome formation and function, compatible with the notion that decreased translation capacity contributes to arresting the cell cycle after abrogation of ribosome biogenesis. Potential implications for the mechanisms of diseases caused by mutations in ribosomal genes (ribosomopathies) are discussed.

show abstract

“…Though not fully understood, tissue-specific defects are the hallmark of ribosomopathies (11,17). Tissues formed from hematopoietic or neural crest cell lineages are disproportionately affected, resulting in anemia, neutropenia, and leukemia, bone marrow failure diseases including Diamond-Blackfan Anemia (DBA) (18)(19)(20)(21)(22)(23) and Shwachman-Diamond syndrome (24)(25)(26), craniofacial, dermatological, and neurological diseases including Treacher Collins syndrome (27)(28)(29) and postaxial acrofacial dysostosis (30), and alopecia, neurologic defects, and endocrinopathy (ANE) syndrome (31)(32)(33)(34).…”

mentioning

confidence: 99%

“…Nop4 (36)(37)(38)(39). Follow-up studies further defined the clinical extent of endocrinopathy (32) and the biochemical mechanisms of hair and skin defects (33) and of inhibited ribosome biogenesis (34,40) due to impaired function of RBM28 or its yeast homolog, Nop4. However, due to the rarity of the disease and lack of sufficient animal model studies, further investigation of ANE syndrome has been limited.…”

mentioning

confidence: 99%

Biallelic splicing variants in the nucleolar 60S assembly factor RBM28 cause the ribosomopathy ANE syndrome

Bryant

Lorea

Almeida

et al. 2021

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

View full text Add to dashboard Cite

Alopecia, neurologic defects, and endocrinopathy (ANE) syndrome is a rare ribosomopathy known to be caused by a p.(Leu351Pro) variant in the essential, conserved, nucleolar large ribosomal subunit (60S) assembly factor RBM28. We report the second family of ANE syndrome to date and a female pediatric ANE syndrome patient. The patient presented with alopecia, craniofacial malformations, hypoplastic pituitary, and hair and skin abnormalities. Unlike the previously reported patients with the p.(Leu351Pro) RBM28 variant, this ANE syndrome patient possesses biallelic precursor messenger RNA (pre-mRNA) splicing variants at the 5′ splice sites of exon 5 (ΔE5) and exon 8 (ΔE8) of RBM28 (NM_018077.2:c.[541+1_541+2delinsA]; [946G > T]). In silico analyses and minigene splicing experiments in cells indicate that each splice variant specifically causes skipping of its respective mutant exon. Because the ΔE5 variant results in an in-frame 31 amino acid deletion (p.(Asp150_Lys180del)) in RBM28 while the ΔE8 variant leads to a premature stop codon in exon 9, we predicted that the ΔE5 variant would produce partially functional RBM28 but the ΔE8 variant would not produce functional protein. Using a yeast model, we demonstrate that the ΔE5 variant does indeed lead to reduced overall growth and large subunit ribosomal RNA (rRNA) production and pre-rRNA processing. In contrast, the ΔE8 variant is comparably null, implying that the partially functional ΔE5 RBM28 protein enables survival but precludes correct development. This discovery further defines the underlying molecular pathology of ANE syndrome to include genetic variants that cause aberrant splicing in RBM28 pre-mRNA and highlights the centrality of nucleolar processes in human genetic disease.

show abstract

The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

Cited by 11 publications

References 38 publications

PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

Analysis of cell cycle parameters during the transition from unhindered growth to ribosomal and translational stress conditions

Biallelic splicing variants in the nucleolar 60S assembly factor RBM28 cause the ribosomopathy ANE syndrome

Contact Info

Product

Resources

About