Aberrant splicing in maize
            <i>rough endosperm3</i>
            reveals a conserved role for U12 splicing in eukaryotic multicellular development

Gault, Christine M.; Martin, Federico; Mei, Wenbin; Bai, Fang; Black, Joseph B.; Barbazuk, W. Brad; Settles, Alexander

doi:10.1073/pnas.1616173114

Cited by 35 publications

(87 citation statements)

References 68 publications

(129 reference statements)

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“…6B). When expressed with U2AF2 fusions, RGH3ΔUHM can give BiFC signal but GFP-RGH3ΔUHM does not co-localize with U2AF2-RFP in the nucleus (Gault et al, 2017).…”

Section: Rbm48 Interacts With U12 and U2 Splicing Factorsmentioning

confidence: 95%

“…A striking example is revealed by mutations of ZRSR2 orthologs in human and maize. Somatic mutations in human ZRSR2 primarily affect U12 splicing and cause myelodysplastic syndrome, a disease that reduces differentiation of mature blood cell types (Madan et al, 2015;Gault et al, 2017). The rgh3 mutation of the maize ZRSR2 ortholog has a conserved U12 splicing function and inhibits differentiation of endosperm cells (Fouquet et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…Biochemical characterization of small nuclear ribonucleoproteins (snRNPs) showed that most minor spliceosome proteins are shared with the major spliceosome with only seven novel proteins uniquely associated with the minor spliceosome (Schneider et al, 2002;Will et al, 2004). Genetic analysis of human ZRSR2, human FUS, mouse SMN1, and maize RGH3 indicates that these factors predominantly affect U12-type intron splicing even though there is substantial evidence for the proteins to participate in other RNA metabolic processes (Gault et al, 2017;Madanieh et al, 2015;Reber et al, 2016). Here we identify the maize RNA Binding Motif Protein (RBM48) as a minor spliceosome factor which functions to promote cell differentiation and repress cell proliferation.…”

Section: Introductionmentioning

confidence: 99%

“…We also compared the two rbm48 alleles with prior mRNA-seq analysis of rgh3 (Gault et al, 2017). Of the 242 U12-type introns tested in all three mutant alleles, 196 (77%) were significantly affected in all experiments (Fig.…”

Section: Aberrant Splicing Of U12-type Introns In Rbm48mentioning

confidence: 99%

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RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

Bai

Corll

Shodja

et al. 2018

Preprint

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The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize RNA Binding Motif Protein48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, ZRSR2/RGH3. Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors may form complexes during intron recognition. Human RBM48 interacts with ARMC7.Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.

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“…6B). When expressed with U2AF2 fusions, RGH3ΔUHM can give BiFC signal but GFP-RGH3ΔUHM does not co-localize with U2AF2-RFP in the nucleus (Gault et al, 2017).…”

Section: Rbm48 Interacts With U12 and U2 Splicing Factorsmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Aberrant Splicing Of U12-type Introns In Rbm48mentioning

confidence: 99%

See 2 more Smart Citations

RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

Bai

Corll

Shodja

et al. 2018

Preprint

Self Cite

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show abstract

“…UBL1, a U6 biogenesis-like-1 gene, also disturbs 1 154 IR events by affecting the 3 0 end process of U6 snRNA in maize (Li et al 2017). RGH3 encodes a U2AF35-related protein that is mainly responsible for U12-type AS (Fouquet et al 2012;Gault et al 2017). Zmsmu2 is a putative RNA splicing factor involved in ribosomal RNA procession and SR-type genes (TRA2 and RSp31B) splicing (Chung et al 2007;Chung et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Dek42 encodes an RNA‐binding protein that affects alternative pre‐mRNA splicing and maize kernel development

Zuo

Feng

et al. 2019

JIPB

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RNA‐binding proteins (RBPs) play an important role in post‐transcriptional gene regulation. However, the functions of RBPs in plants remain poorly understood. Maize kernel mutant dek42 has small defective kernels and lethal seedlings. Dek42 was cloned by Mutator tag isolation and further confirmed by an independent mutant allele and clustered regularly interspaced short palindromic repeats (CRISPR)‐CRISPR‐associated protein 9 materials. Dek42 encodes an RRM_RBM48 type RNA‐binding protein that localizes to the nucleus. Dek42 is constitutively expressed in various maize tissues. The dek42 mutation caused a significant reduction in the accumulation of DEK42 protein in mutant kernels. RNA‐seq analysis showed that the dek42 mutation significantly disturbed the expression of thousands of genes during maize kernel development. Sequence analysis also showed that the dek42 mutation significantly changed alternative splicing in expressed genes, which were especially enriched for the U12‐type intron‐retained type. Yeast two‐hybrid screening identified SF3a1 as a DEK42‐interacting protein. DEK42 also interacts with the spliceosome component U1‐70K. These results suggested that DEK42 participates in the regulation of pre‐messenger RNA splicing through its interaction with other spliceosome components. This study showed the function of a newly identified RBP and provided insights into alternative splicing regulation during maize kernel development.

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Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay

et al. 2020

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Improving the accuracy of variant interpretation during diagnostic sequencing is a major goal for genomic medicine. To explore an often‐overlooked splicing effect of missense variants, we developed the functional assay (“minigene”) for the majority of exons of CAPN3, the gene responsible for limb girdle muscular dystrophy. By systematically screening 21 missense variants distributed along the gene, we found that eight clinically relevant missense variants located at a certain distance from the exon–intron borders (deep exonic missense variants) disrupted normal splicing of CAPN3 exons. Several recent machine learning‐based computational tools failed to predict splicing impact for the majority of these deep exonic missense variants, highlighting the importance of including variants of this type in the training sets during the future algorithm development. Overall, 24 variants in CAPN3 gene were explored, leading to the change in the American College of Medical Genetics and Genomics classification of seven of them when results of the “minigene” functional assay were considered. Our findings reveal previously unknown splicing impact of several clinically important variants in CAPN3 and draw attention to the existence of deep exonic variants with a disruptive effect on gene splicing that could be overlooked by the current approaches in clinical genetics.

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Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development

Cited by 35 publications

References 68 publications

RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

Dek42 encodes an RNA‐binding protein that affects alternative pre‐mRNA splicing and maize kernel development

Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay

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