Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration

Jia, Yichang; Mu, John C.; Ackerman, Susan L.

doi:10.1016/j.cell.2011.11.057

Cited by 100 publications

(121 citation statements)

References 57 publications

Supporting

Mentioning

108

Contrasting

Order By: Relevance

“…Although the U2 snRNA branchpoint interacting sequence is strictly conserved throughout eukaryotic lineages (Marz et al 2008), the density of nucleotide modifications within this branchpoint interacting sequence could further modulate base pair binding possibilities (Yu et al 1998). Furthermore, it was recently shown that different U2 snRNAs genes exhibit cellspecific expression with mutations to a single U2 snRNA resulting in the disruption of a subset of alternative splicing events, including small introns, in a tissue-specific manner (Jia et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide discovery of human splicing branchpoints

et al. 2015

View full text Add to dashboard Cite

During the splicing reaction, the 59 intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 39 splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron-exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.[Supplemental material is available for this article.]The majority of human genes are spliced, a process whereby introns are removed from the nascent RNA and the remaining exonic sequence joined together into a mature RNA transcript. In addition, alternative splicing generates complex networks of isoforms from human gene loci and plays a major role in shaping the diversity of the transcriptome (Kapranov et al. 2005;Gerstein et al. 2007;Djebali et al. 2012).Splicing occurs in the spliceosome, a large ribonucleoprotein complex that recognizes at least three genetic elements within each intron: the 59 splice site (59SS), the 39 splice site (39SS), and the branchpoint (Will and L€ uhrmann 2011). RNU2-1, the U2 spliceosomal RNA (snRNA) base pairs to the sequence surrounding the unpaired branchpoint nucleotide, which then undergoes transesterification with the 59 end of the intron to form a closed lariat structure. The spliceosome then scans for the downstream 39 splice site, which undergoes a second trans-esterification reaction to join together the two exon ends and excise the intron lariat (Fig.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide discovery of human splicing branchpoints

et al. 2015

View full text Add to dashboard Cite

show abstract

“…These observations argue for a more critical role in the process of stochastic intron retention than in the specific identity of retained introns. Interestingly, Ackerman et al (49) recently demonstrated that mutation of one of the multicopy U2 snRNA genes resulted in retention of short introns across broad gene ontologies and subsequent neurodegeneration, further implicating intron retention in neuronal stress.…”

Section: Discussionmentioning

confidence: 99%

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Jangi

Fleet

Cullen

et al. 2017

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

108

111

View full text Add to dashboard Cite

Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. The SMN1 protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as γ-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death.

show abstract

“…Unlike SMA and RP, MOPD I is caused by mutations in an RNA component of the spliceosomes. Although MOPD I is the only reported human disease that is caused by spliceosomal snRNA mutations, a recent report showed that mutations in one of the many genes that code for U2 snRNA in mice causes neurodegeneration and is associated with tissue-specific alternative splicing defects, thus emphasizing the important role of spliceosomal snRNAs in the regulation of mammalian gene expression (Jia et al 2012).…”

Section: U4atac Snrna Defects In Mopd Imentioning

confidence: 99%

Biochemical defects in minor spliceosome function in the developmental disorder MOPD I

Jafarifar

Dietrich

Hiznay

et al. 2014

RNA

View full text Add to dashboard Cite

Biallelic mutations of the human RNU4ATAC gene, which codes for the minor spliceosomal U4atac snRNA, cause the developmental disorder, MOPD I/TALS. To date, nine separate mutations in RNU4ATAC have been identified in MOPD I patients. Evidence suggests that all of these mutations lead to abrogation of U4atac snRNA function and impaired minor intron splicing. However, the molecular basis of these effects is unknown. Here, we use a variety of in vitro and in vivo assays to address this question. We find that only one mutation, 124G>A, leads to significantly reduced expression of U4atac snRNA, whereas four mutations, 30G>A, 50G>A, 50G>C and 51G>A, show impaired binding of essential protein components of the U4atac/U6atac di-snRNP in vitro and in vivo. Analysis of MOPD I patient fibroblasts and iPS cells homozygous for the most common mutation, 51G>A, shows reduced levels of the U4atac/U6atac.U5 tri-snRNP complex as determined by glycerol gradient sedimentation and immunoprecipitation. In this report, we establish a mechanistic basis for MOPD I disease and show that the inefficient splicing of genes containing U12-dependent introns in patient cells is due to defects in minor tri-snRNP formation, and the MOPD I-associated RNU4ATAC mutations can affect multiple facets of minor snRNA function.

show abstract

Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration

Cited by 100 publications

References 57 publications

Genome-wide discovery of human splicing branchpoints

Genome-wide discovery of human splicing branchpoints

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Biochemical defects in minor spliceosome function in the developmental disorder MOPD I

Contact Info

Product

Resources

About