Pre-mRNA Splicing Modulation by Antisense Oligonucleotides.

Pre-mRNA splicing, a dynamic process of intron removal and exon joining, is governed by a combinatorial control exerted by overlapping cis-elements that are unique to each exon and its flanking intronic sequences. Splicing cis-elements are usually 4- to 8-nucleotide-long linear motifs that provide binding sites for specific proteins. Pre-mRNA splicing is also influenced by secondary- and higher-order RNA structures that affect accessibility of splicing cis-elements.

Different factors underlie mild and severe forms of spinal muscular atrophy.

This scientific commentary refers to ‘The systemic complexity of a monogenic disease: the molecular network of spinal muscular atrophy’ by Tapken (https://doi.org/10.1093/brain/awae272).

U1 snRNA interactions with deep intronic sequences regulate splicing of multiple exons of spinal muscular atrophy genes.

Introduction: The U1 small nuclear RNA (snRNA) forms ribonucleoprotein particles (RNPs) such as U1 snRNP and U1-TAF15 snRNP. U1 snRNP is one of the most studied RNPs due to its critical role in pre-mRNA splicing in defining the 5' splice site (5'ss) of every exon through direct interactions with sequences at exon/intron junctions. Recent reports support the role of U1 snRNP in all steps of transcription, namely initiation, elongation, and termination.

Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes.

Spinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells.

Synergistic Effect of an Antisense Oligonucleotide and Small Molecule on Splicing Correction of the Spinal Muscular Atrophy Gene.

Spinal muscular atrophy (SMA) is treated by increasing the level of Survival Motor Neuron (SMN) protein through correction of exon 7 skipping or exogenous expression of SMN through gene therapy. Currently available therapies have multiple shortcomings, including poor body-wide distribution, invasive delivery, and potential negative consequences due to high doses needed for clinical efficacy. Here we test the effects of a combination treatment of a splice-correcting antisense oligonucleotide (ASO) Anti-N1 with the small compounds risdiplam and branaplam.

A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes.

Here we report a Survival Motor Neuron 2 (SMN2) super minigene, SMN2Sup, encompassing its own promoter, all exons, their flanking intronic sequences and the entire 3'-untranslated region. We confirm that the pre-mRNA generated from SMN2Sup undergoes splicing to produce a translation-competent mRNA. We demonstrate that mRNA generated from SMN2Sup produces more SMN than an identical mRNA generated from a cDNA clone.

Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy.

Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials.

Internal Introns Promote Backsplicing to Generate Circular RNAs from Spinal Muscular Atrophy Gene.

Human () codes for SMN, an essential housekeeping protein involved in most aspects of RNA metabolism. Deletions or mutations of lead to spinal muscular atrophy (SMA), a devastating neurodegenerative disease linked to a high rate of infant mortality. , a near identical copy of present in humans, cannot compensate for the loss of due to predominant skipping of exon 7.

Structural Context of a Critical Exon of Spinal Muscular Atrophy Gene.

Humans contain two nearly identical copies of genes, and . Deletion or mutation of causes spinal muscular atrophy (SMA), one of the leading genetic diseases associated with infant mortality. is unable to compensate for the loss of due to predominant exon 7 skipping, leading to the production of a truncated protein.

High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome.

Intronic splicing silencer N1 (ISS-N1) located within () intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h.

Lipid residues in pottery from the Indus Civilisation in northwest India.

This paper presents novel insights into the archaeology of food in ancient South Asia by using lipid residue analysis to investigate what kinds of foodstuffs were used in ceramic vessels by populations of the Indus Civilisation in northwest India. It examines how vessels were used in urban and rural Indus settlements during the Mature Harappan period (.2600/2500-1900 BC), the relationship between vessels and the products within them, and identifies whether changes in vessel use occurred from the Mature Harappan to Late Harappan periods, particularly during climatic instability after 4.

Spinal muscular atrophy: Broad disease spectrum and sex-specific phenotypes.

Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% of cases of SMA result from deletions of or mutations in the Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7.

The First Orally Deliverable Small Molecule for the Treatment of Spinal Muscular Atrophy.

Spinal muscular atrophy (SMA) is 1 of the leading causes of infant mortality. SMA is mostly caused by low levels of Survival Motor Neuron (SMN) protein due to deletion of or mutation in the gene. Its nearly identical copy, , fails to compensate for the loss of due to predominant skipping of exon 7.

Characteristics of circular RNAs generated by human Survival Motor Neuron genes.

Circular RNAs (circRNAs) belong to a diverse class of stable RNAs expressed in all cell types. Their proposed functions include sponging of microRNAs (miRNAs), sequestration and trafficking of proteins, assembly of multimeric complexes, production of peptides, and regulation of transcription. Backsplicing due to RNA structures formed by an exceptionally high number of Alu repeats lead to the production of a vast repertoire of circRNAs by human Survival Motor Neuron genes, SMN1 and SMN2, that code for SMN, an essential multifunctional protein.

RNA in spinal muscular atrophy: therapeutic implications of targeting.

Introduction: Spinal muscular atrophy (SMA) is caused by low levels of the Survival Motor Neuron (SMN) protein due to deletions of or mutations in the gene. Humans carry another nearly identical gene, , which mostly produces a truncated and less stable protein SMNΔ7 due to predominant skipping of exon 7. Elevation of SMN upon correction of exon 7 splicing and gene therapy have been proven to be the effective treatment strategies for SMA.

A survey of transcripts generated by spinal muscular atrophy genes.

Human Survival Motor Neuron (SMN) genes code for SMN, an essential multifunctional protein. Complete loss of SMN is embryonic lethal, while low levels of SMN lead to spinal muscular atrophy (SMA), a major genetic disease of children and infants. Reduced levels of SMN are associated with the abnormal development of heart, lung, muscle, gastro-intestinal system and testis.

How RNA structure dictates the usage of a critical exon of spinal muscular atrophy gene.

Role of RNA structure in pre-mRNA splicing has been implicated for several critical exons associated with genetic disorders. However, much of the structural studies linked to pre-mRNA splicing regulation are limited to terminal stem-loop structures (hairpins) sequestering splice sites. In few instances, role of long-distance interactions is implicated as the major determinant of splicing regulation.

A novel role of U1 snRNP: Splice site selection from a distance.

Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions.

Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs.

Circular RNAs (circRNAs) perform diverse functions, including the regulation of transcription, translation, peptide synthesis, macromolecular sequestration and trafficking. Inverted Alu repeats capable of forming RNA:RNA duplexes that bring splice sites together for backsplicing are known to facilitate circRNA generation. However, higher limits of circRNAs produced by a single Alu-rich gene are currently not predictable due to limitations of amplification and analyses.

Correction: Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China.

[This corrects the article DOI: 10.1371/journal.pone.

Pre-mRNA Splicing Modulation by Antisense Oligonucleotides.

Pre-mRNA splicing, a dynamic process of intron removal and exon joining, is governed by a combinatorial control exerted by overlapping cis-elements that are unique to each exon and its flanking intronic sequences. Splicing cis-elements are usually 4-to-8-nucleotide-long linear motifs that provide binding sites for specific proteins. Pre-mRNA splicing is also influenced by secondary and higher order RNA structures that affect accessibility of splicing cis-elements.

High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs.

The Survival Motor Neuron (SMN) protein is essential for survival of all animal cells. SMN harbors a nucleic acid-binding domain and plays an important role in RNA metabolism. However, the RNA-binding property of SMN is poorly understood.