Expansion and transformation of the minor spliceosomal system in the slime mold Physarum polycephalum

Larue, Graham E.; Eliáš, Marek; Roy, Scott William

doi:10.1016/j.cub.2021.04.050

Cited by 18 publications

(24 citation statements)

References 66 publications

(72 reference statements)

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“…The number of U12-type introns varies between species: for instance, in humans approximately 700 genes contain U12-type introns, while only 19 are found in Drosophila . More recently, an investigation of the genome of slime mold Physarum polycephalum revealed an exceptional case of >20,000 minor introns in a single genome ( Larue et al, 2021 ). The typical architecture of minor intron containing genes (MIGs) includes a single U12-type intron per gene, flanked by multiple U2-type introns.…”

Section: Introductionmentioning

confidence: 99%

At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression

Akinyi

Frilander

2021

Front. Genet.

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Many eukaryotic species contain two separate molecular machineries for removing non-coding intron sequences from pre-mRNA molecules. The majority of introns (more than 99.5% in humans) are recognized and excised by the major spliceosome, which utilizes relatively poorly conserved sequence elements at the 5′ and 3′ ends of the intron that are used for intron recognition and in subsequent catalysis. In contrast, the minor spliceosome targets a rare group of introns (approximately 0.5% in humans) with highly conserved sequences at the 5′ and 3′ ends of the intron. Minor introns coexist in the same genes with major introns and while the two intron types are spliced by separate spliceosomes, the two splicing machineries can interact with one another to shape mRNA processing events in genes containing minor introns. Here, we review known cooperative and competitive interactions between the two spliceosomes and discuss the mechanistic basis of the spliceosome crosstalk, its regulatory significance, and impact on spliceosome diseases.

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Section: Introductionmentioning

confidence: 99%

At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression

Akinyi

Frilander

2021

Front. Genet.

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“…As shown in Fig. 3, the highest known minor intron density is found within the Amoebozoa; our recentlyreported data in the slime mold Physarum polycephalum [41] dwarfs all other known instances of local minor intron enrichment and appears to be an extremely rare example of significant minor intron gain. In the present study, we also find relatively high numbers of minor introns (compared to other amoebozoan species) in both the flagellar amoeba Pelomyxa schiedti (n=90) and the variosean amoeba Protostelium aurantium (labeled Planoprotostelium fungivorum 1 in Fig.…”

Section: Resultsmentioning

confidence: 72%

“…Here, we report a mycorrhizal fungus with only a few cell types and a simple body plan, whose genome contains over 199 minor spliceosomal introns. Whereas two previously reported instances of relatively high minor intron densities outside of animals and plants—in the slime mold Physarum polycephalum [41] and the protist Blastocystis [28]—appear to be largely due to secondary minor intron creation ([41], G.E.L and S.W.R., un-published data and this paper), the R. irregularis minor intron content likely largely reflects retention of ancestral introns, as evidenced by evolutionary conservation of the minor intron positions as well as functional biases of minor intron-containing genes that largely echo those in animals and plants.…”

Section: Discussionmentioning

confidence: 99%

“…Intron splicing efficiency was calculated as previously described [41]. Briefly, RNA-seq reads were mapped to splice-junction sequence constructs using v1.2.3 [40] (excluding multiply-mapping reads using the non-default argument ).…”

Section: Methodsmentioning

confidence: 99%

“…Since minor introns were first documented as having AT-AC termini, it has been shown that the majority of minor introns in most species are in fact of the GT-AG subtype, although an increasing diversity of termini (so-called “non-canonical” introns, with boundaries that aren’t GT-AG, GC-AG or AT-AC) seem to be able to be processed in certain contexts and to varying degrees by both spliceosomes [25, 12, 63, 79, 55]. Until very recently [41], in every genome investigated mi-nor introns have been found to comprise only a tiny fraction (<∼0.05%) of the total set of introns; despite this, they have also been found to be well-conserved over hundreds of mil-lions of years of evolution (e.g., 96% of minor introns in human are conserved in chicken, 83% in octopus (Fig. 2)).…”

Section: Introductionmentioning

confidence: 99%

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Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution

Larue

Roy

2022

Preprint

Self Cite

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Spliceosomal introns are segments of eukaryotic pre-mRNA that are removed ("spliced") during creation of mature mRNA, and are one of the defining and domain-specific features of gene structure in eukaryotes. Introns are spliced by a large, multi-subunit ribonucleoprotein machinery called the spliceosome, and most eukaryotic genomes contain two distinct sets of this machinery - the major (or U2-type) spliceosome is responsible for removal of the vast majority (usually > 99%) of introns in a given genome, with the minor (or U12-type) spliceosome processing the remaining minuscule fraction. Despite in some cases only being responsible for the removal of single-digit numbers of introns in entire genomes, the minor splicing system has been maintained over the roughly 1.5 billion years of eukaryotic evolution since the last eukaryotic common ancestor, and a number of recent studies have suggested that minor introns may be involved in certain aspects of cell cycle regulation and cancer development. It is in this context that we present a broad bioinformatic survey of minor introns across more than 3000 eukaryotic genomes, providing a dramatic increase in information about their distribution in extant species, descriptions of their evolutionary dynamics and features across the eukaryotic tree, and estimates of the minor intron complements of various ancestral nodes.

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Spliceosomal snRNAs, the Essential Players in pre‐mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics

Su,

Wu,

Chen

et al. 2024

Advanced Biology

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Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non‐coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre‐mRNAs). They are transcribed by DNA‐dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3′ end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre‐mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue‐specific regulation of snRNAs.

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Expansion and transformation of the minor spliceosomal system in the slime mold Physarum polycephalum

Cited by 18 publications

References 66 publications

At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression

At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression

Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution

Spliceosomal snRNAs, the Essential Players in pre‐mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics

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