Minimal Introns Are Not “Junk”

Yu, Jun; Yang, Zhaohuai; Kibukawa, Miho; Paddock, Marcia N.; Passey, Douglas A.; Wong, Gane Ka‐Shu

doi:10.1101/gr.224602

Cited by 77 publications

(90 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…First, comparative studies of splicing machineries have pointed out the tempo-spatial features of the different types of introns that all have unique characteristics as we have discussed above in this article and previously elsewhere [6]. Second, evolutionary studies have proven that minimal introns are selected through negative selections on minimal-intron-containing genes and have special sequence contexts in human populations [8,11]. The original design of these experiments is to investigate whether the intron size constraint of human minimal introns is selected in a human population but it has also revealed sequence context relevance [38,11].…”

Section: The Routing Hypothesis Of Intron Processingmentioning

confidence: 99%

“…The trend is clear and firm over the vertebrate lineage. Third, minimal-intron-containing genes are a unique group of genes in both functionality and genomic characteristics [6,8,33,34]. We have previously showed that genes with minimal introns tend to play certain housekeeping roles and are enriched on certain chromosomal territories [35].…”

Section: The Unique Distributions Of Minimal Introns and Their Possibmentioning

confidence: 99%

“…The number and size parameters by and large reflect the nature and efficiency of the intron splicing machinery of particular species or lineages [5][6][7][8][9]. The context parameters are most complicated, concerning the sequence content and context of nucleotide composition (such as GC and purine contents), transposable elements, and functional elements (such as splicing enhancers and the branch point) [10][11][12].…”

mentioning

confidence: 99%

See 2 more Smart Citations

Systematic analysis of intron size and abundance parameters in diverse lineages

Jiayan

Xiao

Wang

et al. 2013

Sci. China Life Sci.

View full text Add to dashboard Cite

All eukaryotic genomes have genes with introns in variable sizes. As far as spliceosomal introns are concerned, there are at least three basic parameters to stratify introns across diverse eukaryotic taxa: size, number, and sequence context. The number parameter is highly variable in lower eukaryotes, especially among protozoan and fungal species, which ranges from less than 4% to 78% of the genes. Over greater evolutionary time scales, the number parameter undoubtedly increases as observed in higher plants and higher vertebrates, reaching greater than 12.5 exons per gene in average among mammalian genomes. The size parameter is more complex, where multiple modes appear at work. Aside from intronless genes, there are three other types of intron-containing genes: half-sized, minimal, and size-expandable introns. The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes. Among the size-expandable introns, the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals, where the larger introns are filled with transposable elements and appear expansion-flexible, reaching several kilobasepairs (kbp) and even thousands of kbp in size. Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality. In particular, the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts. Eukaryotic genes have introns with variable size, number, and sequence context [1][2][3][4]. The number and size parameters by and large reflect the nature and efficiency of the intron splicing machinery of particular species or lineages [5][6][7][8][9]. The context parameters are most complicated, concerning the sequence content and context of nucleotide composition (such as GC and purine contents), transposable elements, and functional elements (such as splicing enhancers and the branch point) [10][11][12]. There are at least three possibilities for the existence and the absence of introns in eukaryotic genes: intronless (no intron), small introns in fixed sizes, and large introns in variable sizes. However, the rules of these intron parameters across diverse taxa have yet to be thoroughly summarized. The spliceosomal machinery is very complex, containing different molecular complexes of proteins and RNAs, which are partitioned into both the nucleus and the cytosol [13,14].

show abstract

Section: The Routing Hypothesis Of Intron Processingmentioning

confidence: 99%

Section: The Unique Distributions Of Minimal Introns and Their Possibmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Systematic analysis of intron size and abundance parameters in diverse lineages

Jiayan

Xiao

Wang

et al. 2013

Sci. China Life Sci.

View full text Add to dashboard Cite

show abstract

“…6), which corresponds perfectly to the length of the minimal intron (61 bp) in Drosophila (Yu et al 2002). Due to snoRNA or snoRNA cluster containing, the host introns can vary in length from 150 bp to 2 kb.…”

Section: Extensive Utilization Of Introns For Snorna-coding In the Drmentioning

confidence: 99%

Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs

Huang¹,

Zhou²,

He³

et al. 2005

RNA

View full text Add to dashboard Cite

Small nucleolar RNAs (snoRNAs) are an abundant group of noncoding RNAs mainly involved in the post-transcriptional modifications of rRNAs in eukaryotes. In this study, a large-scale genome-wide analysis of the two major families of snoRNA genes in the fruit fly Drosophila melanogaster has been performed using experimental and computational RNomics methods. Two hundred and twelve gene variants, encoding 56 box H/ACA and 63 box C/D snoRNAs, were identified, of which 57 novel snoRNAs have been reported for the first time. These snoRNAs were predicted to guide a total of 147 methylations and pseudouridylations on rRNAs and snRNAs, showing a more comprehensive pattern of rRNA modification in the fruit fly. With the exception of nine, all the snoRNAs identified to date in D. melanogaster are intron encoded. Remarkably, the genomic organization of the snoRNAs is characteristic of 8 dUhg genes and 17 intronic gene clusters, demonstrating that distinct organizations dominate the expression of the two families of snoRNAs in the fruit fly. Of the 267 introns in the host genes, more than half have been identified as host introns for coding of snoRNAs. In contrast to mammals, the variation in size of the host introns is mainly due to differences in the number of snoRNAs they contain. These results demonstrate the extensive utilization of introns for coding of snoRNAs in the host genes and shed light on further research of other noncoding RNA genes in the large introns of the Drosophila genome.

show abstract

“…Commonly, we see a bimodal distribution of intron length with a high peak of short (termed 'minimal length') introns and a much flatter peak of longer introns, ranging up to thousands of base pairs in length in humans (Yu et al, 2002). Furthermore, in some organisms there appears to be a functional link between intron length and gene expression, with introns tending to be smaller in highly expressed genes -possibly as a result of a need for transcriptional efficiency.…”

Section: The Diversity Of Intronsmentioning

confidence: 99%

The rise and falls of introns

Belshaw

Bensasson

2006

Heredity

View full text Add to dashboard Cite

There has been a lively debate over the evolution of eukaryote introns: at what point in the tree of life did they appear and from where, and what has been their subsequent pattern of loss and gain? A diverse range of recent research papers is relevant to this debate, and it is timely to bring them together. The absence of introns that are not self-splicing in prokaryotes and several other lines of evidence suggest an ancient eukaryotic origin for these introns, and the subsequent gain and loss of introns appears to be an ongoing process in many organisms. Some introns are now functionally important and there have been suggestions that invoke natural selection for the ancient and recent gain of introns, but it is also possible that fixation and loss of introns can occur in the absence of positive selection.

show abstract

Minimal Introns Are Not “Junk”

Cited by 77 publications

References 36 publications

Systematic analysis of intron size and abundance parameters in diverse lineages

Systematic analysis of intron size and abundance parameters in diverse lineages

Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs

The rise and falls of introns

Contact Info

Product

Resources

About