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Wang B, Mount S. Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR Genom Bioinform 2024; 6:lqae099. [PMID: 39131816 PMCID: PMC11310860 DOI: 10.1093/nargab/lqae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/13/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of distinct alternative motifs, or are best described by base composition. Here we apply the latent Dirichlet allocation (LDA) mixture model to nucleotide sequences. Using positions in an alignment of human or Drosophila splice sites as samples, we show that LDA readily identifies motifs, including such elusive cases as the intron branch site. Using whole sequences with positional k-mers as features, LDA can identify sequence subtypes enriched in long vs. short introns. LDA with bulk k-mers can reliably distinguish reading frame and species of origin in coding sequences from humans and Drosophila. We find that LDA is a useful model for describing heterogeneous signals, for assigning individual sequences to subtypes, and for identifying and characterizing sequences that do not fit recognized subtypes. Because LDA topic models are interpretable, they also aid the discovery of new motifs, even those present in a small fraction of samples. In summary, LDA can identify and characterize signals in nucleotide sequences, including candidate regulatory factors involved in biological processes.
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Affiliation(s)
- Bixuan Wang
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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2
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Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR, Li JJ, Madhani HD. Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell 2019; 173:1014-1030.e17. [PMID: 29727661 DOI: 10.1016/j.cell.2018.03.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 03/07/2018] [Indexed: 11/28/2022]
Abstract
Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam D Longhurst
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daria Merkurjev
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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3
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Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci U S A 2005; 102:16176-81. [PMID: 16260721 PMCID: PMC1283478 DOI: 10.1073/pnas.0508489102] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The exon/intron architecture of genes determines whether components of the spliceosome recognize splice sites across the intron or across the exon. Using in vitro splicing assays, we demonstrate that splice-site recognition across introns ceases when intron size is between 200 and 250 nucleotides. Beyond this threshold, splice sites are recognized across the exon. Splice-site recognition across the intron is significantly more efficient than splice-site recognition across the exon, resulting in enhanced inclusion of exons with weak splice sites. Thus, intron size can profoundly influence the likelihood that an exon is constitutively or alternatively spliced. An EST-based alternative-splicing database was used to determine whether the exon/intron architecture influences the probability of alternative splicing in the Drosophila and human genomes. Drosophila exons flanked by long introns display an up to 90-fold-higher probability of being alternatively spliced compared with exons flanked by two short introns, demonstrating that the exon/intron architecture in Drosophila is a major determinant in governing the frequency of alternative splicing. Exon skipping is also more likely to occur when exons are flanked by long introns in the human genome. Interestingly, experimental and computational analyses show that the length of the upstream intron is more influential in inducing alternative splicing than is the length of the downstream intron. We conclude that the size and location of the flanking introns control the mechanism of splice-site recognition and influence the frequency and the type of alternative splicing that a pre-mRNA transcript undergoes.
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Affiliation(s)
- Kristi L Fox-Walsh
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4025, USA
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Zamoto A, Tsuji M, Wei Q, Cho SH, Shin EH, Kim TS, Leonova GN, Hagiwara K, Asakawa M, Kariwa H, Takashima I, Ishihara C. Epizootiologic survey for Babesia microti among small wild mammals in northeastern Eurasia and a geographic diversity in the beta-tubulin gene sequences. J Vet Med Sci 2004; 66:785-92. [PMID: 15297749 DOI: 10.1292/jvms.66.785] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We previously reported that small wild rodents in Japan harbor two types of novel Babesia microti-like parasites (designated as Hobetsu and Kobe types), but not the type commonly found in the northeastern United States (U.S. type) where human babesiosis is endemic. To determine whether these new types of parasites are distributed in places surrounding Japan, an epizootiologic survey was undertaken in three geographically distant areas in northeastern Eurasia; South Korea, Vladivostok in Russia, and Xinjiang in China. Blood samples were collected from a total of 387 animals comprising 24 species. DNAs extracted from the samples were tested by nested PCR targeting babesial nuclear small-subunit rRNA gene (rDNA), which revealed that small rodents harboring B. microti exist in all three survey areas. Sequence analysis showed that all PCR-positive samples had rDNA sequences virtually identical to that of U.S.-type B. microti. However, when beta-tubulin gene sequences were compared, evident geographic variations were seen. By use of primers specific for each of the beta-tubulin genes of Kobe-, Hobetsu-, and U.S.-type parasites, a type-specific PCR was developed. Parasite with Hobetsu- or Kobe-type sequence was not detected from any of the three survey areas. These findings suggest that U.S.-type B. microti is widely distributed among small wild mammals in temperate zones of not only North America, but also Eurasia, whereas that Hobetsu- and Kobe-type parasites may be uniquely distributed in Japan.
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Affiliation(s)
- Aya Zamoto
- School of Veterinary Medicine, Rakuno-Gakuen University, Ebetsu, Hokkaido, Japan
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Abstract
Using recently available cDNA and genomic data (Berkeley Drosophila Genome Project; http://www.fruitfly.org), we computed a large sample of 10,057 Drosophila splice sites. An information-theoretic analysis of the nucleotide sequences adjacent to these splice sites showed a strong correlation between the sizes of introns and exons and the levels of information, which is a measure of sequence conservation. The strong correlation permitted us to determine extensive consensus sequences at the donor and acceptor sites of longer introns. These sequences were further refined and extended by examining the information in regions around splice sites that only partially matched the consensus. The correlation between length and information provided the basis for determining alternative consensus arrangements associated with shorter introns, as well as general base-composition preferences that likely promote spliceosome function. We also observed a correlation between information near splice sites and the lengths of nonadjacent introns, indicating that there are long-range effects spanning multiple introns. The ordered partitioning approach used in this analysis may become increasingly useful as large genomic data sets become available.
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Affiliation(s)
- Michael Weir
- Department of Biology, Wesleyan University, Middletown, Connecticut 06459, USA.
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Chen Y, Stephan W. Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene. Proc Natl Acad Sci U S A 2003; 100:11499-504. [PMID: 12972637 PMCID: PMC208787 DOI: 10.1073/pnas.1932834100] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evidence for the evolutionary maintenance of a hairpin structure possibly involved in intron processing had been found in intron 1 of the alcohol dehydrogenase gene (Adh) in diverse Drosophila species. In this study, the putative hairpin structure was evaluated systematically in Drosophila melanogaster by elimination of either side of the stem using site-directed mutagenesis. The effects of these mutations and the compensatory double mutant on intron splicing efficiency and ADH protein production were assayed in Drosophila melanogaster Schneider L2 cells and germ-line transformed adult flies. Mutations that disrupt the putative hairpin structure right upstream of the intron branch point were found to cause a significant reduction in both splicing efficiency and ADH protein production. In contrast, the compensatory double mutant that restores the putative hairpin structure was indistinguishable from the WT in both splicing efficiency and ADH level. It was also observed by mutational analysis that a more stable secondary structure (with a longer stem) in this intron decreases both splicing efficiency and ADH protein production. Implications for RNA secondary structure and intron evolution are discussed.
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Affiliation(s)
- Ying Chen
- Department of Biology II, University of Munich, 80333 Munich, Germany
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Lim LP, Burge CB. A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A 2001; 98:11193-8. [PMID: 11572975 PMCID: PMC58706 DOI: 10.1073/pnas.201407298] [Citation(s) in RCA: 258] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2001] [Accepted: 08/02/2001] [Indexed: 11/18/2022] Open
Abstract
Splicing of short introns by the nuclear pre-mRNA splicing machinery is thought to proceed via an "intron definition" mechanism, in which the 5' and 3' splice sites (5'ss, 3'ss, respectively) are initially recognized and paired across the intron. Here, we describe a computational analysis of sequence features involved in recognition of short introns by using available transcript data from five eukaryotes with complete or nearly complete genomic sequences. The information content of five different transcript features was measured by using methods from information theory, and Monte Carlo simulations were used to determine the amount of information required for accurate recognition of short introns in each organism. We conclude: (i) that short introns in Drosophila melanogaster and Caenorhabditis elegans contain essentially all of the information for their recognition by the splicing machinery, and computer programs that simulate splicing specificity can predict the exact boundaries of approximately 95% of short introns in both organisms; (ii) that in yeast, the 5'ss, branch signal, and 3'ss can accurately identify intron locations but do not precisely determine the location of 3' cleavage in every intron; and (iii) that the 5'ss, branch signal, and 3'ss are not sufficient to accurately identify short introns in plant and human transcripts, but that specific subsets of candidate intronic enhancer motifs can be identified in both human and Arabidopsis that contribute dramatically to the accuracy of splicing simulators.
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Affiliation(s)
- L P Lim
- Department of Biology and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Romfo CM, Alvarez CJ, van Heeckeren WJ, Webb CJ, Wise JA. Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe. Mol Cell Biol 2000; 20:7955-70. [PMID: 11027266 PMCID: PMC86406 DOI: 10.1128/mcb.20.21.7955-7970.2000] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Schizosaccharomyces pombe pre-mRNAs are generally multi-intronic and share certain features with pre-mRNAs from Drosophila melanogaster, in which initial splice site pairing can occur via either exon or intron definition. Here, we present three lines of evidence suggesting that, despite these similarities, fission yeast splicing is most likely restricted to intron definition. First, mutating either or both splice sites flanking an internal exon in the S. pombe cdc2 gene produced almost exclusively intron retention, in contrast to the exon skipping observed in vertebrates. Second, we were unable to induce skipping of the internal microexon in fission yeast cgs2, whereas the default splicing pathway excludes extremely small exons in mammals. Because nearly quantitative removal of the downstream intron in cgs2 could be achieved by expanding the microexon, we propose that its retention is due to steric occlusion. Third, several cryptic 5' junctions in the second intron of fission yeast cdc2 are located within the intron, in contrast to their generally exonic locations in metazoa. The effects of expanding and contracting this intron are as predicted by intron definition; in fact, even highly deviant 5' junctions can compete effectively with the standard 5' splice site if they are closer to the 3' splicing signals. Taken together, our data suggest that pairing of splice sites in S. pombe most likely occurs exclusively across introns in a manner that favors excision of the smallest segment possible.
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Affiliation(s)
- C M Romfo
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4960, USA
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Mount SM. Genomic sequence, splicing, and gene annotation. Am J Hum Genet 2000; 67:788-92. [PMID: 10986039 PMCID: PMC1287883 DOI: 10.1086/303098] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2000] [Accepted: 08/15/2000] [Indexed: 11/03/2022] Open
Affiliation(s)
- S M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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Affiliation(s)
- A B Carvalho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil
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11
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Brown SE, Wood SH, Knudson DL. Vertebrate exon trapping methods: implications for transcript mapping with mosquito DNA. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 1999; 29:643-651. [PMID: 10436938 DOI: 10.1016/s0965-1748(99)00042-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Exon trapping methods have played an important role in the development of transcript maps. In one in vivo vertebrate method, exons in a genomic DNA clone are transcribed, and they are recovered without any a priori information on the nature of the expressed transcript. The only requirement is that the genomic DNA clone contains exons separated by intervening introns that are removed by splicing during mRNA transcription and that the splice donor and acceptor site sequences follow those used by vertebrates. It is not known whether invertebrate splice donor and acceptor sites from genes that contain short introns will be processed correctly using an in vivo vertebrate exon trapping method. In this report, an analysis of mosquito splice sites using software designed to identify exons in genomic DNA sequence suggested that the vertebrate exon trapping method could recognize mosquito introns and exons. When a mosquito genomic DNA clone containing the D7 gene was tested experimentally, this method failed to recognize and process small introns (< 63 bp) faithfully. In spite of this failure, exons and exon fragments were recovered. The implications of these findings and their application to map-based positional cloning in mosquito genomics is discussed.
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Affiliation(s)
- S E Brown
- Department of Bioagricultural Sciences and Pest Management, College of Agricultural Sciences, Colorado State University, Fort Collins 80523, USA
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McKenzie RW, Brennan MD. The two small introns of the Drosophila affinidisjuncta Adh gene are required for normal transcription. Nucleic Acids Res 1996; 24:3635-42. [PMID: 8836194 PMCID: PMC146134 DOI: 10.1093/nar/24.18.3635] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
All Drosophila alcohol dehydrogenase (Adh) genes sequenced to date contain two small introns within the coding region. These are conserved in location and, to some extent, in sequence between the various species analyzed. To determine if these introns play a role in Adh gene expression, derivatives of the Drosophila affinidisjuncta Adh gene lacking one or both introns were constructed and analyzed by germline and transient transformation of Drosophila melanogaster. Removal of both introns lowered expression, whether measured by enzyme activity or by RNA levels. The decrease was seen in both germline transformed and transiently transformed larvae, with the effect being larger for germline transformants. Similar decreases (averaging 5-fold) were also seen at the embryonic and adult stages for germline transformants. Nuclear run-off transcription with nuclei from germline transformed embryos indicated that the reduction in RNA levels is due to decreased transcription. However, LacZ fusion constructs designed to test for the presence of a classical enhancer in the introns provided no evidence for such a mechanism. Removal of each intron individually resulted in more complex phenotypes. The introns have smaller, additive effects on expression in adults. In larvae, removal of the upstream intron significantly increases RNA levels but modestly decreases enzyme activity. Removal of the downstream intron lowers expression in both germline and transiently transformed larvae, but also increases position effects in germline transformants. Therefore, the small introns are clearly needed for optimal transcription of this Adh gene, but multiple mechanisms are involved.
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Affiliation(s)
- R W McKenzie
- Department of Biochemistry, School of Medicine, University of Louisville, KY 40292, USA
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