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  1. Article: ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data.

    Taggart, Allison J / Fairbrother, William G

    Quantitative biology (Beijing, China)

    2018  Volume 6, Issue 3, Page(s) 267–274

    Abstract: Background: Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read ... ...

    Abstract Background: Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions.
    Methods: We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape.
    Results: We developed ShapeShifter, a novel approach for identifying and quantifying stable lariat species in RNAseq datasets. We learned a characteristic "lariat" curve from ENCODE RNAseq data and were able to estimate abundances for introns based on read coverage. Using this method we discovered new stable introns in these samples that were not represented using the older, branchpoint-traversing read method.
    Conclusions: ShapeShifter provides a robust approach towards detecting and quantifying stable lariat species.
    Language English
    Publishing date 2018-07-25
    Publishing country China
    Document type Journal Article
    ZDB-ID 2806673-X
    ISSN 2095-4697 ; 2095-4689
    ISSN (online) 2095-4697
    ISSN 2095-4689
    DOI 10.1007/s40484-018-0141-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: RNA structure in splicing: An evolutionary perspective.

    Lin, Chien-Ling / Taggart, Allison J / Fairbrother, William G

    RNA biology

    2016  Volume 13, Issue 9, Page(s) 766–771

    Abstract: Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was recently discovered in fish. Simple expansions of complementary AC and GT dimers at ... ...

    Abstract Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was recently discovered in fish. Simple expansions of complementary AC and GT dimers at opposite boundaries of an intron were found to form a bridging structure, thereby enforcing correct splice site pairing across the intron. In some fish introns, the RNA structures are strong enough to bypass the need of regulatory protein factors for splicing. Here, we discuss the prevalence and potential functions of highly structured introns. In humans, structured introns usually arise through the co-occurrence of C and G-rich repeats at intron boundaries. We explore the potentially instructive example of the HLA receptor genes. In HLA pre-mRNA, structured introns flank the exons that encode the highly polymorphic β sheet cleft, making the processing of the transcript robust to variants that disrupt splicing factor binding. While selective forces that have shaped HLA receptor are fairly atypical, numerous other highly polymorphic genes that encode receptors contain structured introns. Finally, we discuss how the elevated mutation rate associated with the simple repeats that often compose structured intron can make structured introns themselves rapidly evolving elements.
    MeSH term(s) Animals ; Biological Evolution ; Exons ; Humans ; Introns ; Nucleic Acid Conformation ; Polymorphism, Single Nucleotide ; RNA/chemistry ; RNA/genetics ; RNA Precursors/chemistry ; RNA Precursors/genetics ; RNA Splicing ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; Splicing Factor U2AF/metabolism ; Structure-Activity Relationship
    Chemical Substances RNA Precursors ; RNA, Messenger ; Splicing Factor U2AF ; RNA (63231-63-0)
    Language English
    Publishing date 2016-09
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1555-8584
    ISSN (online) 1555-8584
    DOI 10.1080/15476286.2016.1208893
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.

    Buerer, Luke / Clark, Nathaniel E / Welch, Anastasia / Duan, Chaorui / Taggart, Allison J / Townley, Brittany A / Wang, Jing / Soemedi, Rachel / Rong, Stephen / Lin, Chien-Ling / Zeng, Yi / Katolik, Adam / Staley, Jonathan P / Damha, Masad J / Mosammaparast, Nima / Fairbrother, William G

    Research square

    2023  

    Abstract: The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of ... ...

    Abstract The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of the first viable
    Language English
    Publishing date 2023-06-13
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2931976/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1.

    Clark, Nathaniel E / Katolik, Adam / Taggart, Allison J / Buerer, Luke / Holloway, Stephen P / Miller, Nathaniel / Phillips, John D / Farrell, Colin P / Damha, Masad J / Fairbrother, William G

    RNA (New York, N.Y.)

    2022  Volume 28, Issue 7, Page(s) 927–936

    Abstract: In eukaryotic cells, intron lariats produced by the spliceosome contain a 2'5' phosphodiester linkage. The RNA lariat debranching enzyme, Dbr1, is the only enzyme known to hydrolyze this bond. Dbr1 is a member of the metallophosphoesterase (MPE) family ... ...

    Abstract In eukaryotic cells, intron lariats produced by the spliceosome contain a 2'5' phosphodiester linkage. The RNA lariat debranching enzyme, Dbr1, is the only enzyme known to hydrolyze this bond. Dbr1 is a member of the metallophosphoesterase (MPE) family of enzymes, and recent X-ray crystal structures and biochemistry data demonstrate that Dbr1 from
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Humans ; Introns ; Metals ; RNA/chemistry ; RNA Nucleotidyltransferases/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
    Chemical Substances Metals ; RNA (63231-63-0) ; Dbr1 protein, human (EC 2.7.7.-) ; RNA Nucleotidyltransferases (EC 2.7.7.-) ; lariat debranching enzyme (EC 2.7.7.-)
    Language English
    Publishing date 2022-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079159.122
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  5. Article ; Online: Large-scale analysis of branchpoint usage across species and cell lines.

    Taggart, Allison J / Lin, Chien-Ling / Shrestha, Barsha / Heintzelman, Claire / Kim, Seongwon / Fairbrother, William G

    Genome research

    2017  Volume 27, Issue 4, Page(s) 639–649

    Abstract: The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site ... ...

    Abstract The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2-5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.
    Language English
    Publishing date 2017-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.202820.115
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The effects of structure on pre-mRNA processing and stability.

    Soemedi, Rachel / Cygan, Kamil J / Rhine, Christy L / Glidden, David T / Taggart, Allison J / Lin, Chien-Ling / Fredericks, Alger M / Fairbrother, William G

    Methods (San Diego, Calif.)

    2017  Volume 125, Page(s) 36–44

    Abstract: Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and ... ...

    Abstract Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research. The secondary structure of pre-mRNA molecules can have an enhancing or inhibitory effect on pre-mRNA splicing. An example of enhancing structure can be found in a novel class of introns in zebrafish. About 10% of zebrafish genes contain a structured intron that forms a bridging hairpin that enforces correct splice site pairing. Negative examples of splicing include local structures around splice sites that decrease splicing efficiency and potentially cause mis-splicing leading to disease. Splicing mutations are a frequent cause of hereditary disease. The transcripts of disease genes are significantly more structured around the splice sites, and point mutations that increase the local structure often cause splicing disruptions. Post-splicing, RNA secondary structure can also affect the stability of the spliced intron and regulatory RNA interference pathway intermediates, such as pre-microRNAs. Additionally, RNA secondary structure has important roles in the innate immune defense against viruses. Finally, tertiary structure can also play a large role in pre-mRNA splicing. One example is the G-quadruplex structure, which, similar to secondary structure, can either enhance or inhibit splicing through mechanisms such as creating or obscuring RNA binding protein sites.
    MeSH term(s) Animals ; Exons/genetics ; G-Quadruplexes ; Humans ; Immunity, Innate/genetics ; Introns/genetics ; Mutation ; RNA Folding/genetics ; RNA Folding/immunology ; RNA Precursors/chemistry ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Double-Stranded/chemistry ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/immunology ; RNA, Double-Stranded/metabolism ; Zebrafish/genetics
    Chemical Substances RNA Precursors ; RNA, Double-Stranded
    Language English
    Publishing date 2017--01
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2017.06.001
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  7. Article ; Online: Widespread intra-dependencies in the removal of introns from human transcripts.

    Kim, Seong Won / Taggart, Allison J / Heintzelman, Claire / Cygan, Kamil J / Hull, Caitlin G / Wang, Jing / Shrestha, Barsha / Fairbrother, William G

    Nucleic acids research

    2017  Volume 45, Issue 16, Page(s) 9503–9513

    Abstract: Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough ...

    Abstract Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns. We present a genome-wide measurement of the order of splicing within human transcripts. The observed order of splicing cannot be explained by a simple kinetic model. Simulations reveal a bias toward a particular, transcript-specific order of intron removal in human genes. We validate an extreme class of intron that can only splice in a multi-intron context. Special categories of splicing such as exon circularization, first and last intron processing, alternative 5 and 3'ss usage and exon skipping are marked by distinct patterns of ordered intron removal. Excessive intronic length and silencer density tend to delay splicing. Shorter introns that contain enhancers splice early.
    MeSH term(s) Alternative Splicing ; Exons ; Genome, Human ; HEK293 Cells ; Humans ; Introns ; Mutation ; Poly U/genetics ; RNA Splice Sites ; RNA Splicing
    Chemical Substances RNA Splice Sites ; Poly U (27416-86-0)
    Language English
    Publishing date 2017-09-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx661
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  8. Article ; Online: RNA structure replaces the need for U2AF2 in splicing.

    Lin, Chien-Ling / Taggart, Allison J / Lim, Kian Huat / Cygan, Kamil J / Ferraris, Luciana / Creton, Robbert / Huang, Yen-Tsung / Fairbrother, William G

    Genome research

    2015  Volume 26, Issue 1, Page(s) 12–23

    Abstract: RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and ... ...

    Abstract RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
    MeSH term(s) Animals ; Base Sequence ; Computational Biology ; Exons ; Genes, Reporter ; Introns ; Molecular Sequence Data ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Nucleic Acid Conformation ; Phylogeny ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Splicing ; Ribonucleoproteins/genetics ; Ribonucleoproteins/metabolism ; Sequence Analysis, RNA ; Spliceosomes/metabolism ; Zebrafish/genetics
    Chemical Substances Nuclear Proteins ; RNA Precursors ; Ribonucleoproteins
    Language English
    Publishing date 2015-11-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.181008.114
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  9. Article ; Online: Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo.

    Taggart, Allison J / DeSimone, Alec M / Shih, Janice S / Filloux, Madeleine E / Fairbrother, William G

    Nature structural & molecular biology

    2012  Volume 19, Issue 7, Page(s) 719–721

    Abstract: We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From ... ...

    Abstract We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-site selection, identified new mechanisms of alternative splicing and mapped the distribution of splicing factors around branchpoints.
    MeSH term(s) Humans ; Introns ; RNA Precursors/genetics ; RNA, Messenger/genetics
    Chemical Substances RNA Precursors ; RNA, Messenger
    Language English
    Publishing date 2012-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/nsmb.2327
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  10. Article ; Online: Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection.

    Zhang, Shen-Ying / Clark, Nathaniel E / Freije, Catherine A / Pauwels, Elodie / Taggart, Allison J / Okada, Satoshi / Mandel, Hanna / Garcia, Paula / Ciancanelli, Michael J / Biran, Anat / Lafaille, Fabien G / Tsumura, Miyuki / Cobat, Aurélie / Luo, Jingchuan / Volpi, Stefano / Zimmer, Bastian / Sakata, Sonoko / Dinis, Alexandra / Ohara, Osamu /
    Garcia Reino, Eduardo J / Dobbs, Kerry / Hasek, Mary / Holloway, Stephen P / McCammon, Karen / Hussong, Stacy A / DeRosa, Nicholas / Van Skike, Candice E / Katolik, Adam / Lorenzo, Lazaro / Hyodo, Maki / Faria, Emilia / Halwani, Rabih / Fukuhara, Rie / Smith, Gregory A / Galvan, Veronica / Damha, Masad J / Al-Muhsen, Saleh / Itan, Yuval / Boeke, Jef D / Notarangelo, Luigi D / Studer, Lorenz / Kobayashi, Masao / Diogo, Luisa / Fairbrother, William G / Abel, Laurent / Rosenberg, Brad R / Hart, P John / Etzioni, Amos / Casanova, Jean-Laurent

    Cell

    2018  Volume 172, Issue 5, Page(s) 952–965.e18

    Abstract: Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1) ...

    Abstract Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme. We show that DBR1 expression is ubiquitous, but strongest in the spinal cord and brainstem. We also show that all DBR1 mutant alleles are severely hypomorphic, in terms of expression and function. The fibroblasts of DBR1-mutated patients contain higher RNA lariat levels than control cells, this difference becoming even more marked during HSV1 infection. Finally, we show that the patients' fibroblasts are highly susceptible to HSV1. RNA lariat accumulation and viral susceptibility are rescued by wild-type DBR1. Autosomal recessive, partial DBR1 deficiency underlies viral infection of the brainstem in humans through the disruption of tissue-specific and cell-intrinsic immunity to viruses.
    MeSH term(s) Alleles ; Amino Acid Sequence ; Animals ; Brain Diseases, Metabolic, Inborn/genetics ; Brain Diseases, Metabolic, Inborn/pathology ; Brain Stem/metabolism ; Brain Stem/pathology ; Brain Stem/virology ; Encephalitis, Viral/genetics ; Escherichia coli/metabolism ; Female ; Fibroblasts/metabolism ; Fibroblasts/pathology ; Fibroblasts/virology ; Herpesvirus 1, Human ; Humans ; Interferons/metabolism ; Introns/genetics ; Male ; Mice ; Mutant Proteins/metabolism ; Mutation/genetics ; Open Reading Frames/genetics ; Pedigree ; RNA/chemistry ; RNA/metabolism ; RNA Nucleotidyltransferases/chemistry ; RNA Nucleotidyltransferases/deficiency ; RNA Nucleotidyltransferases/genetics ; Toll-Like Receptor 3/metabolism ; Virus Replication
    Chemical Substances Mutant Proteins ; Toll-Like Receptor 3 ; RNA (63231-63-0) ; Interferons (9008-11-1) ; Dbr1 protein, human (EC 2.7.7.-) ; RNA Nucleotidyltransferases (EC 2.7.7.-)
    Language English
    Publishing date 2018-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.02.019
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