1
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Ares M, Igel H, Katzman S, Donohue JP. Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition. Genes Dev 2024; 38:322-335. [PMID: 38724209 DOI: 10.1101/gad.351764.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using Saccharomyces cerevisiae, documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full-length and processed circles. Postsplicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - John P Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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2
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Ares M, Igel H, Katzman S, Donohue JP. Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586863. [PMID: 38585890 PMCID: PMC10996645 DOI: 10.1101/2024.03.26.586863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare, full length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envision and test a hypothesis for their formation using Saccharomyces cerevisiae, documenting full length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron-lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full length and processed circles. Post-splicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - John P. Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz
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3
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, S Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. RNA (NEW YORK, N.Y.) 2024; 30:149-170. [PMID: 38071476 PMCID: PMC10798247 DOI: 10.1261/rna.079866.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after the addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during cotranscriptional splicing in Plad-B using single-molecule intron tracking to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between the binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten the characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Asako Tan
- Illumina, Inc., Madison, Wisconsin 53719, USA
| | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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4
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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5
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.560965. [PMID: 37873484 PMCID: PMC10592967 DOI: 10.1101/2023.10.05.560965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during co-transcriptional splicing in Plad-B using single-molecule intron tracking (SMIT) to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | | | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Melissa Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
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6
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Gaspary A, Laureau R, Dyatel A, Dursuk G, Simon Y, Berchowitz LE. Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision. J Cell Biol 2023; 222:e202302074. [PMID: 37638885 PMCID: PMC10460998 DOI: 10.1083/jcb.202302074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Budding yeast cells have the capacity to adopt few but distinct physiological states depending on environmental conditions. Vegetative cells proliferate rapidly by budding while spores can survive prolonged periods of nutrient deprivation and/or desiccation. Whether or not a yeast cell will enter meiosis and sporulate represents a critical decision that could be lethal if made in error. Most cell fate decisions, including those of yeast, are understood as being triggered by the activation of master transcription factors. However, mechanisms that enforce cell fates posttranscriptionally have been more difficult to attain. Here, we perform a forward genetic screen to determine RNA-binding proteins that affect meiotic entry at the posttranscriptional level. Our screen revealed several candidates with meiotic entry phenotypes, the most significant being RIE1, which encodes an RRM-containing protein. We demonstrate that Rie1 binds RNA, is associated with the translational machinery, and acts posttranscriptionally to enhance protein levels of the master transcription factor Ime1 in sporulation conditions. We also identified a physical binding partner of Rie1, Sgn1, which is another RRM-containing protein that plays a role in timely Ime1 expression. We demonstrate that these proteins act independently of cell size regulation pathways to promote meiotic entry. We propose a model explaining how constitutively expressed RNA-binding proteins, such as Rie1 and Sgn1, can act in cell fate decisions both as switch-like enforcers and as repressors of spurious cell fate activation.
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Affiliation(s)
- Alec Gaspary
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raphaelle Laureau
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Gizem Dursuk
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yael Simon
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Luke E. Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer’s and the Aging Brain, New York, NY, USA
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7
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Hurtig JE, van Hoof A. An unknown essential function of tRNA splicing endonuclease is linked to the integrated stress response and intron debranching. Genetics 2023; 224:iyad044. [PMID: 36943791 PMCID: PMC10213494 DOI: 10.1093/genetics/iyad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
tRNA splicing endonuclease (TSEN) has a well-characterized role in transfer RNA (tRNA) splicing but also other functions. For yeast TSEN, these other functions include degradation of a subset of mRNAs that encode mitochondrial proteins and an unknown essential function. In this study, we use yeast genetics to characterize the unknown tRNA-independent function(s) of TSEN. Using a high-copy suppressor screen, we found that sen2 mutants can be suppressed by overexpression of SEN54. This effect was seen both for tRNA-dependent and tRNA-independent functions indicating that SEN54 is a general suppressor of sen2, likely through structural stabilization. A spontaneous suppressor screen identified mutations in the intron-debranching enzyme, Dbr1, as tRNA splicing-independent suppressors. Transcriptome analysis showed that sen2 mutation activates the Gcn4 stress response. These Gcn4 target transcripts decreased considerably in the sen2 dbr1 double mutant. We propose that Dbr1 and TSEN may compete for a shared substrate, which TSEN normally processes into an essential RNA, while Dbr1 initiates its degradation. These data provide further insight into the essential function(s) of TSEN. Importantly, single amino acid mutations in TSEN cause the generally fatal neuronal disease pontocerebellar hypoplasia (PCH). The mechanism by which defects in TSEN cause this disease is unknown, and our results reveal new possible mechanisms.
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Affiliation(s)
- Jennifer E Hurtig
- Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ambro van Hoof
- Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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8
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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9
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Garcia EL. Allele-specific alternative splicing of Drosophila Ribosomal protein S21 suppresses a lethal mutation in the Phosphorylated adaptor for RNA export ( Phax) gene. G3 GENES|GENOMES|GENETICS 2022; 12:6654594. [PMID: 35920767 PMCID: PMC9434302 DOI: 10.1093/g3journal/jkac195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022]
Abstract
Genetic disruptions to the biogenesis of spliceosomal small-nuclear ribonucleoproteins in Drosophila cause wide-spread alternative splicing changes, including changes to the splicing of pre-mRNA for Ribosomal protein S21 (RpS21). Using a transposon mutant for the Phosphorylated adaptor for RNA export (Phax) gene, we demonstrate that changes in the splicing of RpS21 transcripts have a strong influence on the developmental progression of PhaxSH/SH mutants. Different alleles of the Drosophila RpS21 gene are circulating in common laboratory strains and cell lines. These alleles exhibit differences in RpS21 intron retention and splicing efficiency. Differences in the splicing of RpS21 transcripts account for prior conflicting observations of the phenotypic severity of PhaxSH/SH mutant stocks. The alleles uncover a strong splicing enhancer in RpS21 transcripts that can fully suppress the larval lethality and partially suppress the pupal lethality exhibited by PhaxSH/SH mutant lines. In the absence of the splicing enhancer, the splicing of RpS21 transcripts can be modulated in trans by the SR-rich B52 splicing factor. As PhaxSH/SH mutants exhibit wide-spread splicing changes in transcripts for other genes, findings here establish the importance of a single alternative splicing event, RpS21 splicing or intron retention, to the developmental progression of Drosophila.
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Affiliation(s)
- Eric L Garcia
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine , Lexington, KY 40536, USA
- Department of Biology, University of Kentucky , Lexington, KY 40506, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA
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10
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Sales-Lee J, Perry DS, Bowser BA, Diedrich JK, Rao B, Beusch I, Yates JR, Roy SW, Madhani HD. Coupling of spliceosome complexity to intron diversity. Curr Biol 2021; 31:4898-4910.e4. [PMID: 34555349 DOI: 10.1016/j.cub.2021.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. We found they govern splicing efficiency of introns with divergent spacing between intron elements. Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites. Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G patch/helicase pair that promotes splicing fidelity. We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.
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Affiliation(s)
- Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniela S Perry
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bradley A Bowser
- Department of Molecular and Cellular Biology, University of California, Merced, Merced, CA 95343, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, CA 94132, 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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11
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Wagner AR, Scott HM, West KO, Vail KJ, Fitzsimons TC, Coleman AK, Carter KE, Watson RO, Patrick KL. Global Transcriptomics Uncovers Distinct Contributions From Splicing Regulatory Proteins to the Macrophage Innate Immune Response. Front Immunol 2021; 12:656885. [PMID: 34305890 PMCID: PMC8299563 DOI: 10.3389/fimmu.2021.656885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Pathogen sensing via pattern recognition receptors triggers massive reprogramming of macrophage gene expression. While the signaling cascades and transcription factors that activate these responses are well-known, the role of post-transcriptional RNA processing in modulating innate immune gene expression remains understudied. Given their crucial role in regulating pre-mRNA splicing and other RNA processing steps, we hypothesized that members of the SR/hnRNP protein families regulate innate immune gene expression in distinct ways. We analyzed steady state gene expression and alternatively spliced isoform production in ten SR/hnRNP knockdown RAW 264.7 macrophage-like cell lines following infection with the bacterial pathogen Salmonella enterica serovar Typhimurium (Salmonella). We identified thousands of transcripts whose abundance is increased or decreased by SR/hnRNP knockdown in macrophages. Notably, we observed that SR and hnRNP proteins influence expression of different genes in uninfected versus Salmonella-infected macrophages, suggesting functionalization of these proteins upon pathogen sensing. Likewise, we found that knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for thousands of macrophage transcripts and that these alternative splicing changes were distinct in uninfected and Salmonella-infected macrophages. Finally, having observed a surprising degree of similarity between the differentially expressed genes (DEGs) and DIUs in hnRNP K and U knockdown macrophages, we found that hnRNP K and U knockdown macrophages are both more restrictive to Vesicular Stomatitis Virus (VSV), while hnRNP K knockdown macrophages are more permissive to Salmonella Typhimurium. Based on these findings, we conclude that many innate immune genes evolved to rely on one or more SR/hnRNPs to ensure the proper magnitude of their induction, supporting a model wherein pre-mRNA splicing is critical for regulating innate immune gene expression and controlling infection outcomes in macrophages ex vivo.
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Affiliation(s)
- Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Haley M Scott
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kelsi O West
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Krystal J Vail
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States.,Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Timothy C Fitzsimons
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Aja K Coleman
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kaitlyn E Carter
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health, Bryan, TX, United States
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12
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Hurtig JE, Kim M, Orlando-Coronel LJ, Ewan J, Foreman M, Notice LA, Steiger MA, van Hoof A. Origin, conservation, and loss of alternative splicing events that diversify the proteome in Saccharomycotina budding yeasts. RNA (NEW YORK, N.Y.) 2020; 26:1464-1480. [PMID: 32631843 PMCID: PMC7491326 DOI: 10.1261/rna.075655.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/02/2020] [Indexed: 05/03/2023]
Abstract
Many eukaryotes use RNA processing, including alternative splicing, to express multiple gene products from the same gene. The budding yeast Saccharomyces cerevisiae has been successfully used to study the mechanism of splicing and the splicing machinery, but alternative splicing in yeast is relatively rare and has not been extensively studied. Alternative splicing of SKI7/HBS1 is widely conserved, but yeast and a few other eukaryotes have replaced this one alternatively spliced gene with a pair of duplicated, unspliced genes as part of a whole genome doubling (WGD). We show that other examples of alternative splicing known to have functional consequences are widely conserved within Saccharomycotina. A common mechanism by which alternative splicing has disappeared is by replacement of an alternatively spliced gene with duplicate unspliced genes. This loss of alternative splicing does not always take place soon after duplication, but can take place after sufficient time has elapsed for speciation. Saccharomycetaceae that diverged before WGD use alternative splicing more frequently than S. cerevisiae, suggesting that WGD is a major reason for infrequent alternative splicing in yeast. We anticipate that WGDs in other lineages may have had the same effect. Having observed that two functionally distinct splice-isoforms are often replaced by duplicated genes allowed us to reverse the reasoning. We thereby identify several splice isoforms that are likely to produce two functionally distinct proteins because we find them replaced by duplicated genes in related species. We also identify some alternative splicing events that are not conserved in closely related species and unlikely to produce functionally distinct proteins.
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Affiliation(s)
- Jennifer E Hurtig
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Minseon Kim
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Luisa J Orlando-Coronel
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Jellisa Ewan
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Michelle Foreman
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Lee-Ann Notice
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
| | - Michelle A Steiger
- Department of Chemistry and Biochemistry, University of St. Thomas, Houston, Texas 77006, USA
| | - Ambro van Hoof
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center-Houston, Houston, Texas 77030, USA
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Talkish J, Igel H, Perriman RJ, Shiue L, Katzman S, Munding EM, Shelansky R, Donohue JP, Ares M. Correction: Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. PLoS Genet 2020; 16:e1008854. [PMID: 32459805 PMCID: PMC7252609 DOI: 10.1371/journal.pgen.1008854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5'-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.
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Affiliation(s)
- Tucker J Carrocci
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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