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Brothers WR, Ali F, Kajjo S, Fabian MR. The EDC4-XRN1 interaction controls P-body dynamics to link mRNA decapping with decay. EMBO J 2023; 42:e113933. [PMID: 37621215 PMCID: PMC10620763 DOI: 10.15252/embj.2023113933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
Deadenylation-dependent mRNA decapping and decay is the major cytoplasmic mRNA turnover pathway in eukaryotes. Many mRNA decapping and decay factors are associated with each other via protein-protein interaction motifs. For example, the decapping enzyme DCP2 and the 5'-3' exonuclease XRN1 interact with the enhancer of mRNA-decapping protein 4 (EDC4), a large scaffold that has been reported to stimulate mRNA decapping. mRNA decapping and decay factors are also found in processing bodies (P-bodies), evolutionarily conserved ribonucleoprotein granules that are often enriched with mRNAs targeted for decay, yet paradoxically are not required for mRNA decay to occur. Here, we show that disrupting the EDC4-XRN1 interaction or altering their stoichiometry inhibits mRNA decapping, with microRNA-targeted mRNAs being stabilized in a translationally repressed state. Importantly, we demonstrate that this concomitantly leads to larger P-bodies that are responsible for preventing mRNA decapping. Finally, we demonstrate that P-bodies support cell viability and prevent stress granule formation when XRN1 is limiting. Taken together, these data demonstrate that the interaction between XRN1 and EDC4 regulates P-body dynamics to properly coordinate mRNA decapping with 5'-3' decay in human cells.
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Affiliation(s)
- William R Brothers
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Farah Ali
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Sam Kajjo
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Marc R Fabian
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
- Department of BiochemistryMcGill UniversityMontrealQCCanada
- Department of OncologyMcGill UniversityMontrealQCCanada
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2
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White LK, Strugar SM, MacFadden A, Hesselberth JR. Nanopore sequencing of internal 2'-PO 4 modifications installed by RNA repair. RNA (NEW YORK, N.Y.) 2023; 29:847-861. [PMID: 36854608 PMCID: PMC10187680 DOI: 10.1261/rna.079290.122] [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: 06/04/2022] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
Ligation by plant and fungal RNA ligases yields an internal 2'-phosphate group on each RNA ligation product. In budding yeast, this covalent mark occurs at the splice junction of two targets of ligation: intron-containing tRNAs and the messenger RNA HAC1 The repertoire of RNA molecules repaired by RNA ligation has not been explored due to a lack of unbiased approaches for identifying RNA ligation products. Here, we define several unique signals produced by 2'-phosphorylated RNAs during nanopore sequencing. A 2'-phosphate at the splice junction of HAC1 mRNA inhibits 5' → 3' degradation, enabling detection of decay intermediates in yeast RNA repair mutants by nanopore sequencing. During direct RNA sequencing, intact 2'-phosphorylated RNAs on HAC1 and tRNAs produce diagnostic changes in nanopore current properties and base calling features, including stalls produced as the modified RNA translocates through the nanopore motor protein. These approaches enable directed studies to identify novel RNA repair events in other contexts.
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Affiliation(s)
- Laura K White
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Saylor M Strugar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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3
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Fong N, Sheridan RM, Ramachandran S, Bentley DL. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model. Mol Cell 2022; 82:3632-3645.e4. [PMID: 36206739 PMCID: PMC9555879 DOI: 10.1016/j.molcel.2022.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/24/2022] [Accepted: 08/31/2022] [Indexed: 11/07/2022]
Abstract
The pause-release model of transcription proposes that 40-100 bases from the start site RNA Pol II pauses, followed by release into productive elongation. Pause release is facilitated by the PTEFb phosphorylation of the RNA Pol II elongation factor, Spt5. We mapped paused polymerases by eNET-seq and found frequent pausing in zones that extend ∼0.3-3 kb into genes even when PTEFb is inhibited. The fraction of paused polymerases or pausing propensity declines gradually over several kb and not abruptly as predicted for a discrete pause-release event. Spt5 depletion extends pausing zones, suggesting that it promotes the maturation of elongation complexes to a low-pausing state. The expression of mutants after Spt5 depletion showed that phosphomimetic substitutions in the CTR1 domain diminished pausing throughout genes. By contrast, mutants that prevent the phosphorylation of the Spt5 RNA-binding domain strengthened pausing. Thus, distinct Spt5 phospho-isoforms set the balance between pausing and elongation.
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Affiliation(s)
- Nova Fong
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Srinivas Ramachandran
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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4
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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5
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Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Res 2021; 49:e41. [PMID: 33511416 PMCID: PMC8053086 DOI: 10.1093/nar/gkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
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Affiliation(s)
| | | | - Jacob R Immel
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | - Steven A Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Sunflower Genomics, Inc., Lawrence, KS 66047, USA
- Department of Mechanical Engineering and Bioengineering, University of Kansas, Lawrence, KS 66045, USA
- Department of Cancer Biology and KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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6
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Dai H, Gu W. Strategies and Best Practice in Cloning Small RNAs. GENE TECHNOLOGY 2020; 9:151. [PMID: 32953938 PMCID: PMC7500658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High-throughput sequencing has become a standard and powerful tool for analyzing nucleic acids primarily due to its sensitivity and convenience. Small RNAs play important roles in regulating cellular and viral genes. The conventional methods for small RNA analyses are tedious and often lack accuracy, specificity and sensitivity for many small RNA species. Therefore, high-throughput sequencing becomes an indispensable tool for analyzing small RNAs. However, it is challenging to generate a reliable and representative small RNA library for high-throughput sequencing since small RNAs are usually expressed at extremely low levels and often contain modifications which affect library construction, usually causing biased readouts. This review compares various strategies for generating small RNA libraries of high quality and reliability, and provides recommendations on best practice in preparing high-throughput sequencing RNA libraries.
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Li L, Dai H, Nguyen AP, Gu W. A convenient strategy to clone small RNA and mRNA for high-throughput sequencing. RNA (NEW YORK, N.Y.) 2020; 26:218-227. [PMID: 31754076 PMCID: PMC6961543 DOI: 10.1261/rna.071605.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
High-throughput sequencing has become a standard tool for analyzing RNA and DNA. This method usually needs a cDNA/DNA library ligated with specific 5' and 3' linkers. Unlike mRNA, small RNA often contains modifications including 5' cap or triphosphate and 2'-O-methyl, requiring additional processing steps before linker additions during cloning processes; due to low expression levels, it is difficult to clone small RNA with a small amount of total RNA. Here we present a new strategy to clone 5' modified or unmodified small RNA in an all-liquid-based reaction carried out in a single PCR tube with as little as 20 ng total RNA. The 7-h cloning process only needs ∼1 h of labor. Moreover, this method can also clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA; the barcoded PCR primers are also compatible with non-cDNA cloning applications, including the preparation of genomic libraries. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, versatile, and cost-effective. Moreover, the all-liquid-based reaction can be performed in an automated manner.
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Affiliation(s)
- Lichao Li
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Hui Dai
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - An-Phong Nguyen
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Weifeng Gu
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
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