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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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Liboy-Lugo JM, Espinoza CA, Sheu-Gruttadauria J, Park JE, Xu A, Jowhar Z, Gao AL, Carmona-Negrón JA, Wittmann T, Jura N, Floor SN. Protein-protein interactions with G3BPs drive stress granule condensation and gene expression changes under cellular stress. bioRxiv 2024:2024.02.06.579149. [PMID: 38370785 PMCID: PMC10871250 DOI: 10.1101/2024.02.06.579149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Stress granules (SGs) are macromolecular assemblies that form under cellular stress. Formation of these condensates is driven by the condensation of RNA and RNA-binding proteins such as G3BPs. G3BPs condense into SGs following stress-induced translational arrest. Three G3BP paralogs (G3BP1, G3BP2A, and G3BP2B) have been identified in vertebrates. However, the contribution of different G3BP paralogs to stress granule formation and stress-induced gene expression changes is incompletely understood. Here, we identified key residues for G3BP condensation such as V11. This conserved amino acid is required for formation of the G3BP-Caprin-1 complex, hence promoting SG assembly. Total RNA sequencing and ribosome profiling revealed that disruption of G3BP condensation corresponds to changes in mRNA levels and ribosome engagement during the integrated stress response (ISR). Moreover, we found that G3BP2B preferentially condenses and promotes changes in mRNA expression under endoplasmic reticulum (ER) stress. Together, this work suggests that stress granule assembly promotes changes in gene expression under cellular stress, which is differentially regulated by G3BP paralogs.
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Affiliation(s)
- José M Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Carla A Espinoza
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Sheu-Gruttadauria
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jesslyn E Park
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Ziad Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Angela L Gao
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - José A Carmona-Negrón
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Chemistry, University of Puerto Rico, Mayaguez, Puerto Rico, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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Park JE, Desai H, Liboy-Lugo J, Gu S, Jowhar Z, Xu A, Floor SN. IGHMBP2 deletion suppresses translation and activates the integrated stress response. bioRxiv 2023:2023.12.11.571166. [PMID: 38168189 PMCID: PMC10760061 DOI: 10.1101/2023.12.11.571166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
IGHMBP2 is a non-essential, superfamily 1 DNA/RNA helicase that is mutated in patients with rare neuromuscular diseases SMARD1 and CMT2S. IGHMBP2 is implicated in translational and transcriptional regulation via biochemical association with ribosomal proteins, pre-rRNA processing factors, and tRNA-related species. To uncover the cellular consequences of perturbing IGHMBP2, we generated full and partial IGHMBP2 deletion K562 cell lines. Using polysome profiling and a nascent protein synthesis assay, we found that IGHMBP2 deletion modestly reduces global translation. We performed Ribo-seq and RNA-seq and identified diverse gene expression changes due to IGHMBP2 deletion, including ATF4 upregulation. With recent studies showing the ISR can contribute to tRNA metabolism-linked neuropathies, we asked whether perturbing IGHMBP2 promotes ISR activation. We generated ATF4 reporter cell lines and found IGHMBP2 knockout cells demonstrate basal, chronic ISR activation. Our work expands upon the impact of IGHMBP2 in translation and elucidates molecular mechanisms that may link mutant IGHMBP2 to severe clinical phenotypes.
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Affiliation(s)
- Jesslyn E. Park
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Hetvee Desai
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
| | - José Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Sohyun Gu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Ziad Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Stephen N. Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA, 94143
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. bioRxiv 2023:2023.05.11.540322. [PMID: 37214951 PMCID: PMC10197686 DOI: 10.1101/2023.05.11.540322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
- Department of Cell Biology, Duke University Medical Center, Durham, United States
- Duke Regeneration Center, Duke University Medical Center, Durham, United States
- Department of Neurobiology, Duke University Medical Center, Durham, United States
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, United States
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Helen Diller Family Comprehensive Cancer Center, San Francisco, United States
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Jowhar Z, Shachar S, Gudla PR, Wangsa D, Torres E, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. Effects of human sex chromosome dosage on spatial chromosome organization. Mol Biol Cell 2018; 29:2458-2469. [PMID: 30091656 PMCID: PMC6233059 DOI: 10.1091/mbc.e18-06-0359] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 01/08/2023] Open
Abstract
Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.
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Affiliation(s)
- Ziad Jowhar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Prabhakar R. Gudla
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Erin Torres
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Jill L. Russ
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Armin Raznahan
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
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Jowhar Z, Gudla PR, Shachar S, Wangsa D, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. HiCTMap: Detection and analysis of chromosome territory structure and position by high-throughput imaging. Methods 2018; 142:30-38. [PMID: 29408376 PMCID: PMC5993577 DOI: 10.1016/j.ymeth.2018.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/15/2017] [Accepted: 01/25/2018] [Indexed: 12/23/2022] Open
Abstract
The spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells. HiCTMap is a high-throughput imaging-based chromosome detection method which enables routine analysis of chromosome structure and nuclear position. Using an optimized FISH staining protocol in a 384-well plate format in conjunction with a bespoke automated image analysis workflow, HiCTMap faithfully detects chromosome territories and their position in 2D and 3D in a large population of cells per experimental condition. We apply this novel technique to visualize chromosomes 18, X, and Y in male and female primary human skin fibroblasts, and show accurate detection of the correct number of chromosomes in the respective genotypes. Given the ability to visualize and quantitatively analyze large numbers of nuclei, we use HiCTMap to measure chromosome territory area and volume with high precision and determine the radial position of chromosome territories using either centroid or equidistant-shell analysis. The HiCTMap protocol is also compatible with RNA FISH as demonstrated by simultaneous labeling of X chromosomes and Xist RNA in female cells. We suggest HiCTMap will be a useful tool for routine precision mapping of chromosome territories in a wide range of cell types and tissues.
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MESH Headings
- Animals
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Chromosome Mapping/instrumentation
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 18/metabolism
- Chromosomes, Human, X/genetics
- Chromosomes, Human, X/metabolism
- Chromosomes, Human, Y/genetics
- Chromosomes, Human, Y/metabolism
- Female
- Fibroblasts
- Humans
- Image Processing, Computer-Assisted/instrumentation
- Image Processing, Computer-Assisted/methods
- In Situ Hybridization, Fluorescence/instrumentation
- In Situ Hybridization, Fluorescence/methods
- Male
- Primary Cell Culture/methods
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Skin/cytology
- Staining and Labeling/instrumentation
- Staining and Labeling/methods
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Affiliation(s)
- Ziad Jowhar
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Prabhakar R Gudla
- NCI High-throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Sigal Shachar
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Jill L Russ
- Human Genetics Branch, National Institute of Mental Health, NIH, Bethesda, MD 20892, United States
| | - Gianluca Pegoraro
- NCI High-throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Armin Raznahan
- Human Genetics Branch, National Institute of Mental Health, NIH, Bethesda, MD 20892, United States
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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Mishra PK, Ciftci-Yilmaz S, Reynolds D, Au WC, Boeckmann L, Dittman LE, Jowhar Z, Pachpor T, Yeh E, Baker RE, Hoyt MA, D'Amours D, Bloom K, Basrai MA. Polo kinase Cdc5 associates with centromeres to facilitate the removal of centromeric cohesin during mitosis. Mol Biol Cell 2016; 27:2286-300. [PMID: 27226485 PMCID: PMC4945145 DOI: 10.1091/mbc.e16-01-0004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/20/2022] Open
Abstract
Sister chromatid cohesion is essential for tension-sensing mechanisms that monitor bipolar attachment of replicated chromatids in metaphase. Cohesion is mediated by the association of cohesins along the length of sister chromatid arms. In contrast, centromeric cohesin generates intrastrand cohesion and sister centromeres, while highly cohesin enriched, are separated by >800 nm at metaphase in yeast. Removal of cohesin is necessary for sister chromatid separation during anaphase, and this is regulated by evolutionarily conserved polo-like kinase (Cdc5 in yeast, Plk1 in humans). Here we address how high levels of cohesins at centromeric chromatin are removed. Cdc5 associates with centromeric chromatin and cohesin-associated regions. Maximum enrichment of Cdc5 in centromeric chromatin occurs during the metaphase-to-anaphase transition and coincides with the removal of chromosome-associated cohesin. Cdc5 interacts with cohesin in vivo, and cohesin is required for association of Cdc5 at centromeric chromatin. Cohesin removal from centromeric chromatin requires Cdc5 but removal at distal chromosomal arm sites does not. Our results define a novel role for Cdc5 in regulating removal of centromeric cohesins and faithful chromosome segregation.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Sultan Ciftci-Yilmaz
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Reynolds
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lauren E Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ziad Jowhar
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tejaswini Pachpor
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - M Andrew Hoyt
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Damien D'Amours
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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