1
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024:S1097-2765(24)00511-2. [PMID: 38964322 DOI: 10.1016/j.molcel.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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2
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Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596138. [PMID: 38853896 PMCID: PMC11160661 DOI: 10.1101/2024.05.28.596138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. Hence, we trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs. ProCapNet annotates predictive motifs in nearly all actively transcribed regulatory elements across multiple cell-lines, revealing a shared cis-regulatory logic across promoters and enhancers mediated by a highly epistatic sequence syntax of cooperative and competitive motif interactions. ProCapNet models of RAMPAGE profiles measuring steady-state RNA abundance at TSSs distill initiation signals on par with models trained directly on PRO-cap profiles. ProCapNet learns a largely cell-type-agnostic cis-regulatory code of initiation complementing sequence drivers of cell-type-specific chromatin state critical for accurate prediction of cell-type-specific transcription initiation.
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Affiliation(s)
- Kelly Cochran
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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3
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McShane A, Narayanan IV, Paulsen MT, Ashaka M, Blinkiewicz H, Yang NT, Magnuson B, Bedi K, Wilson TE, Ljungman M. Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588612. [PMID: 38645116 PMCID: PMC11030308 DOI: 10.1101/2024.04.09.588612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Arising as co-products of canonical gene expression, transcription-associated lincRNAs, such as promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and readthrough (RT) transcripts, are often regarded as byproducts of transcription, although they may be important for the expression of nearby genes. We identified regions of nascent expression of these lincRNA in 16 human cell lines using Bru-seq techniques, and found distinctly regulated patterns of PROMPT, eRNA, and RT transcription using the diverse biochemical approaches in the ENCODE4 deeply profiled cell lines collection. Transcription of these lincRNAs was influenced by sequence-specific features and the local or 3D chromatin landscape. However, these sequence and chromatin features do not describe the full spectrum of lincRNA expression variability we identify, highlighting the complexity of their regulation. This may suggest that transcription-associated lincRNAs are not merely byproducts, but rather that the transcript itself, or the act of its transcription, is important for genomic function.
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4
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Jones T, Sigauke RF, Sanford L, Taatjes DJ, Allen MA, Dowell RD. A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585303. [PMID: 38559193 PMCID: PMC10980006 DOI: 10.1101/2024.03.15.585303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
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5
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Zhu X, Joo Y, Bossi S, McDevitt RA, Xie A, Wang Y, Xue Y, Su S, Lee SK, Sah N, Zhang S, Ye R, Pinto A, Zhang Y, Araki K, Araki M, Morales M, Mattson MP, van Praag H, Wang W. Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity. Prog Neurobiol 2024; 233:102568. [PMID: 38216113 PMCID: PMC10922770 DOI: 10.1016/j.pneurobio.2024.102568] [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: 06/02/2023] [Revised: 12/14/2023] [Accepted: 01/06/2024] [Indexed: 01/14/2024]
Abstract
The Topoisomerase 3B (Top3b) - Tudor domain containing 3 (Tdrd3) protein complex is the only dual-activity topoisomerase complex that can alter both DNA and RNA topology in animals. TOP3B mutations in humans are associated with schizophrenia, autism and cognitive disorders; and Top3b-null mice exhibit several phenotypes observed in animal models of psychiatric and cognitive disorders, including impaired cognitive and emotional behaviors, aberrant neurogenesis and synaptic plasticity, and transcriptional defects. Similarly, human TDRD3 genomic variants have been associated with schizophrenia, verbal short-term memory and educational attainment. However, the importance of Tdrd3 in normal brain function has not been examined in animal models. Here we generated a Tdrd3-null mouse strain and demonstrate that these mice display both shared and unique defects when compared to Top3b-null mice. Shared defects were observed in cognitive behaviors, synaptic plasticity, adult neurogenesis, newborn neuron morphology, and neuronal activity-dependent transcription; whereas defects unique to Tdrd3-deficient mice include hyperactivity, changes in anxiety-like behaviors, olfaction, increased new neuron complexity, and reduced myelination. Interestingly, multiple genes critical for neurodevelopment and cognitive function exhibit reduced levels in mature but not nascent transcripts. We infer that the entire Top3b-Tdrd3 complex is essential for normal brain function, and that defective post-transcriptional regulation could contribute to cognitive and psychiatric disorders.
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Affiliation(s)
- Xingliang Zhu
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Yuyoung Joo
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Simone Bossi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Ross A McDevitt
- Comparative Medicine Section, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aoji Xie
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Yue Wang
- Lab of Neuroscience, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Nirnath Sah
- Lab of Neuroscience, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Shiliang Zhang
- Confocal and Electron Microscopy Core, National Institute on Drug Abuse, National Institute of Health, Baltimore, MD 21224, USA
| | - Rong Ye
- Confocal and Electron Microscopy Core, National Institute on Drug Abuse, National Institute of Health, Baltimore, MD 21224, USA
| | - Alejandro Pinto
- Stiles-Nicholson Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1, Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Masatake Araki
- Division of Genomics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1, Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Marisela Morales
- Confocal and Electron Microscopy Core, National Institute on Drug Abuse, National Institute of Health, Baltimore, MD 21224, USA
| | - Mark P Mattson
- Lab of Neuroscience, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA
| | - Henriette van Praag
- Stiles-Nicholson Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institute of Health, Baltimore, MD 21224, USA.
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6
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Vill AC, Rice EJ, De Vlaminck I, Danko CG, Brito IL. Precision run-on sequencing (PRO-seq) for microbiome transcriptomics. Nat Microbiol 2024; 9:241-250. [PMID: 38172625 PMCID: PMC11059318 DOI: 10.1038/s41564-023-01558-w] [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: 02/07/2022] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Bacteria respond to environmental stimuli through precise regulation of transcription initiation and elongation. Bulk RNA sequencing primarily characterizes mature transcripts, so to identify actively transcribed loci we need to capture RNA polymerase (RNAP) complexed with nascent RNA. However, such capture methods have only previously been applied to culturable, genetically tractable organisms such as E. coli and B. subtilis. Here we apply precision run-on sequencing (PRO-seq) to profile nascent transcription in cultured E. coli and diverse uncultured bacteria. We demonstrate that PRO-seq can characterize the transcription of small, structured, or post-transcriptionally modified RNAs, which are often absent from bulk RNA-seq libraries. Applying PRO-seq to the human microbiome highlights taxon-specific RNAP pause motifs and pause-site distributions across non-coding RNA loci that reflect structure-coincident pausing. We also uncover concurrent transcription and cleavage of CRISPR guide RNAs and transfer RNAs. We demonstrate the utility of PRO-seq for exploring transcriptional dynamics in diverse microbial communities.
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Affiliation(s)
- Albert C Vill
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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7
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Pateev I, Seregina K, Ivanov R, Reshetnikov V. Biodistribution of RNA Vaccines and of Their Products: Evidence from Human and Animal Studies. Biomedicines 2023; 12:59. [PMID: 38255166 PMCID: PMC10812935 DOI: 10.3390/biomedicines12010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Explosive developments in mRNA vaccine technology in the last decade have made it possible to achieve great success in clinical trials of mRNA vaccines to prevent infectious diseases and develop cancer treatments and mRNA-based gene therapy products. The approval of the mRNA-1273 and BNT162b2 mRNA vaccines against SARS-CoV-2 by the U.S. Food and Drug Administration has led to mass vaccination (with mRNA vaccines) of several hundred million people around the world, including children. Despite its effectiveness in the fight against COVID-19, rare adverse effects of the vaccination have been shown in some studies, including vascular microcirculation disorders and autoimmune and allergic reactions. The biodistribution of mRNA vaccines remains one of the most poorly investigated topics. This mini-review discussed the results of recent experimental studies on humans and rodents regarding the biodistribution of mRNA vaccines, their constituents (mRNA and lipid nanoparticles), and their encoded antigens. We focused on the dynamics of the biodistribution of mRNA vaccine products and on the possibility of crossing the blood-brain and blood-placental barriers as well as transmission to infants through breast milk. In addition, we critically assessed the strengths and weaknesses of the detection methods that have been applied in these articles, whose results' reliability is becoming a subject of debate.
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Affiliation(s)
- Ildus Pateev
- Translational Medicine Research Center, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Kristina Seregina
- Translational Medicine Research Center, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Roman Ivanov
- Translational Medicine Research Center, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Vasiliy Reshetnikov
- Translational Medicine Research Center, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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8
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Horste EL, Fansler MM, Cai T, Chen X, Mitschka S, Zhen G, Lee FCY, Ule J, Mayr C. Subcytoplasmic location of translation controls protein output. Mol Cell 2023; 83:4509-4523.e11. [PMID: 38134885 PMCID: PMC11146010 DOI: 10.1016/j.molcel.2023.11.025] [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: 01/30/2023] [Revised: 08/15/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.
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Affiliation(s)
- Ellen L Horste
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA
| | - Ting Cai
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Gang Zhen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Flora C Y Lee
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christine Mayr
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA.
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9
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Zhao Y, Liu L, Hassett R, Siepel A. Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Res 2023; 51:e106. [PMID: 37889042 PMCID: PMC10681744 DOI: 10.1093/nar/gkad843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lingjie Liu
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
| | - Rebecca Hassett
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
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10
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Dong S, Xia Q, Pan J, Du XL, Wu YJ, Xie XJ. Hyperbranched polyamidoamine-RGD peptide/si- circICA1 in the treatment of invasive thyroid cancer through targeting of the miR-486-3p/SERPINA1 axis. Nanomedicine (Lond) 2023; 18:2039-2059. [PMID: 38131284 DOI: 10.2217/nnm-2023-0211] [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] [Indexed: 12/23/2023] Open
Abstract
Aim: This study aimed to identify molecular markers associated with papillary thyroid cancer (PTC) and investigate the therapeutic potential of targeted nanoscale drugs. Materials & methods: We analyzed the effects of circICA1 and miR-486-3p on B-CPAP cells' proliferation, apoptosis, migration and invasion. The regulation of the miR-486-3p/SERPINA1 axis was explored using quantitative real-time reverse transcription PCR and western blot analyses for metastasis. In vivo, we evaluated the effects of hyperbranched polyamidoamine-RGD peptide/si-circICA1 on PTC growth and metastasis. Results: Enhanced miR-486-3p expression inhibits B-CPAP cells' proliferation and invasion. si-circICA1 delivered via hyperbranched polyamidoamine-RGD peptide nanoparticles shows potential for treating metastasis in PTC. Conclusion: This study identifies key molecular mechanisms underlying PTC invasiveness and suggests a promising therapeutic strategy for PTC using targeted nanoscale drugs.
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Affiliation(s)
- Shuai Dong
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qing Xia
- Department of Endocrinology, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China
| | - Jun Pan
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiao-Long Du
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yi-Jun Wu
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiao-Jun Xie
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
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11
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Gvozdenov Z, Barcutean Z, Struhl K. Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells. Mol Cell 2023; 83:1786-1797.e5. [PMID: 37137302 PMCID: PMC10247422 DOI: 10.1016/j.molcel.2023.04.010] [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: 10/18/2022] [Revised: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
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Affiliation(s)
- Zlata Gvozdenov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zeno Barcutean
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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12
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Zúñiga-Hernández JM, Olivares GH, Olguín P, Glavic A. Low-nutrient diet in Drosophila larvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting. Open Biol 2023; 13:230049. [PMID: 37161288 PMCID: PMC10170216 DOI: 10.1098/rsob.230049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Nutrient scarcity is a frequent adverse condition that organisms face during their development. This condition may lead to long-lasting effects on the metabolism and behaviour of adults due to developmental epigenetic modifications. Here, we show that reducing nutrient availability during larval development affects adult spontaneous activity and sleep behaviour, together with changes in gene expression and epigenetic marks in the mushroom bodies (MBs). We found that open chromatin regions map to 100 of 241 transcriptionally upregulated genes in the adult MBs, these new opening zones are preferentially located in regulatory zones such as promoter-TSS and introns. Importantly, opened chromatin at the Dopamine 1-like receptor 2 regulatory zones correlate with increased expression. In consequence, adult administration of a dopamine antagonist reverses increased spontaneous activity and diminished sleep time observed in response to early-life nutrient restriction. In comparison, reducing dop1R2 expression in MBs also ameliorates these effects, albeit to a lesser degree. These results lead to the conclusion that increased dopamine signalling in the MBs of flies reared in a poor nutritional environment underlies the behavioural changes observed due to this condition during development.
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Affiliation(s)
- J M Zúñiga-Hernández
- Laboratorio Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Gonzalo H Olivares
- Escuela de Kinesiología, Facultad de Medicina, Center of Integrative Biology (CIB), Universidad Mayor, Chile
| | - Patricio Olguín
- Programa de Genética Humana, ICBM, Biomedical Neuroscience Institute, Departamento de Neurociencia, Facultad de Medicina, Universidad de Chile, Chile
| | - Alvaro Glavic
- Laboratorio Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
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13
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Mimoso CA, Adelman K. U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes. Mol Cell 2023; 83:1264-1279.e10. [PMID: 36965480 PMCID: PMC10135401 DOI: 10.1016/j.molcel.2023.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/06/2023] [Accepted: 02/28/2023] [Indexed: 03/27/2023]
Abstract
The expansion of introns within mammalian genomes poses a challenge for the production of full-length messenger RNAs (mRNAs), with increasing evidence that these long AT-rich sequences present obstacles to transcription. Here, we investigate RNA polymerase II (RNAPII) elongation at high resolution in mammalian cells and demonstrate that RNAPII transcribes faster across introns. Moreover, we find that this acceleration requires the association of U1 snRNP (U1) with the elongation complex at 5' splice sites. The role of U1 to stimulate elongation rate through introns reduces the frequency of both premature termination and transcriptional arrest, thereby dramatically increasing RNA production. We further show that changes in RNAPII elongation rate due to AT content and U1 binding explain previous reports of pausing or termination at splice junctions and the edge of CpG islands. We propose that U1-mediated acceleration of elongation has evolved to mitigate the risks that long AT-rich introns pose to transcript completion.
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Affiliation(s)
- Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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14
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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. NATURE AGING 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Zhu X, Joo Y, Bossi S, McDevitt R, Xie A, Wang Y, Xue Y, Su S, Lee SK, Sah N, Zhang S, Ye R, Pinto A, Zhang Y, Araki K, Araki M, Morales M, Mattson M, van Praag H, Wang W. Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity. RESEARCH SQUARE 2023:rs.3.rs-2597043. [PMID: 36909584 PMCID: PMC10002826 DOI: 10.21203/rs.3.rs-2597043/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The Topoisomerase 3B (Top3b) - Tudor domain containing 3 (Tdrd3) protein complex is the only dual-activity topoisomerase complex in animals that can alter the topology of both DNA and RNA. TOP3B mutations in humans are associated with schizophrenia, autism and cognitive disorders; and Top3b-null mice exhibit several phenotypes observed in animal models of psychiatric and cognitive disorders, including impairments in cognitive and emotional behaviors, aberrant neurogenesis and synaptic plasticity, and transcriptional defects. Similarly, human TDRD3 genomic variants have been associated with schizophrenia, verbal shorten-memory and learning, and educational attainment. However, the importance of Tdrd3 in normal brain function has not been examined in animal models. Here we built a Tdrd3-null mouse strain and demonstrate that these mice display both shared and unique defects when compared to Top3b-null mice. Shared defects were observed in cognitive behaviors, synaptic plasticity, adult neurogenesis, newborn neuron morphology, and neuronal activity-dependent transcription; whereas defects unique to Tdrd3-deficient mice include hyperactivity, changes in anxiety-like behaviors, increased new neuron complexity, and reduced myelination. Interestingly, multiple genes critical for neurodevelopment and cognitive function exhibit reduced levels in mature but not nascent transcripts. We infer that the entire Top3b-Tdrd3 complex is essential for normal brain function, and that defective post-transcriptional regulation could contribute to cognitive impairment and psychiatric disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University
| | | | - Mark Mattson
- Department of Neuroscience, Johns Hopkins University School of Medicine
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16
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Agarwal V, Kelley DR. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 2022; 23:245. [PMID: 36419176 PMCID: PMC9684954 DOI: 10.1186/s13059-022-02811-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more precise identification of variants that perturb gene expression through post-transcriptional gene regulatory mechanisms. RESULTS We establish a compendium of 39 human and 27 mouse transcriptome-wide mRNA decay rate datasets. A meta-analysis of these data identified a prevalence of technical noise and measurement bias, induced partially by the underlying experimental strategy. Correcting for these biases allowed us to derive more precise, consensus measurements of half-life which exhibit enhanced consistency between species. We trained substantially improved statistical models based upon genetic and biochemical features to better predict half-life and characterize the factors molding it. Our state-of-the-art model, Saluki, is a hybrid convolutional and recurrent deep neural network which relies only upon an mRNA sequence annotated with coding frame and splice sites to predict half-life (r=0.77). The key novel principle learned by Saluki is that the spatial positioning of splice sites, codons, and RNA-binding motifs within an mRNA is strongly associated with mRNA half-life. Saluki predicts the impact of RNA sequences and genetic mutations therein on mRNA stability, in agreement with functional measurements derived from massively parallel reporter assays. CONCLUSIONS Our work produces a more robust ground truth for transcriptome-wide mRNA half-lives in mammalian cells. Using these revised measurements, we trained Saluki, a model that is over 50% more accurate in predicting half-life from sequence than existing models. Saluki succinctly captures many of the known determinants of mRNA half-life and can be rapidly deployed to predict the functional consequences of arbitrary mutations in the transcriptome.
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Affiliation(s)
- Vikram Agarwal
- grid.497059.6Calico Life Sciences LLC, South San Francisco, CA 94080 USA ,grid.417555.70000 0000 8814 392XPresent Address: mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA 02451 USA
| | - David R. Kelley
- grid.497059.6Calico Life Sciences LLC, South San Francisco, CA 94080 USA
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17
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Flores BCT, Chawla S, Ma N, Sanada C, Kujur PK, Yeung R, Bellon MB, Hukari K, Fowler B, Lynch M, Chinen LTD, Ramalingam N, Sengupta D, Jeffrey SS. Microfluidic live tracking and transcriptomics of cancer-immune cell doublets link intercellular proximity and gene regulation. Commun Biol 2022; 5:1231. [DOI: 10.1038/s42003-022-04205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 11/01/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractCell–cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell–cell interactions. We track the temporal variations in natural killer—triple-negative breast cancer cell distances and compare them with terminal cellular transcriptome profiles. The results show the time-bound activities of regulatory modules and allude to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live-cell interactions at doublet resolution. Together, our findings highlight the use of our approach across different cancers and cell types.
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18
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Kwak Y, Daly CWP, Fogarty EA, Grimson A, Kwak H. Dynamic and widespread control of poly(A) tail length during macrophage activation. RNA (NEW YORK, N.Y.) 2022; 28:947-971. [PMID: 35512831 PMCID: PMC9202586 DOI: 10.1261/rna.078918.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
The poly(A) tail enhances translation and transcript stability, and tail length is under dynamic control during cell state transitions. Tail regulation plays essential roles in translational timing and fertilization in early development, but poly(A) tail dynamics have not been fully explored in post-embryonic systems. Here, we examined the landscape and impact of tail length control during macrophage activation. Upon activation, more than 1500 mRNAs, including proinflammatory genes, underwent distinctive changes in tail lengths. Increases in tail length correlated with mRNA levels regardless of transcriptional activity, and many mRNAs that underwent tail extension encode proteins necessary for immune function and post-transcriptional regulation. Strikingly, we found that ZFP36, whose protein product destabilizes target transcripts, undergoes tail extension. Our analyses indicate that many mRNAs undergoing tail lengthening are, in turn, degraded by elevated levels of ZFP36, constituting a post-transcriptional feedback loop that ensures transient regulation of transcripts integral to macrophage activation. Taken together, this study establishes the complexity, relevance, and widespread nature of poly(A) tail dynamics, and the resulting post-transcriptional regulation during macrophage activation.
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Affiliation(s)
- Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Ciarán W P Daly
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, New York 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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19
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Chou SP, Alexander AK, Rice EJ, Choate LA, Danko CG. Genetic dissection of the RNA polymerase II transcription cycle. eLife 2022; 11:78458. [PMID: 35775732 PMCID: PMC9286732 DOI: 10.7554/elife.78458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here, we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate DNA sequence, including both known and novel DNA sequence motifs, as key determinants of the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to Brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
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Affiliation(s)
- Shao-Pei Chou
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Adriana K Alexander
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Edward J Rice
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Lauren A Choate
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
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20
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Su S, Xue Y, Sharov A, Zhang Y, Lee SK, Martindale J, Li W, Ku WL, Zhao K, De S, Shen W, Sen P, Gorospe M, Xu D, Wang W. A dual-activity topoisomerase complex regulates mRNA translation and turnover. Nucleic Acids Res 2022; 50:7013-7033. [PMID: 35748872 PMCID: PMC9262614 DOI: 10.1093/nar/gkac538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/06/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation-enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Weidong Wang
- To whom correspondence should be addressed. Tel: +1 410 454 8418; Fax: +1 410 558 8331.
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21
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Todero JE, Koch-Laskowski K, Shi Q, Kanke M, Hung YH, Beck R, Styblo M, Sethupathy P. Candidate master microRNA regulator of arsenic-induced pancreatic beta cell impairment revealed by multi-omics analysis. Arch Toxicol 2022; 96:1685-1699. [PMID: 35314868 PMCID: PMC9095563 DOI: 10.1007/s00204-022-03263-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/17/2022] [Indexed: 02/05/2023]
Abstract
Arsenic is a pervasive environmental toxin that is listed as the top priority for investigation by the Agency for Toxic Substance and Disease Registry. While chronic exposure to arsenic is associated with type 2 diabetes (T2D), the underlying mechanisms are largely unknown. We have recently demonstrated that arsenic treatment of INS-1 832/13 pancreatic beta cells impairs glucose-stimulated insulin secretion (GSIS), a T2D hallmark. We have also shown that arsenic alters the microRNA profile of beta cells. MicroRNAs have a well-established post-transcriptional regulatory role in both normal beta cell function and T2D pathogenesis. We hypothesized that there are microRNA master regulators that shape beta cell gene expression in pathways pertinent to GSIS after exposure to arsenicals. To test this hypothesis, we first treated INS-1 832/13 beta cells with either inorganic arsenic (iAsIII) or monomethylarsenite (MAsIII) and confirmed GSIS impairment. We then performed multi-omic analysis using chromatin run-on sequencing, RNA-sequencing, and small RNA-sequencing to define profiles of transcription, gene expression, and microRNAs, respectively. Integrating across these data sets, we first showed that genes downregulated by iAsIII treatment are enriched in insulin secretion and T2D pathways, whereas genes downregulated by MAsIII treatment are enriched in cell cycle and critical beta cell maintenance factors. We also defined the genes that are subject primarily to post-transcriptional control in response to arsenicals and demonstrated that miR-29a is the top candidate master regulator of these genes. Our results highlight the importance of microRNAs in arsenical-induced beta cell dysfunction and reveal both shared and unique mechanisms between iAsIII and MAsIII.
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Affiliation(s)
- Jenna E Todero
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kieran Koch-Laskowski
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rowan Beck
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miroslav Styblo
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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22
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Coordination of mitochondrial and nuclear gene expression regulation in health, evolution and disease. CURRENT OPINION IN PHYSIOLOGY 2022. [DOI: 10.1016/j.cophys.2022.100554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Moqtaderi Z, Geisberg JV, Struhl K. A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast. Proc Natl Acad Sci U S A 2022; 119:e2121488119. [PMID: 35058367 PMCID: PMC8794773 DOI: 10.1073/pnas.2121488119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/18/2021] [Indexed: 12/20/2022] Open
Abstract
Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and messenger RNA (mRNA) turnover in the cytoplasm. On a global basis, same-gene 3' mRNA isoforms with twofold or greater differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of 2. In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3' mRNA isoform. This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested. These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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24
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Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics 2021; 37:4727-4736. [PMID: 34382072 PMCID: PMC8665767 DOI: 10.1093/bioinformatics/btab582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Motivation Quantification of isoform abundance has been extensively studied at the mature RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Results We address this problem with a new computational method called Deconvolution of Expression for Nascent RNA-sequencing data (DENR), which models nascent RNA-sequencing read-counts as a mixture of user-provided isoforms. The baseline algorithm is enhanced by machine-learning predictions of active transcription start sites and an adjustment for the typical ‘shape profile’ of read-counts along a transcription unit. We show that DENR outperforms simple read-count-based methods for estimating gene and isoform abundances, and that transcription of multiple pre-RNA isoforms per gene is widespread, with frequent differences between cell types. In addition, we provide evidence that a majority of human isoform diversity derives from primary transcription rather than from post-transcriptional processes. Availability and implementation DENR and nascentRNASim are freely available at https://github.com/CshlSiepelLab/DENR (version v1.0.0) and https://github.com/CshlSiepelLab/nascentRNASim (version v0.3.0). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Shushan Toneyan
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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25
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Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M. One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife 2021; 10:59303. [PMID: 33594971 PMCID: PMC7932693 DOI: 10.7554/elife.59303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
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Affiliation(s)
| | | | | | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Daniele Peroni
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Romina Belli
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jacopo Zasso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
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