1
|
Nadimpalli HP, Katsioudi G, Arpa ES, Chikhaoui L, Arpat AB, Liechti A, Palais G, Tessmer C, Hofmann I, Galy B, Gatfield D. Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms. Genome Biol 2024; 25:128. [PMID: 38773499 PMCID: PMC11106963 DOI: 10.1186/s13059-024-03270-2] [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: 01/12/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Cellular iron homeostasis is regulated by iron regulatory proteins (IRP1 and IRP2) that sense iron levels (and other metabolic cues) and modulate mRNA translation or stability via interaction with iron regulatory elements (IREs). IRP2 is viewed as the primary regulator in the liver, yet our previous datasets showing diurnal rhythms for certain IRE-containing mRNAs suggest a nuanced temporal control mechanism. The purpose of this study is to gain insights into the daily regulatory dynamics across IRE-bearing mRNAs, specific IRP involvement, and underlying systemic and cellular rhythmicity cues in mouse liver. RESULTS We uncover high-amplitude diurnal oscillations in the regulation of key IRE-containing transcripts in the liver, compatible with maximal IRP activity at the onset of the dark phase. Although IRP2 protein levels also exhibit some diurnal variations and peak at the light-dark transition, ribosome profiling in IRP2-deficient mice reveals that maximal repression of target mRNAs at this timepoint still occurs. We further find that diurnal regulation of IRE-containing mRNAs can continue in the absence of a functional circadian clock as long as feeding is rhythmic. CONCLUSIONS Our findings suggest temporally controlled redundancy in IRP activities, with IRP2 mediating regulation of IRE-containing transcripts in the light phase and redundancy, conceivably with IRP1, at dark onset. Moreover, we highlight the significance of feeding-associated signals in driving rhythmicity. Our work highlights the dynamic nature and regulatory complexity in a metabolic pathway that had previously been considered well-understood.
Collapse
Affiliation(s)
| | - Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Enes Salih Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lies Chikhaoui
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Gaël Palais
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Claudia Tessmer
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Ilse Hofmann
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
| |
Collapse
|
2
|
Lei T, Chang Y, Yao C, Zhang H. A systematic evaluation of computational methods for predicting translated non-canonical ORFs from ribosome profiling data. J Genet Genomics 2024; 51:105-108. [PMID: 37673174 DOI: 10.1016/j.jgg.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Affiliation(s)
- Tianyu Lei
- College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yue Chang
- College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Chao Yao
- Cuiying Honors College, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hong Zhang
- College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China.
| |
Collapse
|
3
|
Shi Y, Guo Z, Liu F, Pan S, Gao D, Zhou S, Liu Z, Wang F, Liu D, Liu Z. Analysis of potential biomarkers for diabetic kidney disease based on single-cell RNA-sequencing integrated with a single-cell sequencing assay for transposase-accessible chromatin. Aging (Albany NY) 2023; 15:10681-10704. [PMID: 37827693 PMCID: PMC10599739 DOI: 10.18632/aging.205107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Diabetic kidney disease (DKD) is a renal microvascular disease caused by hyperglycemia that involves metabolic remodeling, oxidative stress, inflammation, and other factors. The mechanism is complex and not fully unraveled. We performed an integrated single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) and single-cell RNA-sequencing (scRNA-seq) analyses of kidneys from db/db and db/m mice to identify differential open chromatin regions and gene expression, particularly in genes related to proximal tubular reabsorption and secretion. We identified 9,776 differentially expressed genes (DEGs) and 884 cell type-specific transcription factors (TFs) across 15 cell types. Glucose and lipid transporters, and TFs related to the circadian rhythm in the proximal tubules had significantly higher expression in db/db mice than in db/m mice (P<0.01). Crosstalk between podocytes and tubular cells in the proximal tubules was enhanced, and renal inflammation, oxidative stress, and fibrosis pathways were activated in db/db mice. Western blotting and immunohistochemical staining results showed that Wfdc2 expression in the urine and kidneys of DKD patients was higher than that in non-diabetic kidney disease (NDKD) controls. The revealed landscape of chromatin accessibility and transcriptional profiles in db/db mice provide insights into the pathological mechanism of DKD.
Collapse
Affiliation(s)
- Yan Shi
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zuishuang Guo
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Fengxun Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Shaokang Pan
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Dan Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Sijie Zhou
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zhenjie Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Feng Wang
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Department of Nephrology, Shanghai Eighth People’s Hospital, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, P.R. China
| | - Dongwei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zhangsuo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| |
Collapse
|
4
|
Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [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: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
Collapse
Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| |
Collapse
|
5
|
Yanaizu M, Adachi H, Araki M, Kontani K, Kino Y. Translational regulation and protein-coding capacity of the 5' untranslated region of human TREM2. Commun Biol 2023; 6:616. [PMID: 37291187 PMCID: PMC10250343 DOI: 10.1038/s42003-023-04998-6] [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: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
TREM2 is a transmembrane receptor expressed in microglia and macrophages. Elevated TREM2 levels in these cells are associated with age-related pathological conditions, including Alzheimer's disease. However, the regulatory mechanism underlying the protein expression of TREM2 remains unclear. In this study, we uncover the role of the 5' untranslated region (5'-UTR) of human TREM2 in translation. An upstream start codon (uAUG) in the 5'-UTR of TREM2 is specific to some primates, including humans. The expression of the conventional TREM2 protein, starting from the downstream AUG (dTREM2), is repressed by the 5'-UTR in a uAUG-mediated manner. We also detect a TREM2 protein isoform starting from uAUG (uTREM2) that is largely degraded by proteasomes. Finally, the 5'-UTR is essential for the downregulation of dTREM2 expression in response to amino acid starvation. Collectively, our study identifies a species-specific regulatory role of the 5'-UTR in TREM2 translation.
Collapse
Affiliation(s)
- Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Haruka Adachi
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
| |
Collapse
|
6
|
Bowazolo C, Morse D. Insights into daily metabolic changes of the dinoflagellate Lingulodinium from ribosome profiling. Cell Cycle 2023; 22:1343-1352. [PMID: 37125841 PMCID: PMC10228409 DOI: 10.1080/15384101.2023.2206771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 05/02/2023] Open
Abstract
The dinoflagellate Lingulodinium specializes its metabolism to perform different tasks better at specific times of day. For example, cells are specialized for photosynthesis during the day and bioluminescence and cell division at night. These rhythms are circadian as they are controlled by an endogenous circadian clock whose mechanism is currently unknown. Despite this, the metabolic rhythms follow coordinated changes in gene expression that occur at a translational level. These changes are revealed by ribosome profiling, a surrogate measure of protein synthesis rates in vivo. Lingulodinium regulates the synthesis rate of over three thousand transcripts. Peak synthesis rates for the different transcripts are clustered around three different times over a light/dark cycle. Furthermore, transcripts involved in the same metabolic process are coordinately regulated. We review the basic principles underlying the correlation of coordinated translation of cell metabolic pathway enzymes with known circadian rhythms, and offer examples where previously unsuspected rhythms are suggested by synchronized changes in gene expression.
Collapse
Affiliation(s)
- Carl Bowazolo
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| |
Collapse
|
7
|
Anisimova AS, Kolyupanova NM, Makarova NE, Egorov AA, Kulakovskiy IV, Dmitriev SE. Human Tissues Exhibit Diverse Composition of Translation Machinery. Int J Mol Sci 2023; 24:ijms24098361. [PMID: 37176068 PMCID: PMC10179197 DOI: 10.3390/ijms24098361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas, we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g., PABP and eRF3 paralogs, eIF2B and eIF3 subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified the testis and brain as organs with the most diverged expression of translation-associated genes.
Collapse
Affiliation(s)
- Aleksandra S Anisimova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalia M Kolyupanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artyom A Egorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| |
Collapse
|
8
|
Hsu C, He Z, Le Henaff C, Partridge NC. Differential effects of parathyroid hormone, parathyroid hormone-related protein, and abaloparatide on collagen 1 expression by mouse cementoblasts and mouse tooth root density. Am J Orthod Dentofacial Orthop 2023; 163:378-388.e1. [PMID: 36543659 PMCID: PMC9991996 DOI: 10.1016/j.ajodo.2021.12.023] [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: 08/01/2020] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Parathyroid hormone (PTH) plays an important role in maintaining mineral homeostasis by regulating calcium and phosphate levels. Clinical trials have shown that peptides of PTH (1-34), PTH-related protein (PTHrP 1-36), and the new peptide modeled on PTHrP, abaloparatide, can have different anabolic effects on osteoporotic subjects, but the underlying mechanisms are still unclear. The prevalence of moderate and major gingival recession has been shown to be higher in postmenopausal women with osteoporosis. In addition, there is a significant association between osteoporosis and tooth loss. METHODS We investigated the actions of these peptides on the cementoblasts and teeth of mice. The murine cementoblast line, OCCM-30, known to express collagen I (Col1a1), was treated with intermittent PTH (1-34), PTHrP (1-36), or abaloparatide for 6 h/d for 3 days. Microcomputed tomography was performed on the teeth of mice receiving daily injections of phosphate-buffered saline, PTH (1-34), or abaloparatide. Statistical differences were analyzed by a 2-way or 1-way analysis of variance followed by a Tukey's post-hoc test. Results are expressed as mean ± standard deviation, and P <0.05 was considered significant. RESULTS Gene expression showed regulation of Bsp, Col1a1, Opg, Rankl, and Mmp13 by the 3 peptides in these cells. Western blots revealed that after intermittent treatment for 3 days, PTH (1-34) caused an increase in COL1A1 protein immediately after treatment. In contrast, abaloparatide showed a latent effect in increasing COL1A1 protein 18 hours after treatment. PTHrP had no effect on COL1A1 expression. Immunofluorescence confirmed the same result as the Western blots. Microcomputed tomography of teeth showed PTH (1-34) injections increased molar root mineral density in mice, whereas abaloparatide increased density in roots of incisors and molars. CONCLUSIONS This study reveals the differential anabolic effects of intermittent PTH (1-34), PTHrP (1-36), and abaloparatide on cementoblasts, as revealed by COL1A1 expression and root mineral density. Abaloparatide may be a potential therapeutic approach for achieving improved cementogenesis.
Collapse
Affiliation(s)
- Chingyun Hsu
- Formerly, Departments of Molecular Pathobiology and Orthodontics, New York University College of Dentistry, New York, NY; currently, Department of Orthodontics, Oregon Health Sciences University, Portland, OR
| | - Zhiming He
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY
| | - Carole Le Henaff
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY
| | - Nicola C Partridge
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY.
| |
Collapse
|
9
|
Cordes H, Rapp H. Gene expression databases for physiologically based pharmacokinetic modeling of humans and animal species. CPT Pharmacometrics Syst Pharmacol 2023; 12:311-319. [PMID: 36715173 PMCID: PMC10014062 DOI: 10.1002/psp4.12904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 01/31/2023] Open
Abstract
In drug research, developing a sound understanding of the key mechanistic drivers of pharmacokinetics (PK) for new molecular entities is essential for human PK and dose predictions. Here, characterizing the absorption, distribution, metabolism, and excretion (ADME) processes is crucial for a mechanistic understanding of the drug-target and drug-body interactions. Sufficient knowledge on ADME processes enables reliable interspecies and human PK estimations beyond allometric scaling. The physiologically based PK (PBPK) modeling framework allows the explicit consideration of organ-specific ADME processes. The sum of all passive and active ADME processes results in the observed plasma PK. Gene expression information can be used as surrogate for protein abundance and activity within PBPK models. The absolute and relative expression of ADME genes can differ between species and strains. This is affecting both, the PK and pharmacodynamics and is therefore posing a challenge for the extrapolation from preclinical findings to humans. We developed an automated workflow that generates whole-body gene expression databases for humans and other species relevant in drug development, animal health, nutritional sciences, and toxicology. Solely, bulk RNA-seq data curated and provided by the Swiss Institute of Bioinformatics from healthy, normal, and untreated primary tissue samples were considered as an unbiased reference of normal gene expression. The databases are interoperable with the Open Systems Pharmacology Suite (PK-Sim and MoBi) and enable seamless access to a central source of curated cross-species gene expression data. This will increase data transparency, increase reliability and reproducibility of PBPK model simulations, and accelerate mechanistic PBPK model development in the future.
Collapse
Affiliation(s)
- Henrik Cordes
- Drug Metabolism & Pharmacokinetics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt am Main, Germany
| | - Hermann Rapp
- Research Drug Metabolism & Pharmacokinetics, Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| |
Collapse
|
10
|
Miyake T, Inoue Y, Shao X, Seta T, Aoki Y, Nguyen Pham KT, Shichino Y, Sasaki J, Sasaki T, Ikawa M, Yamaguchi Y, Okamura H, Iwasaki S, Doi M. Minimal upstream open reading frame of Per2 mediates phase fitness of the circadian clock to day/night physiological body temperature rhythm. Cell Rep 2023; 42:112157. [PMID: 36882059 DOI: 10.1016/j.celrep.2023.112157] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/29/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Body temperature in homeothermic animals does not remain constant but displays a regular circadian fluctuation within a physiological range (e.g., 35°C-38.5°C in mice), constituting a fundamental systemic signal to harmonize circadian clock-regulated physiology. Here, we find the minimal upstream open reading frame (uORF) encoded by the 5' UTR of the mammalian core clock gene Per2 and reveal its role as a regulatory module for temperature-dependent circadian clock entrainment. A temperature shift within the physiological range does not affect transcription but instead increases translation of Per2 through its minimal uORF. Genetic ablation of the Per2 minimal uORF and inhibition of phosphoinositide-3-kinase, lying upstream of temperature-dependent Per2 protein synthesis, perturb the entrainment of cells to simulated body temperature cycles. At the organismal level, Per2 minimal uORF mutant skin shows delayed wound healing, indicating that uORF-mediated Per2 modulation is crucial for optimal tissue homeostasis. Combined with transcriptional regulation, Per2 minimal uORF-mediated translation may enhance the fitness of circadian physiology.
Collapse
Affiliation(s)
- Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Yuichi Inoue
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Xinyan Shao
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Takehito Seta
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Yuto Aoki
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Khanh Tien Nguyen Pham
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Junko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyō-ku, Tokyo 113-8510, Japan; Department of Cellular and Molecular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyō-ku, Tokyo 113-8510, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyō-ku, Tokyo 113-8510, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshiaki Yamaguchi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Hitoshi Okamura
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan; Division of Physiology and Neurobiology, Graduate School of Medicine, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto 606-8501, Japan.
| |
Collapse
|
11
|
Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [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] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
Collapse
Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
| |
Collapse
|
12
|
Song Y, Zhang Y, Qu Q, Zhang X, Lu T, Xu J, Ma W, Zhu M, Huang C, Xiong R. Biomaterials based on hyaluronic acid, collagen and peptides for three-dimensional cell culture and their application in stem cell differentiation. Int J Biol Macromol 2023; 226:14-36. [PMID: 36436602 DOI: 10.1016/j.ijbiomac.2022.11.213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
In recent decades, three-dimensional (3D) cell culture technologies have been developed rapidly in the field of tissue engineering and regeneration, and have shown unique advantages and great prospects in the differentiation of stem cells. Herein, the article reviews the progress and advantages of 3D cell culture technologies in the field of stem cell differentiation. Firstly, 3D cell culture technologies are divided into two main categories: scaffoldless and scaffolds. Secondly, the effects of hydrogels scaffolds and porous scaffolds on stem cell differentiation in the scaffold category were mainly reviewed. Among them, hydrogels scaffolds are divided into natural hydrogels and synthetic hydrogels. Natural materials include polysaccharides, proteins, and their derivatives, focusing on hyaluronic acid, collagen and polypeptides. Synthetic materials mainly include polyethylene glycol (PEG), polyacrylic acid (PAA), polyvinyl alcohol (PVA), etc. In addition, since the preparation techniques have a large impact on the properties of porous scaffolds, several techniques for preparing porous scaffolds based on different macromolecular materials are reviewed. Finally, the future prospects and challenges of 3D cell culture in the field of stem cell differentiation are reviewed. This review will provide a useful guideline for the selection of materials and techniques for 3D cell culture in stem cell differentiation.
Collapse
Affiliation(s)
- Yuanyuan Song
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Yingying Zhang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Qingli Qu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Xiaoli Zhang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Tao Lu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Jianhua Xu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Wenjing Ma
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Miaomiao Zhu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Chaobo Huang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China.
| | - Ranhua Xiong
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China.
| |
Collapse
|
13
|
Schaefer M, Nabih A, Spies D, Hermes V, Bodak M, Wischnewski H, Stalder P, Ngondo RP, Liechti LA, Sajic T, Aebersold R, Gatfield D, Ciaudo C. Global and precise identification of functional
miRNA
targets in
mESCs
by integrative analysis. EMBO Rep 2022; 23:e54762. [PMID: 35899551 PMCID: PMC9442311 DOI: 10.15252/embr.202254762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject to miRNA‐mediated regulation, but it remains largely unknown which fraction of these interactions are functional in a specific cellular context. Here, we integrate transcriptome data from a set of miRNA‐depleted mouse embryonic stem cell (mESC) lines with published miRNA interaction predictions and AGO‐binding profiles. Using this integrative approach, combined with molecular validation data, we present evidence that < 10% of expressed genes are functionally and directly regulated by miRNAs in mESCs. In addition, analyses of the stem cell‐specific miR‐290‐295 cluster target genes identify TFAP4 as an important transcription factor for early development. The extensive datasets developed in this study will support the development of improved predictive models for miRNA‐mRNA functional interactions.
Collapse
Affiliation(s)
- Moritz Schaefer
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Amena Nabih
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Daniel Spies
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Maxime Bodak
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Harry Wischnewski
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Tatjana Sajic
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - Ruedi Aebersold
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - David Gatfield
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| |
Collapse
|
14
|
Dong Y, Cheng L, Zhao Y. Resetting the circadian clock of Alzheimer’s mice via GLP-1 injection combined with time-restricted feeding. Front Physiol 2022; 13:911437. [PMID: 36148311 PMCID: PMC9487156 DOI: 10.3389/fphys.2022.911437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythm disturbances are the most common symptoms during the early onset of AD. Circadian rhythm disorders aggravate the deposition of amyloid plaques in the brains of AD patients. Therefore, improving the circadian rhythm of AD patients might slow down the pathological development of neurodegeneration. Circadian regulation is driven by a master clock in suprachiasmatic nuclei (SCN) and peripheral clock located in peripheral organs. The rhythmic feeding–fasting cycle has been proved to dominant cue to entrain peripheral clocks. We hypothesized that dietary intervention to a certain period of time during the dark phase might entrain the clock and reset the disrupted daily rhythms of AD mice. In this study, exogenous glucagon-like peptide-1 (GLP-1) treatment, time-restricted feeding (TRF), and the combination were used to examine the effect of overall circadian rhythm and neurodegenerative pathogenesis of transgenic AD mice. It was confirmed that GLP-1 administration together with time-restricted feeding improves circadian rhythm of 5 × FAD mice including the physiological rhythm of the activity–rest cycle, feeding–fasting cycle, core body temperature, and hormone secretion. Furthermore, GLP-1 and TRF treatments improved the diurnal metabolic homeostasis, spatial cognition, and learning of 5 × FAD mice. The aberrant expression of clock genes, including Baml1, Clock, and Dbp, was improved in the hypothalamus, and pathological changes in neurodegeneration and neuroinflammation were also observed in AD mice with dual treatment.
Collapse
Affiliation(s)
- Yanqiong Dong
- Department of Basic Medicine Sciences, School of Basic Medical Sciences, Dali University, Dali, Yunnan, China
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, China
| | - Le Cheng
- Department of Basic Medicine Sciences, School of Basic Medical Sciences, Dali University, Dali, Yunnan, China
- BGI-Yunnan, BGI-Shenzhen, Kunming, Yunnan, China
| | - Yingying Zhao
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, China
- *Correspondence: Yingying Zhao,
| |
Collapse
|
15
|
Orchestrated translation specializes dinoflagellate metabolism three times per day. Proc Natl Acad Sci U S A 2022; 119:e2122335119. [PMID: 35858433 PMCID: PMC9335273 DOI: 10.1073/pnas.2122335119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many cells specialize for different metabolic tasks at different times over their normal ZT cycle by changes in gene expression. However, in most cases, circadian gene expression has been assessed at the mRNA accumulation level, which may not faithfully reflect protein synthesis rates. Here, we use ribosome profiling in the dinoflagellate Lingulodinium polyedra to identify thousands of transcripts showing coordinated translation. All of the components in carbon fixation are concurrently regulated at ZT0, predicting the known rhythm of carbon fixation, and many enzymes involved in DNA replication are concurrently regulated at ZT12, also predicting the known rhythm in this process. Most of the enzymes in glycolysis and the TCA cycle are also regulated together, suggesting rhythms in these processes as well. Surprisingly, a third cluster of transcripts show peak translation at approximately ZT16, and these transcripts encode enzymes involved in transcription, translation, and amino acid biosynthesis. The latter has physiological consequences, as measured free amino acid levels increase at night and thus represent a previously undocumented rhythm in this model. Our results suggest that ribosome profiling may be a more accurate predictor of changed metabolic state than transcriptomics.
Collapse
|
16
|
Eisen TJ, Li JJ, Bartel DP. The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation. RNA (NEW YORK, N.Y.) 2022; 28:808-831. [PMID: 35273099 PMCID: PMC9074895 DOI: 10.1261/rna.079046.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), considering the interplay between TE, mRNA poly(A)-tail lengths, microRNAs, and neuronal activation. In neurons and brain tissues, TE correlates with tail length, and a few dozen mRNAs appear to undergo cytoplasmic polyadenylation upon light or chemical stimulation. However, the correlation between TE and tail length is modest, explaining <5% of TE variance, and even this modest relationship diminishes when accounting for other mRNA features. Thus, tail length appears to affect TE only minimally. Accordingly, miRNAs, which accelerate deadenylation of their mRNA targets, primarily influence target mRNA levels, with no detectable effect on either steady-state tail lengths or TE. Larger correlates with TE include codon composition and predicted mRNA folding energy. When combined in a model, the identified correlates explain 38%-45% of TE variance. These results provide a framework for considering the relative impact of factors that contribute to translational control in neurons. They indicate that when examined in bulk, translational control in neurons largely resembles that of other types of post-embryonic cells. Thus, detection of more specialized control might require analyses that can distinguish translation occurring in neuronal processes from that occurring in cell bodies.
Collapse
Affiliation(s)
- Timothy J Eisen
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Jingyi Jessica Li
- Department of Statistics, Department of Biostatistics, Department of Computational Medicine, and Department of Human Genetics, University of California, Los Angeles, California 90095, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
17
|
Terrey M, Adamson SI, Chuang JH, Ackerman SL. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology. eLife 2021; 10:e66904. [PMID: 33899734 PMCID: PMC8075583 DOI: 10.7554/elife.66904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD), and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical in mice for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant mouse embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, including mTOR activation, the translatome and mouse cerebellar development were observed upon deletion of the NMD factor Upf2. Our data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.
Collapse
Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
| |
Collapse
|
18
|
Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Collapse
Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
19
|
Terrey M, Adamson SI, Gibson AL, Deng T, Ishimura R, Chuang JH, Ackerman SL. GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis. eLife 2020; 9:e62731. [PMID: 33186095 PMCID: PMC7665888 DOI: 10.7554/elife.62731] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of a tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here, we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant GTPases function in the same pathway to mitigate ribosome pausing. As observed in Gtpbp2-/- mice (Ishimura et al., 2016), GCN2-mediated activation of the integrated stress response (ISR) was apparent in the Gtpbp1-/- brain. We observed decreased mTORC1 signaling which increased neuronal death, whereas ISR activation was neuroprotective. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective elongation.
Collapse
Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Alana L Gibson
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Tianda Deng
- Division of Biological Sciences, Section of Molecular Biology, University of California, San DiegoSan DiegoUnited States
| | - Ryuta Ishimura
- The Jackson Laboratory for Mammalian GeneticsBar HarborUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| |
Collapse
|
20
|
Wang D, Yang J, Fan J, Chen W, Nikolic‐Paterson DJ, Li J. Omics technologies for kidney disease research. Anat Rec (Hoboken) 2020; 303:2729-2742. [PMID: 32592293 DOI: 10.1002/ar.24413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jiayi Yang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jinjin Fan
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | | | - Jinhua Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
- Shunde Women and Children Hospital, Guangdong Medical University Shunde Guangdong China
- The Second Clinical College, Guangdong Medical University Dongguan Guangdong China
- Department of Anatomy and Developmental BiologyMonash Biomedicine Discovery Institute, Monash University Clayton Victoria Australia
| |
Collapse
|
21
|
Multifaceted deregulation of gene expression and protein synthesis with age. Proc Natl Acad Sci U S A 2020; 117:15581-15590. [PMID: 32576685 DOI: 10.1073/pnas.2001788117] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis represents a major metabolic activity of the cell. However, how it is affected by aging and how this in turn impacts cell function remains largely unexplored. To address this question, herein we characterized age-related changes in both the transcriptome and translatome of mouse tissues over the entire life span. We showed that the transcriptome changes govern those in the translatome and are associated with altered expression of genes involved in inflammation, extracellular matrix, and lipid metabolism. We also identified genes that may serve as candidate biomarkers of aging. At the translational level, we uncovered sustained down-regulation of a set of 5'-terminal oligopyrimidine (5'-TOP) transcripts encoding protein synthesis and ribosome biogenesis machinery and regulated by the mTOR pathway. For many of them, ribosome occupancy dropped twofold or even more. Moreover, with age, ribosome coverage gradually decreased in the vicinity of start codons and increased near stop codons, revealing complex age-related changes in the translation process. Taken together, our results reveal systematic and multidimensional deregulation of protein synthesis, showing how this major cellular process declines with age.
Collapse
|
22
|
Castelo-Szekely V, Gatfield D. Emerging Roles of Translational Control in Circadian Timekeeping. J Mol Biol 2020; 432:3483-3497. [PMID: 32246961 DOI: 10.1016/j.jmb.2020.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/07/2023]
Abstract
A large part of mammalian physiology and behaviour shows regular daily variations. This temporal organisation is driven by the activity of an endogenous circadian clock, whose molecular basis consists of diurnal waves in gene expression. Circadian transcription is the major driver of these rhythms, yet post-transcriptional mechanisms, some of which occur in response to systemic cues and in a tissue-specific fashion, have central roles in ultimately establishing the oscillatory gene expression programme as well. Regulatory control that occurs at the level of translation is emerging as an important player in the generation and modulation of protein accumulation rhythms. As a mechanism, translation lies at a privileged position to integrate genetically encoded rhythmic signals with other, external and internal stimuli, including nutrient-derived cues. In this review, we summarise our current knowledge of how diurnal control of translation affects both bulk protein levels and gene-specific protein biosynthesis. We discuss mechanisms of regulation, in particular with regard to the complex interplay between circadian cycles and feeding/fasting cycles, as well as emerging roles for upstream open reading frames in clock control.
Collapse
Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland.
| |
Collapse
|
23
|
Gobet C, Weger BD, Marquis J, Martin E, Neelagandan N, Gachon F, Naef F. Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver. Proc Natl Acad Sci U S A 2020; 117:9630-9641. [PMID: 32295881 PMCID: PMC7196831 DOI: 10.1073/pnas.1918145117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) profiling to investigate the relations between translation elongation rates, (aminoacyl-) tRNA levels, and codon usage in mammals. We modeled codon-specific ribosome dwell times from ribosome profiling, considering codon pair interactions between ribosome sites. In mouse liver, the model revealed site- and codon-specific dwell times that differed from those in yeast, as well as pairs of adjacent codons in the P and A site that markedly slow down or speed up elongation. While translation efficiencies vary across diurnal time and feeding regimen, codon dwell times were highly stable and conserved in human. Measured tRNA levels correlated with codon usage and several tRNAs showed reduced aminoacylation, which was conserved in fasted mice. Finally, we uncovered that the longest codon dwell times could be explained by aminoacylation levels or high codon usage relative to tRNA abundance.
Collapse
Affiliation(s)
- Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Benjamin Dieter Weger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | | | - Eva Martin
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Nagammal Neelagandan
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | | | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland;
| |
Collapse
|
24
|
Cui H, Hu H, Zeng J, Chen T. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. BMC Bioinformatics 2019; 20:678. [PMID: 31861979 PMCID: PMC6923924 DOI: 10.1186/s12859-019-3244-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mapped reads to similar isoforms. Existing methods either discard the multiple mapped-reads, or allocate them randomly, or assign them proportionally according to transcript abundance estimated from RNA-seq data. Results Here we present DeepShape, an RNA-seq free computational method to estimate ribosome abundance of isoforms, and simultaneously compute their ribosome profiles using a deep learning model. Our simulation results demonstrate that DeepShape can provide more accurate estimations on both ribosome abundance and profiles when compared to state-of-the-art methods. We applied DeepShape to a set of Ribo-seq data from PC3 human prostate cancer cells with and without PP242 treatment. In the four cell invasion/metastasis genes that are translationally regulated by PP242 treatment, different isoforms show very different characteristics of translational efficiency and regulation patterns. Transcript level ribosome distributions were analyzed by “Codon Residence Index (CRI)” proposed in this study to investigate the relative speed that a ribosome moves on a codon compared to its synonymous codons. We observe consistent CRI patterns in PC3 cells. We found that the translation of several codons could be regulated by PP242 treatment. Conclusion In summary, we demonstrate that DeepShape can serve as a powerful tool for Ribo-seq data analysis.
Collapse
Affiliation(s)
- Hongfei Cui
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China.,DonLinks School of Economics and Management, University of Science and Technology Beijing, Beijing, China
| | - Hailin Hu
- School of Medicine, Tsinghua University, Beijing, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China.
| |
Collapse
|
25
|
Archakov AI, Aseev AL, Bykov VA, Grigoriev AI, Govorun VM, Ilgisonis EV, Ivanov YD, Ivanov VT, Kiseleva OI, Kopylov AT, Lisitsa AV, Mazurenko SN, Makarov AA, Naryzhny SN, Pleshakova TO, Ponomarenko EA, Poverennaya EV, Pyatnitskii MA, Sagdeev RZ, Skryabin KG, Zgoda VG. Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium. J Proteome Res 2019; 18:4206-4214. [PMID: 31599598 DOI: 10.1021/acs.jproteome.9b00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.
Collapse
Affiliation(s)
| | | | | | | | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine , Moscow 119435 , Russia
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| | - Vadim T Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow 117997 , Russia
| | | | | | | | - Sergey N Mazurenko
- Joint Institute for Nuclear Research , Dubna, Moscow region 141980 , Russia
| | | | | | | | | | | | | | - Renad Z Sagdeev
- International Tomography Center , Novosibirsk 630090 , Russia
| | - Konstantin G Skryabin
- The Federal Research Centre "Fundamentals of Biotechnology" , Moscow 119071 , Russia
| | - Victor G Zgoda
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| |
Collapse
|
26
|
Abstract
Numerous physiological functions exhibit substantial circadian oscillations. In the kidneys, renal plasma flow, the glomerular filtration rate and tubular reabsorption and/or secretion processes have been shown to peak during the active phase and decline during the inactive phase. These functional rhythms are driven, at least in part, by a self-sustaining cellular mechanism termed the circadian clock. The circadian clock controls different cellular functions, including transcription, translation and protein post-translational modifications (such as phosphorylation, acetylation and ubiquitylation) and degradation. Disruption of the circadian clock in animal models results in the loss of blood pressure control and substantial changes in the circadian pattern of water and electrolyte excretion in the urine. Kidney-specific suppression of the circadian clock in animals implicates both the intrinsic renal and the extrarenal circadian clocks in these pathologies. Alterations in the circadian rhythm of renal functions are associated with the development of hypertension, chronic kidney disease, renal fibrosis and kidney stones. Furthermore, renal circadian clocks might interfere with the pharmacokinetics and/or pharmacodynamics of various drugs and are therefore an important consideration in the treatment of some renal diseases or disorders.
Collapse
Affiliation(s)
- Dmitri Firsov
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland.
| | - Olivier Bonny
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland. .,Service of Nephrology, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.
| |
Collapse
|
27
|
Chowdhury D, Wang C, Lu AP, Zhu HL. Understanding Quantitative Circadian Regulations Are Crucial Towards Advancing Chronotherapy. Cells 2019; 8:cells8080883. [PMID: 31412622 PMCID: PMC6721722 DOI: 10.3390/cells8080883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/01/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022] Open
Abstract
Circadian rhythms have a deep impact on most aspects of physiology. In most organisms, especially mammals, the biological rhythms are maintained by the indigenous circadian clockwork around geophysical time (~24-h). These rhythms originate inside cells. Several core components are interconnected through transcriptional/translational feedback loops to generate molecular oscillations. They are tightly controlled over time. Also, they exert temporal controls over many fundamental physiological activities. This helps in coordinating the body’s internal time with the external environments. The mammalian circadian clockwork is composed of a hierarchy of oscillators, which play roles at molecular, cellular, and higher levels. The master oscillation has been found to be developed at the hypothalamic suprachiasmatic nucleus in the brain. It acts as the core pacemaker and drives the transmission of the oscillation signals. These signals are distributed across different peripheral tissues through humoral and neural connections. The synchronization among the master oscillator and tissue-specific oscillators offer overall temporal stability to mammals. Recent technological advancements help us to study the circadian rhythms at dynamic scale and systems level. Here, we outline the current understanding of circadian clockwork in terms of molecular mechanisms and interdisciplinary concepts. We have also focused on the importance of the integrative approach to decode several crucial intricacies. This review indicates the emergence of such a comprehensive approach. It will essentially accelerate the circadian research with more innovative strategies, such as developing evidence-based chronotherapeutics to restore de-synchronized circadian rhythms.
Collapse
Affiliation(s)
- Debajyoti Chowdhury
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Wang
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Ai-Ping Lu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Hai-Long Zhu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| |
Collapse
|
28
|
Li JJ, Chew GL, Biggin MD. Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes. Genome Biol 2019; 20:162. [PMID: 31399036 PMCID: PMC6689182 DOI: 10.1186/s13059-019-1761-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
Background General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood. Results Here, we show that these sequence features specify 42–81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25–60 nucleotide segments within mRNA 5′ regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5′ regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA. Conclusions Our work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell. Electronic supplementary material The online version of this article (10.1186/s13059-019-1761-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics, Department of Biomathematics, and Department of Human Genetics, University of California, Los Angeles, CA, 90095, USA.
| | - Guo-Liang Chew
- Computational Biology Program, Public Health Sciences and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Mark Douglas Biggin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94708, USA.
| |
Collapse
|
29
|
Abstract
PURPOSE OF REVIEW The purpose of this review is to provide a brief summary about the current state of knowledge regarding the circadian rhythm in the regulation of normal renal function. RECENT FINDINGS There is a lack of information regarding how the circadian clock mechanisms may contribute to the development of diabetic kidney disease. We discuss recent findings regarding mechanisms that are established in diabetic kidney disease and are known to be linked to the circadian clock as possible connections between these two areas. Here, we hypothesize various mechanisms that may provide a link between the clock mechanism and kidney disease in diabetes based on available data from humans and rodent models.
Collapse
Affiliation(s)
- Olanrewaju A Olaoye
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, 1600 SW Archer Road, Box 100224, Gainesville, FL, 32610, USA
| | - Sarah H Masten
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, 1600 SW Archer Road, Box 100224, Gainesville, FL, 32610, USA
| | - Rajesh Mohandas
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, 1600 SW Archer Road, Box 100224, Gainesville, FL, 32610, USA
- North Florida/South Georgia Veterans Health System, Gainesville, FL, USA
| | - Michelle L Gumz
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, 1600 SW Archer Road, Box 100224, Gainesville, FL, 32610, USA.
- North Florida/South Georgia Veterans Health System, Gainesville, FL, USA.
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
30
|
Castelo-Szekely V, De Matos M, Tusup M, Pascolo S, Ule J, Gatfield D. Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Res 2019; 47:5193-5209. [PMID: 30982898 PMCID: PMC6547434 DOI: 10.1093/nar/gkz261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 02/05/2023] Open
Abstract
The non-canonical initiation factor DENR promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). Moreover, DENR depletion shortens circadian period in mouse fibroblasts, suggesting involvement of uORF usage and reinitiation in clock regulation. To identify DENR-regulated translation events transcriptome-wide and, in particular, specific core clock transcripts affected by this mechanism, we have used ribosome profiling in DENR-deficient NIH3T3 cells. We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract 5' UTR features predictive of DENR dependence. Among core clock genes, we identified Clock as a DENR target. Using Clock 5' UTR mutants, we mapped the specific uORF through which DENR acts to regulate CLOCK protein biosynthesis. Notably, these experiments revealed an alternative downstream start codon, likely representing the bona fide CLOCK N-terminus. Our findings provide insights into uORF-mediated translational regulation that can regulate the mammalian circadian clock and gene expression at large.
Collapse
Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Jernej Ule
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| |
Collapse
|
31
|
Wang S, Chen Y. Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize. FRONTIERS IN PLANT SCIENCE 2019; 10:534. [PMID: 31156655 PMCID: PMC6530396 DOI: 10.3389/fpls.2019.00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/05/2019] [Indexed: 06/01/2023]
Abstract
Plant genomes are extensively shaped by various types of gene duplication. However, in this active area of investigation, the vast majority of studies focus on the sequence and transcription of duplicate genes, leaving open the question of how translational regulation impacts the expression and evolution of duplicate genes. We explored this issue by analyzing the ribo- and mRNA-seq data sets across six tissue types and stress conditions in Arabidopsis thaliana and maize (Zea mays). We dissected the relative contributions of transcriptional and translational regulation to the divergence in the abundance of ribosome footprint (RF) for different types of duplicate genes. We found that the divergence in RF abundance was largely programmed at the transcription level and that translational regulation plays more of a modulatory role. Intriguingly, translational regulation is characterized by its strong directionality, with the divergence in translational efficiency (TE) globally counteracting the divergence in mRNA abundance, indicating partial buffering of the transcriptional divergence between paralogs by translational regulation. Divergence in TE was associated with several sequence features. The faster-evolving copy in a duplicate pair was more likely to show lower RF abundance, which possibly results from relaxed purifying selection compared with its paralog. A considerable proportion of duplicates displayed differential TE across tissue types and stress conditions, most of which were enriched in photosynthesis, energy production, and translation-related processes. Additionally, we constructed a database TDPDG-DB (http://www.plantdupribo.tk), providing an online platform for data exploration. Overall, our study illustrates the roles of translational regulation in fine-tuning duplicate gene expression in plants.
Collapse
Affiliation(s)
- Sishuo Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Department of Botany, Faculty of Science, The University of British Columbia, Vancouver, BC, Canada
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
32
|
Egorov AA, Sakharova EA, Anisimova AS, Dmitriev SE, Gladyshev VN, Kulakovskiy IV. svist4get: a simple visualization tool for genomic tracks from sequencing experiments. BMC Bioinformatics 2019; 20:113. [PMID: 30841857 PMCID: PMC6404320 DOI: 10.1186/s12859-019-2706-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track constructed by short read mapping to a particular genome assembly. There are many software tools to visualize genomic tracks in a web browser or with a stand-alone graphical user interface. However, there are only few command-line applications suitable for automated usage or production of publication-ready visualizations. RESULTS Here we present svist4get, a command-line tool for customizable generation of publication-quality figures based on data from genomic signal tracks. Similarly to generic genome browser software, svist4get visualizes signal tracks at a given genomic location and is able to aggregate data from several tracks on a single plot along with the transcriptome annotation. The resulting plots can be saved as the vector or high-resolution bitmap images. We demonstrate practical use cases of svist4get for Ribo-Seq and RNA-Seq data. CONCLUSIONS svist4get is implemented in Python 3 and runs on Linux. The command-line interface of svist4get allows for easy integration into bioinformatics pipelines in a console environment. Extra customization is possible through configuration files and Python API. For convenience, svist4get is provided as pypi package. The source code is available at https://bitbucket.org/artegorov/svist4get/.
Collapse
Affiliation(s)
- Artyom A Egorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia. .,Department of Medical Physics, Faculty of Physics, Lomonosov Moscow State University, Leninskiye gory 1-2, Moscow, 119991, Russia.
| | - Ekaterina A Sakharova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia
| | - Aleksandra S Anisimova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, Moscow, 119234, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
| | - Vadim N Gladyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ivan V Kulakovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia. .,Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia. .,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia. .,Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, 142290, Moscow Region, Russia.
| |
Collapse
|
33
|
Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
Collapse
Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
34
|
Podkolodnaya OV, Tverdokhleb NN, Podkolodnyy NL. Detection and analysis of dynamic patterns of diurnal expression of mammalian genes. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj18.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The purpose of the study is to identify and analyze patterns of the diurnal dynamics of the expression of genes that differ in the shape of the curve. It can be expected that the similarity of the patterns of daily expression (shape of the curve) of genes is a reflection of the synchronization of gene expression by common external and internal signals or participation in similar biological processes. Different signals that have daily dynamics (light, activity, nutrition, stress, temperature, etc.) can affect different levels of expression regulation, which can be manifested in various forms of patterns of daily gene expression. In our research, we used experimental data on gene expression at the level of translation (ribosome profling) in the liver and kidney of a mouse (GSE67305 and GSE81283). To identify genes with a daily rhythm of expression, we used a oneway analysis of variance. To identify similarinshape curves of the daily dynamics of gene expression, we propose an approach based on cluster analysis. The distance between the genes was calculated by aligning the phases and fnding the maximum crosscorrelation between the patterns of the daily expression of these genes by the cyclic shift. This approach allowed us to identify genes that have not only expression patterns with a single maximum (sinusoidal, asymmetrical, shifted to the left or right, pulsed), but also complex composite signals with several extremes. As a result, the groups of genes united by the similarity of the shape of the daily expression curve without regard to their phase characteristics were identifed. GO enrichment analysis of groups of genes with sharply different patterns of daily expression (sinusoidal and pulsed) in the mouse kidneys and liver showed that the group of genes with a sinusoidal pattern was more associated with regulation of circadian rhythm and metabolism. The group of genes with a pulsed pattern is largely associated with the protective functions of the organism, which require the quick response. Thus, our studies have confrmed the effectiveness of the proposed approach to the analysis of the diurnal dynamics of gene expression. The identifed dynamic patterns of diurnal expression are important for the further study of complex circadian regulation, synchronization and interaction of biological processes with diurnal dynamics in mammals.
Collapse
Affiliation(s)
| | - N. N. Tverdokhleb
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - N. L. Podkolodnyy
- Institute of Cytology and Genetics, SB RAS; Institute of Computational Mathematics and Mathematical Geophysics, SB RAS
| |
Collapse
|
35
|
|
36
|
Seimetz J, Arif W, Bangru S, Hernaez M, Kalsotra A. Cell-type specific polysome profiling from mammalian tissues. Methods 2018; 155:131-139. [PMID: 30500367 DOI: 10.1016/j.ymeth.2018.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/29/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022] Open
Abstract
The regulation of gene expression occurs through complex relationships between transcription, processing, turnover, and translation, which are only beginning to be elucidated. We know that at least for certain messenger (m) RNAs, processing, modifications, and sequence elements can greatly influence their translational output through recognition by translation and turn-over machinery. Recently, we and others have combined high-throughput sequencing technologies with traditional biochemical methods of studying translation to extend our understanding of these relationships. Additionally, there is growing importance given to how these processes may be regulated across varied cell types as a means to achieve tissue-specific expression of proteins. Here, we provide an in-depth methodology for polysome profiling to dissect the composition of mRNAs and proteins that make up the translatome from both whole tissues and a specific cell type isolated from mammalian tissue. Also, we provide a detailed computational workflow for the analysis of the next-generation sequencing data generated from these experiments.
Collapse
Affiliation(s)
- Joseph Seimetz
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Waqar Arif
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Mikel Hernaez
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@ Illinois, University of Illinois, Urbana-Champaign, IL, USA.
| |
Collapse
|
37
|
Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
Collapse
|
38
|
Smit E, Caiment F, Piepers J, Kleinjans JCS, van den Beucken T. Translational regulation is a key determinant of the cellular response to benzo[a]pyrene. Toxicol Lett 2018; 295:144-152. [PMID: 29906497 DOI: 10.1016/j.toxlet.2018.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 11/19/2022]
Abstract
Translational control is a cellular response mechanism which initiates adaptation during various stress situations. Here, we investigated the role of translational control after benzo[a]pyrene (BaP) exposure in primary mouse hepatocytes. Translated mRNAs were separated and captured based on the number of associated ribosomes using sucrose gradients and subjected to RNA sequencing (RNAseq) to investigate translational changes. Furthermore, unseparated RNA (total RNA) was used for RNAseq to determine the transcriptional alterations. We showed that, after 24 h of exposure to 10 μM BaP, the number of genes altered by changes in mRNA translation was substantially higher compared with the number of genes altered by transcription. Although part of the BaP regulated genes were regulated by both transcription and translation, we identified genes that were uniquely regulated by mRNA translation. These mRNA transcripts encode proteins that are involved in biological processes that are not affected by transcriptional regulation. Al together this work identified a new layer of gene expression regulation that might contribute to BaP-induced carcinogenesis.
Collapse
Affiliation(s)
- Evelyn Smit
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6200MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6200MD, The Netherlands
| | - Jolanda Piepers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6200MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6200MD, The Netherlands
| | - Twan van den Beucken
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6200MD, The Netherlands.
| |
Collapse
|
39
|
Eastman G, Smircich P, Sotelo-Silveira JR. Following Ribosome Footprints to Understand Translation at a Genome Wide Level. Comput Struct Biotechnol J 2018; 16:167-176. [PMID: 30069283 PMCID: PMC6066590 DOI: 10.1016/j.csbj.2018.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/11/2022] Open
Abstract
Protein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the main conclusions raised in different models.
Collapse
Affiliation(s)
- Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - José R. Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| |
Collapse
|
40
|
Abstract
In most organisms, gene expression over the course of the day is under the control of the circadian clock. The canonical clock operates as a gene expression circuit that is controlled at the level of transcription, and transcriptional control is also a major clock output. However, rhythmic transcription cannot explain all the observed rhythms in protein accumulation. Although it is clear that rhythmic gene expression also involves RNA processing and protein turnover, until two years ago little was known in any eukaryote about diel dynamics of mRNA translation into protein. A recent series of studies in animals and plants demonstrated that diel cycles of translation efficiency are widespread across the tree of life and its transcriptomes. There are surprising parallels between the patterns of diel translation in mammals and plants. For example, ribosomal proteins and mitochondrial proteins are under translational control in mouse liver, human tissue culture, and Arabidopsis seedlings. In contrast, the way in which the circadian clock, light-dark changes, and other environmental factors such as nutritional signals interact to drive the cycles of translation may differ between organisms. Further investigation is needed to identify the signaling pathways, biochemical mechanisms, RNA sequence features, and the physiological implications of diel translation.
Collapse
Affiliation(s)
- Sarah Catherine Mills
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA
| | - Ramya Enganti
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA
| | - Albrecht G von Arnim
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA.,b UT-ORNL Graduate School of Genome Science and Technology , The University of Tennessee , Knoxville , TN , USA
| |
Collapse
|
41
|
Poverennaya EV, Ilgisonis EV, Ponomarenko EA, Kopylov AT, Zgoda VG, Radko SP, Lisitsa AV, Archakov AI. Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J Proteome Res 2017; 16:4311-4318. [PMID: 28956606 DOI: 10.1021/acs.jproteome.7b00348] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.
Collapse
Affiliation(s)
| | | | | | | | - Victor G Zgoda
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | | | | |
Collapse
|