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Muino JM, Ruwe H, Qu Y, Maschmann S, Chen W, Zoschke R, Ohler U, Kaufmann K, Schmitz-Linneweber C. MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39074058 DOI: 10.1111/tpj.16945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024]
Abstract
The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5'-splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA-K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK-matK over-expressor exhibited elevated levels of the spliced tRNA-K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up-shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA-K(UUU), enabling the differential expression of functional chloroplast gene groups.
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Affiliation(s)
- Jose M Muino
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Hannes Ruwe
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Yujiao Qu
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Sascha Maschmann
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
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Lirakis M, Nolte V, Schlötterer C. Pool-GWAS on reproductive dormancy in Drosophila simulans suggests a polygenic architecture. G3 GENES|GENOMES|GENETICS 2022; 12:6523974. [PMID: 35137042 PMCID: PMC8895979 DOI: 10.1093/g3journal/jkac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022]
Abstract
The genetic basis of adaptation to different environments has been of long-standing interest to evolutionary biologists. Dormancy is a well-studied adaptation to facilitate overwintering. In Drosophila melanogaster, a moderate number of genes with large effects have been described, which suggests a simple genetic basis of dormancy. On the other hand, genome-wide scans for dormancy suggest a polygenic architecture in insects. In D. melanogaster, the analysis of the genetic architecture of dormancy is complicated by the presence of cosmopolitan inversions. Here, we performed a genome-wide scan to characterize the genetic basis of this ecologically extremely important trait in the sibling species of D. melanogaster, D. simulans that lacks cosmopolitan inversions. We performed Pool-GWAS in a South African D. simulans population for dormancy incidence at 2 temperature regimes (10 and 12°C, LD 10:14). We identified several genes with SNPs that showed a significant association with dormancy (P-value < 1e-13), but the overall modest response suggests that dormancy is a polygenic trait with many loci of small effect. Our results shed light on controversies on reproductive dormancy in Drosophila and have important implications for the characterization of the genetic basis of this trait.
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Affiliation(s)
- Manolis Lirakis
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans. Genes (Basel) 2021; 12:genes12101576. [PMID: 34680971 PMCID: PMC8535304 DOI: 10.3390/genes12101576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI's Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.
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Ecdysone-Induced 3D Chromatin Reorganization Involves Active Enhancers Bound by Pipsqueak and Polycomb. Cell Rep 2020; 28:2715-2727.e5. [PMID: 31484080 PMCID: PMC6754745 DOI: 10.1016/j.celrep.2019.07.096] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Evidence suggests that Polycomb (Pc) is present at chromatin loop anchors in Drosophila. Pc is recruited to DNA through interactions with the GAGA binding factors GAF and Pipsqueak (Psq). Using HiChIP in Drosophila cells, we find that the psq gene, which has diverse roles in development and tumorigenesis, encodes distinct isoforms with unanticipated roles in genome 3D architecture. The BR-C, ttk, and bab domain (BTB)-containing Psq isoform (PsqL) colocalizes genome-wide with known architectural proteins. Conversely, Psq lacking the BTB domain (PsqS) is consistently found at Pc loop anchors and at active enhancers, including those that respond to the hormone ecdysone. After stimulation by this hormone, chromatin 3D organization is altered to connect promoters and ecdysone-responsive enhancers bound by PsqS. Our findings link Psq variants lacking the BTB domain to Pc-bound active enhancers, thus shedding light into their molecular function in chromatin changes underlying the response to hormone stimulus.
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Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
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Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Van Bortle K, Phanstiel DH, Snyder MP. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. Genome Biol 2017; 18:180. [PMID: 28931413 PMCID: PMC5607496 DOI: 10.1186/s13059-017-1310-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing. We therefore devised integrated tDNA expression profiling, a method that combines RNAPIII mapping with biotin-capture of nascent tRNAs. We apply this method to the study of dynamic tRNA gene regulation during macrophage development and further integrate these data with high-resolution maps of 3D chromatin structure. Results Integrated tDNA expression profiling reveals domain-level and loop-based organization of tRNA gene transcription during cellular differentiation. tRNA genes connected by DNA loops, which are proximal to CTCF binding sites and expressed at elevated levels compared to non-loop tDNAs, change coordinately with tDNAs and protein-coding genes at distal ends of interactions mapped by in situ Hi-C. We find that downregulated tRNA genes are specifically marked by enhanced promoter-proximal binding of MAF1, a transcriptional repressor of RNAPIII activity, altogether revealing multiple levels of tDNA regulation during cellular differentiation. Conclusions We present evidence of both local and coordinated long-range regulation of human tDNA expression, suggesting the location and organization of tRNA genes contribute to dynamic tDNA activity during macrophage development. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1310-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin Van Bortle
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Douglas H Phanstiel
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA.,Thurston Arthritis Research Center and Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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