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Liao M, Cao J, Chen W, Wang M, Jin Z, Ye J, Ren Y, Wei Y, Xue Y, Chen D, Zhang Y, Chen S. HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells. BMC Genomics 2024; 25:345. [PMID: 38580917 PMCID: PMC10996203 DOI: 10.1186/s12864-024-10204-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND High-mobility group B1 (HMGB1) is both a DNA binding nuclear factor modulating transcription and a crucial cytokine that mediates the response to both infectious and noninfectious inflammation such as autoimmunity, cancer, trauma, and ischemia reperfusion injury. HMGB1 has been proposed to control ribosome biogenesis, similar as the other members of a class of HMGB proteins. RESULTS Here, we report that HMGB1 selectively promotes transcription of genes involved in the regulation of transcription, osteoclast differentiation and apoptotic process. Improved RNA immunoprecipitation by UV cross-linking and deep sequencing (iRIP-seq) experiment revealed that HMGB1 selectively bound to mRNAs functioning not only in signal transduction and gene expression, but also in axon guidance, focal adhesion, and extracellular matrix organization. Importantly, HMGB1-bound reads were strongly enriched in specific structured RNAs, including the domain II of 28S rRNA, H/ACA box snoRNAs including snoRNA63 and scaRNAs. RTL-P experiment showed that overexpression of HMGB1 led to a decreased methylation modification of 28S rRNA at position Am2388, Cm2409, and Gm2411. We further showed that HMGB1 overexpression increased ribosome RNA expression levels and enhanced protein synthesis. CONCLUSION Taken together, our results support a model in which HMGB1 binds to multiple RNA species in human cancer cells, which could at least partially contribute to HMGB1-modulated rRNA modification, protein synthesis function of ribosomes, and differential gene expression including rRNA genes. These findings provide additional mechanistic clues to HMGB1 functions in cancers and cell differentiation.
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Affiliation(s)
- Meimei Liao
- Department of Ultrasound Imaging, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jiarui Cao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Wen Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Mengwei Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Zhihui Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jia Ye
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yijun Ren
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yaqiang Xue
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Sen Chen
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China.
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Mehta D, Ramesh A. Diversity and prevalence of ANTAR RNAs across actinobacteria. BMC Microbiol 2021; 21:159. [PMID: 34051745 PMCID: PMC8164766 DOI: 10.1186/s12866-021-02234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Background Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their target RNAs haven’t been identified in certain bacterial phyla such as actinobacteria. Results Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes. Conclusion In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. These findings now provide a starting point to investigate the actinobacterial processes that are regulated by ANTAR. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02234-x.
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Affiliation(s)
- Dolly Mehta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.,SASTRA University, Tirumalaisamudram, Thanjavur, 613401, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.
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Mirihana Arachchilage G, Hetti Arachchilage M, Venkataraman A, Piontkivska H, Basu S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 2019; 696:149-161. [PMID: 30753890 DOI: 10.1016/j.gene.2019.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.
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Affiliation(s)
| | | | - Aparna Venkataraman
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America.
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