1
|
Angelo M, Bhargava Y, Aoki ST. A primer for junior trainees: Recognition of RNA modifications by RNA-binding proteins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024. [PMID: 39037148 DOI: 10.1002/bmb.21854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
The complexity of RNA cannot be fully expressed with the canonical A, C, G, and U alphabet. To date, over 170 distinct chemical modifications to RNA have been discovered in living systems. RNA modifications can profoundly impact the cellular outcomes of messenger RNAs (mRNAs), transfer and ribosomal RNAs, and noncoding RNAs. Additionally, aberrant RNA modifications are associated with human disease. RNA modifications are a rising topic within the fields of biochemistry and molecular biology. The role of RNA modifications in gene regulation, disease pathogenesis, and therapeutic applications increasingly captures the attention of the scientific community. This review aims to provide undergraduates, junior trainees, and educators with an appreciation for the significance of RNA modifications in eukaryotic organisms, alongside the skills required to identify and analyze fundamental RNA-protein interactions. The pumilio RNA-binding protein and YT521-B homology (YTH) family of modified RNA-binding proteins serve as examples to highlight the fundamental biochemical interactions that underlie the specific recognition of both unmodified and modified ribonucleotides, respectively. By instilling these foundational, textbook concepts through practical examples, this review contributes an analytical toolkit that facilitates engagement with RNA modifications research at large.
Collapse
Affiliation(s)
- Murphy Angelo
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Yash Bhargava
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Scott Takeo Aoki
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| |
Collapse
|
2
|
Danga AK, Kour S, Kumari A, Rath PC. Cell-type specific and differential expression of LINC-RSAS long noncoding RNA declines in the testes during ageing of the rat. Biogerontology 2024; 25:543-566. [PMID: 38353919 DOI: 10.1007/s10522-023-10088-1] [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: 10/14/2023] [Accepted: 12/15/2023] [Indexed: 03/26/2024]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as major regulators of gene expression, chromatin structure, epigenetic changes, post-transcriptional processing of RNAs, translation of mRNAs into proteins as well as contributing to the process of ageing. Ageing is a universal, slow, progressive change in almost all physiological processes of organisms after attaining reproductive maturity and often associated with age-related diseases. Mammalian testes contain various cell-types, vast reservoir of transcriptome complexity, produce haploid male gametes for reproduction and testosterone for development and maintenance of male sexual characters as well as contribute genetic variation to the species. We report age-related decline in expression and cellular localization of Long intergenic noncoding repeat-rich sense-antisense (LINC-RSAS) RNA in the testes and its major cell-types such as primary spermatocytes, Leydig cells and Sertoli cells during ageing of the rat. LINC-RSAS expression in testes increased from immature (4-weeks) to adult (16- and 44-weeks) and declined from adult (44-weeks) to nearly-old (70-weeks) rats. Genomic DNA methylation in the testes showed a similar pattern. Cell-type specific higher expression of LINC-RSAS was observed in primary spermatocytes (pachytene cells), Leydig cells and Sertoli cells of testes of adult rats. Over-expression of LINC-RSAS in cultured human cell lines revealed its possible role in cell-cycle control and apoptosis. We propose that LINC-RSAS expression is involved in molecular physiology of primary spermatocytes, Leydig cells and Sertoli cells of adult testes and its decline is associated with diminishing function of testes during ageing of the rat.
Collapse
Affiliation(s)
- Ajay Kumar Danga
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Anita Kumari
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
3
|
Ille AM, Mathews MB. AI interprets the Central Dogma and Genetic Code. Trends Biochem Sci 2023; 48:1014-1018. [PMID: 37833131 DOI: 10.1016/j.tibs.2023.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Generative artificial intelligence (AI) is a burgeoning field with widespread applications, including in science. Here, we explore two paradigms that provide insight into the capabilities and limitations of Chat Generative Pre-trained Transformer (ChatGPT): its ability to (i) define a core biological concept (the Central Dogma of molecular biology); and (ii) interpret the genetic code.
Collapse
Affiliation(s)
- Alexander M Ille
- School of Graduate Studies, Rutgers University, Newark, NJ, USA.
| | - Michael B Mathews
- School of Graduate Studies, Rutgers University, Newark, NJ, USA; Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA.
| |
Collapse
|
4
|
Greslehner GP. "Molecular Biology"-Pleonasm or Denotation for a Discipline of Its Own? Reflections on the Origins of Molecular Biology and Its Situation Today. Biomolecules 2023; 13:1511. [PMID: 37892193 PMCID: PMC10605324 DOI: 10.3390/biom13101511] [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: 06/24/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The disciplinary identity of molecular biology has frequently been called into question. Although the debates might sometimes have been more about creating or debunking myths, defending intellectual territory and the distribution of resources, there are interesting underlying questions about this area of biology and how it is conceptually organized. By looking at the history of molecular biology, its origins and development, I examine the possible criteria for its status as a scientific discipline. Doing so allows us to answer the title question in such a way that offers a reasonable middle ground, where molecular biology can be properly viewed as a viable interdisciplinary program that can very well be called a discipline in its own right, even if no strict boundaries can be established. In addition to this historical analysis, a couple of systematic issues from a philosophy of science perspective allow for some assessment of the current situation and the future of molecular biology.
Collapse
Affiliation(s)
- Gregor P Greslehner
- Department of Philosophy, University of Vienna, Universitätsstraße 7, 1010 Vienna, Austria
| |
Collapse
|
5
|
Hallee L, Rafailidis N, Gleghorn JP. cdsBERT - Extending Protein Language Models with Codon Awareness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558027. [PMID: 37745387 PMCID: PMC10516008 DOI: 10.1101/2023.09.15.558027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Recent advancements in Protein Language Models (pLMs) have enabled high-throughput analysis of proteins through primary sequence alone. At the same time, newfound evidence illustrates that codon usage bias is remarkably predictive and can even change the final structure of a protein. Here, we explore these findings by extending the traditional vocabulary of pLMs from amino acids to codons to encapsulate more information inside CoDing Sequences (CDS). We build upon traditional transfer learning techniques with a novel pipeline of token embedding matrix seeding, masked language modeling, and student-teacher knowledge distillation, called MELD. This transformed the pretrained ProtBERT into cdsBERT; a pLM with a codon vocabulary trained on a massive corpus of CDS. Interestingly, cdsBERT variants produced a highly biochemically relevant latent space, outperforming their amino acid-based counterparts on enzyme commission number prediction. Further analysis revealed that synonymous codon token embeddings moved distinctly in the embedding space, showcasing unique additions of information across broad phylogeny inside these traditionally "silent" mutations. This embedding movement correlated significantly with average usage bias across phylogeny. Future fine-tuned organism-specific codon pLMs may potentially have a more significant increase in codon usage fidelity. This work enables an exciting potential in using the codon vocabulary to improve current state-of-the-art structure and function prediction that necessitates the creation of a codon pLM foundation model alongside the addition of high-quality CDS to large-scale protein databases.
Collapse
Affiliation(s)
- Logan Hallee
- Center for Bioinformatics and Computational Biology, University of Delaware
| | | | | |
Collapse
|
6
|
Zagrovic B, Adlhart M, Kapral TH. Coding From Binding? Molecular Interactions at the Heart of Translation. Annu Rev Biophys 2023; 52:69-89. [PMID: 36626765 DOI: 10.1146/annurev-biophys-090622-102329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.
Collapse
Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| |
Collapse
|
7
|
Wang Z, Zeng Z, Gao F, Gui Z, Du J, Shen N, Shang Y, Yang Z, Shang L, Wei R, Ma W, Wang C. Osteosarcoma transcriptome data exploration reveals STC2 as a novel risk indicator in disease progression. BMC Med Genomics 2023; 16:30. [PMID: 36803385 PMCID: PMC9942349 DOI: 10.1186/s12920-023-01456-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/11/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Osteosarcoma has been the most common primary bone malignant tumor in children and adolescents. Despite the considerable improvement in the understanding of genetic events attributing to the rapid development of molecular pathology, the current information is still lacking, partly due to the comprehensive and highly heterogeneous nature of osteosarcoma. The study is to identify more potential responsible genes during the development of osteosarcoma, thus identifying promising gene indicators and aiding more precise interpretation of the disease. METHODS Firstly, from GEO database, osteosarcoma transcriptome microarrays were used to screen the differential expression genes (DEGS) in cancer comparing to normal bone samples, followed by GO/KEGG interpretation, risk score assessment and survival analysis of the genes, for the purpose of selecting a credible key gene. Further, the basic physicochemical properties, predicted cellular location, gene expression in human cancers, the association with clinical pathological features and potential signaling pathways involved in the key gene's regulation on osteosarcoma development were in succession explored. RESULTS Based on the selected GEO osteosarcoma expression profiles, we identified the differential expression genes in osteosarcoma versus normal bone samples, and the genes were classified into four groups based on the difference level, further genes interpretation indicated that the high differently level (> 8 fold) genes were mainly located extracellular and related to matrix structural constituent regulation. Meanwhile, module function analysis of the 67 high differential level (> 8 fold) DEGS revealed a 22-gene containing extracellular matrix regulation associated hub gene cluster. Further survival analysis of the 22 genes revealed that STC2 was an independent prognosis indicator in osteosarcoma. Moreover, after validating the differential expression of STC2 in cancer vs. normal tissues using local hospital osteosarcoma samples by IHC and qRT-PCR experiment, the gene's physicochemical property revealed STC2 as a cellular stable and hydrophilic protein, and the gene's association with osteosarcoma clinical pathological parameters, expression in pan-cancers and the probable biological functions and signaling pathways it involved were explored. CONCLUSION Using multiple bioinformatic analysis and local hospital samples validation, we revealed the gain of expression of STC2 in osteosarcoma, which associated statistical significantly with patients survival, and the gene's clinical features and potential biological functions were also explored. Although the results shall provide inspiring insights into further understanding of the disease, further experiments and detailed rigorous clinical trials are needed to reveal its potential drug-target role in clinical medical use.
Collapse
Affiliation(s)
- Ziyue Wang
- grid.24696.3f0000 0004 0369 153XDepartment of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Zixin Zeng
- grid.263452.40000 0004 1798 4018Basic Medical school of ShanXi Medical University, Tai Yuan city, ShanXi Province China
| | - Feng Gao
- grid.263452.40000 0004 1798 4018Department of Orthopedics, The Six Clinical Medical School of ShanXi Medical University, Tai Yuan, ShanXi Province China
| | - Ziwei Gui
- grid.263452.40000 0004 1798 4018Basic Medical school of ShanXi Medical University, Tai Yuan city, ShanXi Province China
| | - Juan Du
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Ningning Shen
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Yangwei Shang
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Zhiqing Yang
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Lifang Shang
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Rong Wei
- grid.452845.a0000 0004 1799 2077Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000 Tai Yuan City, ShanXi Province China
| | - Wenxia Ma
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000, Tai Yuan City, ShanXi Province, China.
| | - Chen Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, 030000, Tai Yuan City, ShanXi Province, China.
| |
Collapse
|
8
|
Cheng L, Lu L, Chen Z, Ma D, Xi Z. Multiple-Gene Regulation for Enhanced Antitumor Efficacy with Branch-PCR-Assembled TP53 and MYC Gene Nanovector. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206943. [PMID: 36296536 PMCID: PMC9609172 DOI: 10.3390/molecules27206943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Multiple proteins are involved in network regulation through the crosstalk of different signaling pathways in cancers. Here, we propose a novel strategy of genome therapy with branch-PCR-assembled gene nanovectors to perform network-based gene regulation at multiple levels for cancer therapy. To validate network-based multiplex-gene regulation for genome therapy, we chose to simultaneously target one tumor suppressor gene (TP53) and one oncogene (MYC) in two different signaling pathways. The results showed that, compared to gene nanovectors targeting single genes (NP-TP53 and NP-shMYC), branch-PCR-assembled gene nanovectors simultaneously expressing p53 proteins and MYC shRNA arrays (NP-TP53-shMYC) showed enhanced antitumor efficacy in both MDA-MB-231 cancer cells and an MDA-MB-231-tumor-bearing mouse model. These findings indicate the feasibility and effectiveness of genome therapy in cancer therapy.
Collapse
Affiliation(s)
| | | | | | - Dejun Ma
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
| | - Zhen Xi
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
| |
Collapse
|