Transcriptional Regulation

What is transcriptional regulation?

Transcription is fundamental to information transfer from the genome to the proteome (1, 2). The first step in gene expression involves making an RNA copy called the messenger RNA (mRNA) of a gene’s DNA sequence.  Each mRNA carries the information for making a protein from the nucleus to the cytoplasm, where the machinery for protein synthesis, called the ribosome, resides. Ribosomal RNA (rRNA) molecules are a vital component of the ribosomes (3). Whereas, transfer RNA (tRNA) molecules provide ribosomes with amino acids during protein synthesis. The mRNA, rRNA, and tRNA are the main types of RNA molecules involved in protein synthesis, and each of them needs to be transcribed from the DNA.

Transcriptional regulation is a strictly coordinated process involving a variety of transcription factors a complex transcriptional apparatus that includes RNA polymerase, and chromatin and its regulators. Transcription factors (TFs) are proteins that recognize and bind to DNA regions, called transcription factor binding sites, in the promoter or enhancer region. TFs initiate and regulate transcription and are a crucial mechanism for gene expression. Any dysfunction in TFs can cause aberrant gene expression, resulting in disease onset (4).   Chromatin is a combination of DNA and proteins that forms chromosomes in the nucleus of cells (5). Chromatin influences cellular processes including transcription, gene regulation, mRNA production, DNA replication and repair, and genetic recombination. A set of RNA polymerases transcribe DNA to RNA guided by interactions with the chromatin and TFs via the rest of the transcriptional apparatus.

Transcriptional regulation modulates cellular processes, such as differentiation, development, and apoptosis. It also enables cells to establish and maintain cell identity and respond to internal and external signals through signal transduction pathways. This regulatory network is essential to the health and functioning of biological systems. Deregulation impairs cellular processes and is associated with diseases, including cancer, autoimmune diseases, metabolic diseases, and cardiovascular diseases. 

A deeper understanding of mechanisms involved in transcriptional regulation and its components can enhance our knowledge of the pathological events that drive many diseases.

Stages of transcription

Transcription is a three-step process consisting of initiation, elongation, and termination.

Transcription initiation begins with the binding of RNA polymerase to the DNA at the promoter region (6).  It ends when the RNA polymerase leaves the promoter region after synthesizing about the first nine nucleotides (7).

Transcription elongation is the next phase after initiation. It occurs when an RNA polymerase moves along DNA, adding nucleotides to nascent RNA strands (8).

Termination concludes the transcription process. It occurs when nucleotide addition ends, and the RNA is released from the RNA polymerase (8).

Also significant to the transcription process is pre-mRNA cleavage, capping, and polyadenylation. It is an extended processing that involves cutting nascent mRNA to remove introns that are not part of the protein-coding sequence, adding a methylated 5’ guanosine, and adding a polyadenylate or poly(A) tail (9). This step is required for the maturation of pre-mRNA molecules into functional mRNAs that can exit from the nucleus and be translated in the cytoplasm (10).

DNA methylation for transcription silencing

DNA methylation is a process of transferring a methyl group to DNA that occurs during cell division. It is regulated by DNA methyltransferases (DNMTs): DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L. DNA methylation represses transcription as a mechanism to regulate gene expression. It is essential for normal development, and its alteration contributes to cardiovascular diseases, cancer, autoimmune diseases, neurological disorders, and more (11).

The role of RNA polymerase in health and diseases

RNA polymerase is an enzyme in all organisms and a core transcription component. It is a complex molecule composed of protein subunits. It transcribes DNA into RNA and works with transcription activators and repressors (12, 13).

RNA polymerase mutations may contribute to disease development, and causing defects in the structure and function of rRNA genes that may lead to ribosomopathies. For example, dysregulated rRNA synthesis through RNA Polymerase I (Pol I) has been associated with Treacher Collins syndrome, Diamond-Blackfan anemia, 5q minus syndrome, and Blooms and Werner syndrome. Mutations affecting RNA processing and modification are linked to diseases such as Shwachman-Diamond syndrome, Bowen-Conradi syndrome, dyskeratosis congenita, and alopecia, neurological defect and endocrinopathy (ANE) syndrome (14).

Three RNA polymerases—RNA polymerase I, II, and III—transcribe cellular genomes in eukaryotes. They are classified based on the type of gene they transcribe (13).  

RNA Polymerase I

RNA polymerase I (Pol I) is a 14-subunit enzyme located in the nucleolus (15). It transcribes genes for large rRNA molecules and 5.8S rRNA. Pol I is responsible for up to 60% of cellular transcriptional activity, regulating cell growth, proliferation, and more (16).

Its dysregulation results in diseases including cancer, like colorectal and endometrial cancers, and ribosomopathies, including severe neurodegenerative diseases, acrofacial dysostosis-type Cincinnati (AFDCIN), and Treacher Collins Syndrome (TCS) (17). For instance, the POLR1A subunit has been shown to be overexpressed in colorectal cancer, and POLR1B is usually upregulated in many cancers, including non-small cell lung cancer (NSCLC). Hence, Pol I transcription machinery is a potential target for treating these diseases.

RNA Polymerase II

RNA polymerase II (Pol II) is a 12-subunit enzyme, the largest of which is  subunit A, encoded by POLR2A. Pol II transcribes most eukaryotic protein-coding genes into mRNA (18).

POLR2A subunit plays a crucial role in the Pol II active site and is indispensable to gene and oncogene transcription. It is significantly expressed in tumor tissue and can support tumor cell proliferation and prevent apoptosis. Studies have found its upregulation in cancers such as gastric cancer, ovarian cancer, and acute myeloid leukemia (13).

Studies have shown that POLR2A polymorphisms are associated with poor prognosis in non-small cell lung cancer. Moreover, suppressing POLR2A using siRNA has been observed to decrease tumor growth and enhance tumor suppression. These findings suggest targeting POLR2A could be a potential treatment approach for cancer (13).

RNA Polymerases III

Pol III is the largest of the three polymerases and is pivotal to cellular growth and lifespan in eukaryotes. These large proteins consist of 17 subunits. They transcribe the genes for small, nonprotein-coding RNA molecules, including tRNA and 5S rRNA (19, 20).

Pol III transcription defects are associated with many diseases, including neurodegenerative diseases like Alzheimer's disease, hypomyelinating leukodystrophy, Leigh syndrome, and Fragile X-syndrome, hypersensitivity to viral infection, and cancer, notably ovarian and breast cancer. These diseases may occur due to mutations in Pol III leading to decreased or defective Pol III transcription or defective synthesis of a Pol III product (21).

For instance, patients who experience hypersensitivity to viral infections have been observed to have Pol III mutations. Mutations in the POLR3A, POLR3C, POLR3E, and POLR3F subunits are implicated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. Mutations in POLR3A, POLR3B, POLR1C, and POLR3K contribute to the development of neurodegenerative diseases (22).

Researchers have recognized the potential of Pol III as a promising therapeutic target for various diseases, owing to its crucial role in cellular health and diseases. However, while the relationship between Pol III dysregulation and the development of diseases is well-established, the precise pathogenic mechanisms of these diseases still need to be fully understood (22).

Transcription is a fundamental process that occurs in all organisms, including bacteria, viruses, and cancer cells. Because of its central role in gene expression, cellular health, and diseases, the transcription machinery is an attractive target for developing new therapies.

References

1. Polouliakh, N. (2018). In Silico Transcription Factor Discovery via Bioinformatics Approach: Application on iPSC Reprogramming Resistant Genes. Leveraging Biomedical and Healthcare Data, 183-193.
2. National Human Genome Research Institute https://www.genome.gov/genetics-glossary/Transcription#  (Accessed April 16, 2024)
3. Scitable by Nature Education https://www.nature.com/scitable/topicpage/ribosomes-transcription-and-translation-14120660/  (Accessed April 16, 2024)
4. He H, Yang M, Li S, et al. Mechanisms and biotechnological applications of transcription factors. Synth Syst Biotechnol. 2023;8(4):565-577. Published 2023 Aug 31.
5. National Cancer Institute https://www.cancer.gov/publications/dictionaries/cancer-terms/def/chromatin  (Accessed April 16, 2024)
6. ScienceDirect https://www.sciencedirect.com/topics/medicine-and-dentistry/rna-synthesis  (Accessed April 16, 2024)
7. ScienceDirect https://www.sciencedirect.com/topics/neuroscience/transcription-initiation (Accessed April 16, 2024)
8. Mohamed AA, Vazquez Nunez R, Vos SM. Structural advances in transcription elongation. Curr Opin Struct Biol. 2022;75:102422.
9. Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA. 2012;3(3):385-396.
10. Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol. 2017;14(7):865-890.
11. Kandi V, Vadakedath S. Effect of DNA Methylation in Various Diseases and the Probable Protective Role of Nutrition: A Mini-Review. Cureus. 2015;7(8):e309. Published 2015 Aug 24.
12. National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/books/NBK26887/#:~:text=Not%20only%20does%20the%20polymerase,appropriate%20(more...)  (Accessed April 16, 2024)
13. Muste Sadurni, M., & Saponaro, M. (2023). Deregulations of RNA Pol II Subunits in Cancer. Applied Biosciences, 2(3), 459-476.
14. National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/books/NBK545212/ (Accessed April 16, 2024)
15. ScienceDirect https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/rna-polymerase-i  (Accessed April 16, 2024)
16. Zhao D, Liu W, Chen K, Wu Z, Yang H, Xu Y. Structure of the human RNA polymerase I elongation complex. Cell Discov. 2021;7(1):97. Published 2021 Oct 20.
17. Xing X, Jin N, Wang J. Polymerase Epsilon-Associated Ultramutagenesis in Cancer. Cancers (Basel). 2022;14(6):1467. Published 2022 Mar 12.
18. Hansen AW, Arora P, Khayat MM, et al. Germline mutation in POLR2A: a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation. HGG Adv. 2021;2(1):100014.
19. Kulaberoglu Y, Malik Y, Borland G, Selman C, Alic N, Tullet JMA. RNA Polymerase III, Ageing and Longevity [published correction appears in Front Genet. 2021 Sep 02;12:758135]. Front Genet. 2021;12:705122. Published 2021 Jul 6.
20. Ramsay EP, Abascal-Palacios G, Daiß JL, et al. Structure of human RNA polymerase III. Nat Commun. 2020;11(1):6409. Published 2020 Dec 17.
21. Yeganeh M, Hernandez N. RNA polymerase III transcription as a disease factor. Genes Dev. 2020;34(13-14):865-882.
22. Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci. 2021;8:696438. Published 2021 Jul 30.