Mechanism of transcription-coupled DNA modification recognition
© The Author(s) 2017
Received: 1 October 2016
Accepted: 2 November 2016
Published: 22 February 2017
As a key enzyme for gene expression, RNA polymerase II (pol II) reads along the DNA template and catalyzes accurate mRNA synthesis during transcription. On the other hand, genomic DNA is under constant attack by endogenous and environmental stresses. These attack cause many DNA lesions. Pol II functions as a specific sensor that is able to recognize changes in DNA sequences and structures and induces different outcomes. A critical question in the field is how Pol II recognizes and senses these DNA modifications or lesions. Recent studies provided new insights into understanding this critical question. In this mini-review, we would like to focus on three classes of DNA lesions/modifications: (1) Bulky, DNA-distorting lesions that block pol II transcription, (2) small DNA lesions that promote pol II pausing and error-prone transcriptional bypass, and (3) endogenous enzyme-catalyzed DNA modifications that lead to pol II pausing and error-free transcriptional bypass.
KeywordsTranscription RNA polymerase II DNA damage Transcription-coupled repair Transcriptional pausing Transcriptional arrest Transcriptional lesion bypass UV DNA damage Oxidative DNA lesions 8-Oxo-2′-deoxyguanosine
RNA polymerase II (pol II) is the enzyme responsible for the transcription and synthesis of pre-messenger RNA and noncoding RNA transcripts . During the process of transcription, pol II reads along the template strand of genomic DNA and incorporates the matched nucleotide substrate with high fidelity to ensure accurate genetic transfer and minimize transcriptional errors. Transcriptional fidelity during elongation is maintained via at least three fidelity checkpoint steps: the nucleotide insertion step, RNA transcript extension step, and proofreading step . Unavoidably, pol II may encounter various DNA modifications or lesions during its long transcriptional ‘journey’ moving along the DNA template. In such situations, pol II utilizes several important motifs to ‘sense’ these DNA modifications. The distinct interactions between pol II conserved motifs and these DNA modifications also induce appropriate transcription-coupled responses, which may lead to transcriptional mutagenesis, transcription-coupled repair pathway, or apoptosis [2–4].
Some small DNA lesions do not affect the DNA backbone significantly and therefore do not block transcription elongation. Rather, some of these DNA lesions cause error-prone transcriptional lesion bypass. For example, 8-Oxo-2′-deoxyguanosine (8-oxo-dG), a common endogenous oxidative damage, is one such mutagenic DNA lesion . Pol II can either insert a matched cytosine or a mismatched adenine when it encounters 8-oxo-dG during transcription [16, 17]. However, the presence of the 8-carbonyl group of 8-oxo-dG destabilizes the canonical anti conformation of template base, making ATP misinsertion and extension much more energy favorable . Consequently, the presence of 8-oxoG at the DNA template causes a specific C→A mutation in the RNA transcript, termed transcriptional mutagenesis . Emerging evidence suggests that transcriptional mutagenesis could contribute to cancer, aging, and a variety of neurodegenerative diseases.
Taken together, the different mechanisms of pol II arrest or bypass of a variety of lesions or modifications support the idea that pol II is a specific sensor that detects DNA modifications during transcription. The specific interactions between DNA lesions/modifications and pol II govern the specific transcriptional outcomes: transcriptional arrest, pausing, and error-prone or error-free transcriptional lesion bypass. For bulky, DNA-distorting lesions such as cis-syn CPD and CydA lesions, the presence of DNA lesions compromises DNA backbone flexibility and greatly slows down the bridge helix crossover step during translocation, thus forming a strong road block for pol II transcription elongation . This DNA-lesion induced pol II arrest initiates transcription-coupled nucleotide excision repair . For the 8-oxo-dG lesion, the interaction between the 8-oxo-dG and the active site of pol II promotes the mis-incorporation of an adenine base opposite the lesion and leads to error-prone transcriptional bypass. 8-oxo-dG is a common type of oxidative DNA damage and can be effectively repaired by the base excision repair pathway. Whether 8-oxo-dG is subject to transcription-coupled repair has been an interesting debatable topic for decades, but emerging new evidence suggests that 8-oxoG is preferentially repaired in the transcribed strand in vivo, yet the detailed molecular mechanism remains to be established . With regards to the enzyme-catalyzed 5caC modifications, RNA pol II can directly sense the 5caC modification via the specific interaction between pol II and 5caC . This 5caC-induced transcriptional pausing may suggest another layer of functional interplay between epigenetic DNA modifications and pol II transcription machinery in the fine-tuning of transcriptional dynamics and gene expression [25, 26].
Conclusively, RNA polymerase II can sense a variety of different DNA structures/lesions during transcription and induce specific transcription-coupled responses including transcriptional lesion bypass, transcriptional pausing and arrest, which may consequently trigger DNA repair or cell death. As RNA pol II scans along significant portions of the genomic DNA during transcription, the sensory function of pol II possibly may have developed as an evolutionary mechanism for the cell to maintain genomic integrity, to respond a variety of environmental cues or stress, and to determine how and when the cell’s energy and resources should be optimally utilized.
- pol II:
RNA polymerase II
ten eleven translocation proteins
thymine DNA glycosylase
cyclobutane pyrimidine dimer lesions
JHS, LX and DW wrote the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
This work was supported by funding from National Institutes of Health (R01GM102362 to D.W).
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