The DOI matches its Crossref record; 92 of the 92 references it cites were found in a registry or an index.
Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond
Open accessAbstract
Modification of DNA bases plays vital roles in the epigenetic control of gene expression in both animals and plants. Though much attention is given to the conventional epigenetic signature 5-methylcytosine (5-mC), the field of epigenetics is attracting increased scientific interest through the discovery of additional modifications of DNA bases and their roles in controlling gene expression. Theoretically, each of the DNA bases can be modified; however, modifications of cytosine and adenine only are known so far. This review focuses on the recent findings of the well-studied cytosine modifications and yet poorly characterized adenine modification which serve as an additional layer of epigenetic regulation in animals and discuss their potential roles in plants. Cytosine modification at symmetric (CG, CHG) and asymmetric (CHH) contexts is a key epigenetic feature. In addition to the ROS1 family mediated demethylation, Ten-Eleven Translocation family proteins-mediated hydroxylation of 5-mC to 5-hydroxymethylcytosine as additional active demethylation pathway are also discussed. The epigenetic marks are known to be associated with the regulation of several cellular and developmental processes, pluripotency of stem cells, neuron cell development, and tumor development in animals. Therefore, the most recently discovered N6-methyladenine, an additional epigenetic mark with regulatory potential, is also described. Interestingly, these newly discovered modifications are also found in the genomes which lack canonical 5-mC, signifying their independent epigenetic functions. These modified DNA bases are considered to be important players in epigenomics. The potential for combinatorial interaction among the known modified DNA bases suggests that epigenetic codon is likely to be substantially more complicated than it is thought today.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
Law, J. A., & Jacobsen, S. E. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2719 · Cited by 3,850
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825 · cited 1×
“Discovery of flexibility in sgRNA has created the possibility of inserting additional RNA elements (Konermann et al., 2015) which can be recognized by RNA-specific binding protein effectors leading to improved efficacy of targeted dCas9-mediated functional moieties (Zalatan et al., 2015).”
BackgroundThe molecular hallmarks of epigenetic control
Allis, C. D., & Jenuwein, T. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.59 · Cited by 2,809
Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA
He, Y.-F., Li, B.-Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L., et al. (2011) · Science · doi:10.1126/science.1210944 · Cited by 2,770
The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700 · cited 2×
“5-hmC content in mammalian tissues is about 0.1% but can vary greatly (Globisch et al., 2010) with the highest level in the brain where it can go up to 1% (Kriaucionis and Heintz, 2009).”
BackgroundInfluentialIto, S., D’Alessio, A. C., Taranova, O. V., Hong, K., Sowers, L. C., & Zhang, Y. (2010) · Nature · doi:10.1038/nature09303 · Cited by 2,373
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., Pradhan, S., Nelson, S. F., Pellegrini, M., & Jacobsen, S. E. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,256
Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., Harmer, S. L., & Zilberman, D. (2013) · Cell · doi:10.1016/j.cell.2013.02.033 · Cited by 1,180
Cited by
Dynamics of dna methylation and its functions in plant growth and development
Kumar, S., & Mohapatra, T. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.596236 · Cited by 227
Self-citationRNA m6A regulates transcription via DNA demethylation and chromatin accessibility
Deng, S., Zhang, J., Su, J., Zuo, Z., Zeng, L., Liu, K., Zheng, Y., Huang, X., Bai, R., Zhuang, L., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01173-1 · Cited by 187
Epigenetic signature in neural plasticity: the journey so far and journey ahead
Nayak, M., Das, D., Pradhan, J., Ahmed, R. G., Laureano-Melo, R., & Dandapat, J. (2022) · Heliyon · doi:10.1016/j.heliyon.2022.e12292 · Cited by 42
Metadata
- Authors
- Kumar, S., Chinnusamy, V., & Mohapatra, T.
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2018-12-18
- Volume
- 9
- Pages
- 640-640
- ISSN
- 1664-8021 (ISSN-L)
- OpenAlex
- W2904369742
- Cited by
- 283
- References
- 92
- FWCI
- 6.98
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond. https://app.cochat.ai/papers/10.3389/fgene.2018.00640
- The paper
- Kumar, S., Chinnusamy, V., & Mohapatra, T. (2018). Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond. Frontiers in Genetics. https://doi.org/10.3389/fgene.2018.00640
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
