The molecular basis of depression: implications of sex-related differences in epigenetic regulation
Open accessAbstract
Major depressive disorder (MDD) is a leading cause of disability worldwide. Although the etiology and pathophysiology of MDD remain poorly understood, aberrant neuroplasticity mediated by the epigenetic dysregulation of gene expression within the brain, which may occur due to genetic and environmental factors, may increase the risk of this disorder. Evidence has also been reported for sex-related differences in the pathophysiology of MDD, with female patients showing a greater severity of symptoms, higher degree of functional impairment, and more atypical depressive symptoms. Males and females also differ in their responsiveness to antidepressants. These clinical findings suggest that sex-dependent molecular and neural mechanisms may underlie the development of depression and the actions of antidepressant medications. This review discusses recent advances regarding the role of epigenetics in stress and depression. The first section presents a brief introduction of the basic mechanisms of epigenetic regulation, including histone modifications, DNA methylation, and non-coding RNAs. The second section reviews their contributions to neural plasticity, the risk of depression, and resilience against depression, with a particular focus on epigenetic modulators that have causal relationships with stress and depression in both clinical and animal studies. The third section highlights studies exploring sex-dependent epigenetic alterations associated with susceptibility to stress and depression. Finally, we discuss future directions to understand the etiology and pathophysiology of MDD, which would contribute to optimized and personalized therapy.
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Female patients are more likely to exhibit promoter hypermethylation of stress-related genes, including NR3C1 and SLC6A4, which has been associated with increased vulnerability to depression and differential treatment response.
“Accumulating evidence suggests that female patients are more likely to exhibit promoter hypermethylation of stress-related genes, including NR3C1 and SLC6A4, which has been associated with increased vulnerability to depression and differential treatment response (Kawatake-Kuno et al., 2021).”
From Histone modifications and depression: epigenetic mechanisms, therapeutic targets, and translational outlook (2026) · cites this paper as Kawatake-Kuno et al., 2021
The sex-related DNA methylation section (page unavailable) reports higher SLC6A4 promoter methylation in women than men. Its NR3C1 findings concern girls under a specific maternal-depression condition and adult male suicide victims, not a general tendency toward NR3C1 promoter hypermethylation in female patients. The DNA Methylation section (page unavailable) links SLC6A4 promoter methylation to depression and antidepressant responsiveness, but does not establish a female-specific difference in treatment response. (LLM, conf=0.87)
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Shors, T. J., Falduto, J., & Leuner, B. (2003) · European Journal of Neuroscience · doi:10.1046/j.1460-9568.2003.03065.x · Cited by 105 · see citing works
Altered HDAC5 and CREB mRNA expressions in the peripheral leukocytes of major depression
Iga, J.-I., Ueno, S.-I., Yamauchi, K., Numata, S., Kinouchi, S., Tayoshi-Shibuya, S., Song, H., & Ohmori, T. (2007) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2006.12.014 · Cited by 105 · see citing works
Estrogen-dependent association of HDAC4 with fear in female mice and women with PTSD
Maddox, S. A., Kilaru, V., Shin, J. H., Jovanović, T., Almli, L. M., Dias, B. G., Norrholm, S. D., Fani, N., Michopoulos, V., Ding, Z., et al. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.250 · Cited by 104 · see citing works
O'Connor, R. M., Grenham, S., Dinan, T. G., & Cryan, J. F. (2013) · International Journal of Neuropsychopharmacology · doi:10.1017/s1461145713000448 · Cited by 101 · see citing works
Nagy, C., Torres-Platas, S. G., Mechawar, N., & Turecki, G. (2016) · International Journal of Neuropsychopharmacology · doi:10.1093/ijnp/pyw071 · Cited by 98 · see citing works
Number of manic episodes is associated with elevated DNA oxidation in bipolar I disorder
Soeiro‐de‐Souza, M. G., Andreazza, A. C., Carvalho, A. F., Machado‐Vieira, R., Young, L. T., & Moreno, R. A. (2013) · The International Journal of Neuropsychopharmacology · doi:10.1017/s1461145713000047 · Cited by 97 · see citing works
Zuloaga, D. G., Heck, A., Guzman, R. M. D., & Handa, R. J. (2020) · Biology of Sex Differences · doi:10.1186/s13293-020-00319-2 · Cited by 96 · see citing works
He, S., Liu, X., Jiang, K., Peng, D., Hong, W., Fang, Y., Qian, Y., Yu, S., & Li, H. (2016) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2016.03.015 · Cited by 94 · see citing works
Cruceanu, C., Alda, M., Nagy, C., Freemantle, E., Rouleau, G. A., & Turecki, G. (2013) · International Journal of Neuropsychopharmacology · doi:10.1017/s1461145712000363 · Cited by 93 · see citing works
Miller, W. J. S., Suzuki, S., Miller, L. K., Handa, R. J., & Uht, R. M. (2004) · Journal of Neuroscience · doi:10.1523/jneurosci.5540-03.2004 · Cited by 93 · see citing works
Shen, E., Ahern, T. H., Cheung, I. K., Straubhaar, J., Dincer, A., Houston, I. B., Vries, G. J. D., Akbarian, S., & Forger, N. G. (2014) · Experimental Neurology · doi:10.1016/j.expneurol.2014.08.006 · Cited by 91 · see citing works
Fang, Y., Qiu, Q., Zhang, S., Sun, L., Li, G., Xiao, S., & Li, X. (2018) · Journal of Affective Disorders · doi:10.1016/j.jad.2017.11.090 · Cited by 90 · see citing works
Zhang, Y., Zhu, X., Bai, M., Zhang, L., Xue, L., & Yi, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069934 · Cited by 83 · see citing works
Non-Coding RNAs in Psychiatric Disorders and Suicidal Behavior
Yoshino, Y., & Dwivedi, Y. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.543893 · Cited by 82 · see citing works
Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse
Reinius, B., Shi, C., Hengshuo, L., Sandhu, K. S., Radomska, K. J., Rosen, G. D., Lu, L., Kullander, K., Williams, R. W., & JAZIN, E. E. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-614 · Cited by 81 · see citing works
Flagged first, then by citations
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Sorted by citations
Li, H., Kawatake-Kuno, A., Inaba, H., Miyake, Y., Itoh, Y., Ueki, T., Oishi, N., Murai, T., Suzuki, T., & Uchida, S. (2024) · Neuron · doi:10.1016/j.neuron.2023.12.004 · Cited by 31 · see citing works
Kawatake-Kuno, A., Li, H., Inaba, H., Hikosaka, M., Ishimori, E., Ueki, T., Garkun, Y., Morishita, H., Narumiya, S., Oishi, N., et al. (2024) · Neuron · doi:10.1016/j.neuron.2024.01.023 · Cited by 30 · see citing works
Inaba, H., Li, H., Kawatake-Kuno, A., Dewa, K., Nagai, J., Oishi, N., Murai, T., & Uchida, S. (2023) · Science Advances · doi:10.1126/sciadv.ade5397 · Cited by 30 · see citing works
Kawatake-Kuno, A., Murai, T., & Uchida, S. (2021) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2021.749180 · Cited by 26 · see citing works
Zha, B., Cai, A., Yu, H., & Wang, Z. (2025) · Journal of Affective Disorders · doi:10.1016/j.jad.2025.04.139 · Cited by 17 · see citing works
Funayama, Y., Li, H., Ishimori, E., Kawatake-Kuno, A., Inaba, H., Yamagata, H., Seki, T., Nakagawa, S., Watanabe, Y., Murai, T., et al. (2022) · Biological Psychiatry Global Open Science · doi:10.1016/j.bpsgos.2021.12.009 · Cited by 16 · see citing works
Sawaguchi, E., Nakamura, S., Watanabe, K., Tsuno, K., Ikegami, H., Shinmura, N., Saito, Y., & Narimatsu, H. (2022) · Frontiers in Public Health · doi:10.3389/fpubh.2022.1010720 · Cited by 16 · see citing works
Zhang, Y., Wang, M., Zhang, X., Jiang, Z.-Y., Zhang, Y., Fu, X., Li, Y., Cao, D., Han, J. H., & Tong, J. (2022) · Contrast Media & Molecular Imaging · doi:10.1155/2022/9242827 · Cited by 13 · see citing works
RetractedSex Significantly Impacts the Function of Major Depression–Linked Variants In Vivo
Mulvey, B., Selmanovic, D., & Dougherty, J. D. (2021) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.02.009 · Cited by 12 · see citing works
Identification of Specific Plasma miRNAs as Potential Biomarkers for Major Depressive Disorder
Prodan-Bărbulescu, C., Alin, C. D., Faur, F. I., Bujor, G. C., Șeclăman, E. P., ENĂTESCU, V. R., Dănilă, A.-I., Dăescu, E., Hajjar, R., Ghenciu, L. A., et al. (2024) · Biomedicines · doi:10.3390/biomedicines12102165 · Cited by 6 · see citing works
Lv, L.-Z., Wang, Z.-D., Ren, J.-J., Li, L.-H., Liu, X.-B., Li, J.-L., Zhu, H., Jiang, B., Han, Y.-P., Zhou, X.-M., et al. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2025.1722453 · Cited by 7 · see citing works
Tran, S. H., Zhang, S., Lee, H., Hitayezu, E., Nguyen, U. T. T., Lee, S., Kang, S. W., Park, K., Kim, S. H., Kwon, H. C., et al. (2025) · Phytomedicine · doi:10.1016/j.phymed.2025.157581 · Cited by 4 · see citing works
Depression: epigenetics and epitranscriptomic modifications
Banerjee, S., Shrilaxmi, M. S., Banerjee, S., Prajwal, B. G., Smith, C., D’Mello, S. R., & Dastidar, S. G. (2025) · The World Journal of Biological Psychiatry · doi:10.1080/15622975.2025.2602171 · Cited by 4 · see citing works
Li, B., Zhao, H., & Sun, J. (2022) · Computational and Mathematical Methods in Medicine · doi:10.1155/2022/4244425 · Cited by 3 · see citing works
Retractedda Silva, S. V., Santos, I. S., Bivanco-Lima, D., Goulart, A. C., Varella, A. C., Lotufo, P. A., Brunoni, A. R., & Benseñor, I. M. (2024) · Clinics · doi:10.1016/j.clinsp.2024.100488 · Cited by 1 · see citing works
Depression and Cancer: The Inflammatory Bridge
Leite, F., & Leite, Â. M. T. (2023) · Interdisciplinary cancer research · doi:10.1007/16833_2022_106 · Cited by 1 · see citing works
Gao, J., Wang, Q., Liu, J., Zheng, S., Liu, J., Gao, Z., & Zhu, C. (2025) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2025.1564095 · Cited by 1 · see citing works
Sex significantly impacts the function of major depression-linked variants in vivoPreprint
Mulvey, B., Selmanovic, D., & Dougherty, J. D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.01.466849 · Cited by 1 · see citing works
Jiang, W., Chen, C., Wang, S., Liu, Y., Li, P., & Zhang, B. (2025) · Brain Imaging and Behavior · doi:10.1007/s11682-025-01062-1
Distinct prefrontal neuronal circuits determine repeated stress-induced behavioral styles in mice
Uchida, S. (2026) · Folia Pharmacologica Japonica · doi:10.1254/fpj.25040
Corral-Castillo, D. A., Blanco-Salazar, A., Garcia-Murillo, O. G., Ruiz-Olvera, A., Hernández-Lepe, M. A., Llamas-Alonso, L. A., Amaro‐Gahete, F. J., Egan, B., & Chávez-Guevara, I. A. (2026) · Translational Journal of the American College of Sports Medicine · doi:10.1249/tjx.0000000000000345
Comparative evaluation of two chronic stress models in zebrafish for advancing depression research
Tripathy, C., Dhaygude, S. S., Vijay, V., Mondal, A., Soren, K., Kumar, A. T. R., & Chakravarty, S. (2026) · Physiology & Behavior · doi:10.1016/j.physbeh.2026.115453
- Authors
- Kawatake-Kuno, A., Murai, T., & Uchida, S.
- Affiliations
- Kyoto University (JP)
- Corresponding author
- Uchida, Shusaku
- Venue
- Frontiers in Molecular Neuroscience
- Publisher
- Frontiers Media SA
- Published
- 2021-07-01
- Volume
- 14
- Pages
- 708004-708004
- ISSN
- 1662-5099 (ISSN-L)
- PMC
- PMC8282210
- OpenAlex
- W3182076372
- Cited by
- 23
- References
- 251
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 5 · 2023: 3 · 2022: 4 · 2021: 2
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Molecular Neuroscience (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Japan Society for the Promotion of Science
- Japan Agency for Medical Research and Development
- Ministry of Education, Culture, Sports, Science and Technology
- Topics
- Health Sciences › Medicine › Pharmacology › Treatment of Major Depression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Neuroscience › Behavioral Neuroscience › Stress Responses and Cortisol
- Keywords
- major depressive disorder, sex differences, epigenetic regulation, DNA methylation, histone modifications, non-coding RNA, neuroplasticity, stress, antidepressant response, depression resilience, depression vulnerability, personalized treatment
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.
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