top of page


Cytosine Modifications in Development and Stem Cells

Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P.*, and He, C*. (2010) A Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology, 29(1): 68-72. (*:Co-Corresponding authors) PMC3107705


Yu, M., Hon, G.C., Szulwach, K.E., Song, C.X., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., Min, J.H., Jin, P. *, Ren, B. *, and He. C. * (2012) Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell, 149: 1368-1380. (*: Co-Corresponding authors). PMC3589129

Song, C.X., Szulwach, K.E., Dai, Q., Fu, Y., Mao, S.Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., Gao, J., Liu, P., Li, L., Xu, G.L., Jin, P.*, and He, C.* Genome-wide Profiling of 5-Formylcytosine reveals its roles in epigenetic priming. Cell, 153: 678-691. (*:Co-Corresponding authors)  PMC3657391

Wang, T., Wu, H., Li, Y., Szulwach, K.E., Lin, L., Li, X., Chen, I.P., Goldlust, I.S., Chamberlain, S.J., Ananiev, G., Mowrey, J., Han, J.W., Yoon, Y., Rudd, M.K., Song, C.X., He, C., Chang, Q., Warren, S.T., and Jin, P. (2013) Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nature Cell Biology, 15: 700-711.  PMC3998089


Szulwach, K.E., Li, X., Li, Y., Song, C.X., Wu, H., Dai, Q., Irier, H., Upadhyay, A.K., Gearing, M., Levey, A.I., Vasanthakumar, A., Godley, L.A., Chang, Q., Cheng, X., He, C. and Jin, P. (2011) 5-hydroxymethylcytosine-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nature Neuroscience, 14: 1607-1616.  PMC3292193

Yao, B., Lin, L., Street, R.C., Zalewski, Z.A., Galloway, J.N., Wu, H., Nelson, D.L., and Jin, P. (2013) Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome. Human Molecular Genetics, 23: 1095-1107.  PMC3900112

Yao B, Cheng Y, Wang Z, Li Y, Chen L, Huang L, Zhang W, Chen D, Wu H, Tang B and Jin P. (2017) DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nature Communications, 8: 1122. PMC5654764

Yao B, Li, Y., Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Philips BL, Xu T, Duan R, Moberg KH, Wu H, Jin P (2018) Active N6-Methyladenine demethylation by DMAD regulates gene expression by coordinating with Polycomb protein in neurons. Molecular Cell, 71: 848-857. PMC6136845

Tet-mediated epigenetic modulation in development and diseases

Zeng Y, Yao B, Shin J, Lin L, Kim N, Song Q, Liu S, Su Y, Guo JU, Huang L, Wan J, Wu H, Qian J, Cheng X, Zhu H, Ming GL, Jin P*, Song H*. (2016). Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Molecular Cell, 61, 153-160. (*: Co-Corresponding authors) PMC4779955


Yao, B. and Jin, P. (2014) Unlocking epigenetic codes in neurogenesis. Genes & Development, 28, 1253-1271.  PMC4066397


Li X, Yao B, Chen L, Kang Y, Li Y, Cheng Y, Li L, Lin L, Wang Z, Wang M, Pan F, Dai Q, Zhang W, Wu H, Shu Q, Qin Z, He C, Xu M, Jin P. (2017) Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. Nature Communications, 8:15903. PMC5493768


Cheng Y, Sun M, Chen L, Li Y, Lin L, Yao B, Li Z, Wang Z, Chen J, Miao Z, Xin N, Huang L, Allen EG, Wu H, Xu X, Jin P. (2018) Distinct roles of Ten-eleven translocation protein 1 and 2 in response to environmental stress. Cell Reports, 25: 3194-3203.

RNA Dysregulation in Neurological Disorders

Jin, P., Zarnescu, D.C., Zhang, F., Pearson, C.E., Lucchesi, J.C., Moses, K and Warren, S.T. (2003). RNA-mediated neurodegeneration caused by the fragile X premutation rCGG repeats in Drosophila. Neuron, 39, 739-747. (PMID: 12948442)


Sofola, O.A.*, Jin, P.* (equal contribution), Qin, Y., Duan, R., Liu, H., de Haro, M., Nelson, D.L., and Botas, J. (2007). RNA binding proteins hnRNP A2/B1 and CUGBP1 suppress Fragile X CGG premutation repeat-induced neurodegeneration in a Drosophila model of FXTAS. Neuron, 16, 565-571. PMC2215388


Jin, P.*, Duan, R., Qurashi, A., Qin, Y., Tian, D., Rosser, T.C., Liu, H., Feng, Y., and Warren, S.T.* (2007). Pur a binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of Fragile X Tremor/Ataxia Syndrome. Neuron, 16, 556-564. (*:Co-Corresponding authors) PMC1994817


Xu, Z., Poidevin, M., Li, X., Li, Y., Shu, L., Nelson, D.L., Li, H., Gearing, M., Wingo, T.S., and Jin, P. (2013) Expanded Hexanucleotide GGGGCC Repeat RNA Associated with ALS/FTD Causes Neurodegeneration. Proceedings of the National Academy of Sciences, 110: 7778-7783.  PMC3651485

MicroRNAs and Human Diseases

Szulwach K. E., Li, X., Smrt, R.D., Li, Y., Luo, Y., Lin, L., Satistevan, N.J., Li, W. Zhao, X., and Jin, P. (2010) Cross talk between microRNA and epigenetic regulation in adult neurogenesis. Journal of Cell Biology, 189, 127-141.  PMC2854370


Jin, P., Zarnescu, D.C., Ceman, S., Nakamoto, M., Mowrey, J., Jongens, T.A., Nelson, D.L., Moses, K., and Warren, S.T. (2004). Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature Neuroscience, 7, 113-117.


Cheng Y, Wang ZM, Tan W, Wang X, Li Y, Bai B, Li Y, Zhang SF, Yan HL, Chen ZL, Liu CM, Mi TW, Xia S, Zhou Z, Liu A, Tang GB, Liu C, Dai ZJ, Wang YY, Wang H, Wang X, Kang Y, Lin L, Chen Z, Xie N, Sun Q, Xie W, Peng J, Chen D, Teng ZQ, Jin P. (2018) Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a. Nature Neuroscience, Epub 2018/11/07. PubMed PMID: 30397325.

Small Molecules and RNAi

Shan, G.*, Li, Y.* (*Equal Contribution), Zhang, J., Li, W., Szulwach, K., Duan, R., Faghihi, M.A., Khalil, A., Lu, L., Paroo, Z., Chan, A.W.S., Shi, Z., Liu, Q., Wahlestedt, C., He, C., and Jin, P. (2008). A small molecule enhances RNA interference and promotes microRNA processing. Nature Biotechnology, 8, 933-940. PMC2831467


Li, X. and Jin, P. (2010). Roles of small regulatory RNAs in determining neuronal identity. Nature Reviews Neuroscience, 11(5): 329-338.


Li, Y., He, C. and Jin, P. (2010). Emergence of Chemical Biology Approaches to the RNAi/miRNA Pathway. Chemistry & Biology, 17(6): 584-589.  PMC2901241


Li, Y., Lin, L., Li, Z., Ye, X., Xiong, K., Aryal, B., Xu, Z., Paroo, Z., Liu, Q., He, C., and Jin, P. (2012) Iron Homeostasis Regulates the Activity of the MicroRNA Pathway through Poly(C)-Binding Protein 2. Cell Metabolism, 15, 895-904.  PMC3613991



Cheng Y, Jin P. Dysfunction of Habituation Learning: A Novel Pathogenic Paradigm of Intellectual Disability and Autism Spectrum Disorder. Biol Psychiatry. 2019 Aug 15;86(4):253-254. doi: 10.1016/j.biopsych.2019.06.012. PubMed PMID: 31370964.


Armstrong MJ, Jin Y, Allen EG, Jin P. Diverse and Dynamic DNA Modifications in Brain and Diseases. Hum Mol Genet. 2019 Jul 26;. doi: 10.1093/hmg/ddz179. [Epub ahead of print] PubMed PMID: 31348493.


He H, Huang W, Wang R, Lin Y, Guo Y, Deng J, Deng H, Zhu Y, Allen EG, Jin P, Duan R. Amyotrophic Lateral Sclerosis-associated GGGGCC repeat expansion promotes Tau phosphorylation and toxicity. Neurobiol Dis. 2019 Jun 6;:104493. doi: 10.1016/j.nbd.2019.104493. [Epub ahead of print] PubMed PMID: 31176718.


Tian Y, Wang JL, Huang W, Zeng S, Jiao B, Liu Z, Chen Z, Li Y, Wang Y, Min HX, Wang XJ, You Y, Zhang RX, Chen XY, Yi F, Zhou YF, Long HY, Zhou CJ, Hou X, Wang JP, Xie B, Liang F, Yang ZY, Sun QY, Allen EG, Shafik AM, Kong HE, Guo JF, Yan XX, Hu ZM, Xia K, Jiang H, Xu HW, Duan RH, Jin P, Tang BS, Shen L. Expansion of Human-Specific GGC Repeat in Neuronal Intranuclear Inclusion Disease-Related Disorders. Am J Hum Genet. 2019 May 27;. doi: 10.1016/j.ajhg.2019.05.013. [Epub ahead of print] PubMed PMID: 31178126.


Kim H, Lim J, Bao H, Jiao B, Canon SM, Epstein MP, Xu K, Jiang J, Parameswaran J, Li Y, Moberg KH, Landers JE, Fournier C, Allen EG, Glass JD, Wingo TS, Jin P. Rare variants in MYH15 modify amyotrophic lateral sclerosis risk. Hum Mol Genet.2019 Apr 1;. doi: 10.1093/hmg/ddz063. [Epub ahead of print] PubMed PMID: 30985904.


Li Z, Wu Z, Jin P, Wu H. Dissecting differential signals in high-throughput data from complex tissues. Bioinformatics. 2019 Mar 23;. doi: 10.1093/bioinformatics/btz196. [Epub ahead of print] PubMed PMID: 30903684.


Aoued HS, Sannigrahi S, Doshi N, Morrison FG, Linsenbaum H, Hunter SC, Walum H, Baman J, Yao B, Jin P, Ressler KJ, Dias BG. Reversing Behavioral, Neuroanatomical, and Germline Influences of Intergenerational Stress. Biol Psychiatry.2019 Feb 1;85(3):248-256. doi: 10.1016/j.biopsych.2018.07.028. Epub 2018 Aug 27. PubMed PMID: 30292395; PubMed Central PMCID: PMC6326876.


Kong HE, Lim J, Jin P. Application of Drosophila Model Toward Understanding the Molecular Basis of Fragile X Syndrome. Methods Mol Biol. 2019;1942:141-153. doi: 10.1007/978-1-4939-9080-1_12. PubMed PMID: 30900182.


Cheng Y, Sun M, Chen L, Li Y, Lin L, Yao B, Li Z, Wang Z, Chen J, Miao Z, Xin N, Huang L, Allen EG, Wu H, Xu X, Jin P. Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice. Cell Rep. 2018 Dec 11;25(11):3194-3203.e4. doi: 10.1016/j.celrep.2018.11.061. PubMed PMID: 30540950; PubMed Central PMCID: PMC6350936.


Cheng Y, Wang ZM, Tan W, Wang X, Li Y, Bai B, Li Y, Zhang SF, Yan HL, Chen ZL, Liu CM, Mi TW, Xia S, Zhou Z, Liu A, Tang GB, Liu C, Dai ZJ, Wang YY, Wang H, Wang X, Kang Y, Lin L, Chen Z, Xie N, Sun Q, Xie W, Peng J, Chen D, Teng ZQ, Jin P. Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a. Nat Neurosci. 2018 Dec;21(12):1689-1703. doi: 10.1038/s41593-018-0261-7. Epub 2018 Nov 5. PubMed PMID: 30397325; PubMed Central PMCID: PMC6261680.


Kong HE, Lim J, Zhang F, Huang L, Gu Y, Nelson DL, Allen EG, Jin P. Metabolic pathways modulate the neuronal toxicity associated with Fragile X-Associated Tremor/Ataxia Syndrome. Hum Mol Genet. 2018 Nov 26;. doi: 10.1093/hmg/ddy410. [Epub ahead of print] PubMed PMID: 30476102; PubMed Central PMCID: PMC6400045.


Xu T, Zheng X, Li B, Jin P, Qin Z, Wu H. A comprehensive review of computational prediction of genome-wide features.Brief Bioinform. 2018 Nov 16;. doi: 10.1093/bib/bby110. [Epub ahead of print] PubMed PMID: 30462144.


Zhang F, Kang Y, Wang M, Li Y, Xu T, Yang W, Song H, Wu H, Shu Q, Jin P. Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets. Hum Mol Genet. 2018 Nov 15;27(22):3936-3950. doi: 10.1093/hmg/ddy292. PubMed PMID: 30107516; PubMed Central PMCID: PMC6216232.


Yao B, Li Y, Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Phillips BL, Xu T, Duan R, Moberg KH, Wu H, Jin P. Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell. 2018 Sep 6;71(5):848-857.e6. doi: 10.1016/j.molcel.2018.07.005. Epub 2018 Aug 2. PubMed PMID: 30078725; PubMed Central PMCID: PMC6136845.


Cheng Y, Li Z, Manupipatpong S, Lin L, Li X, Xu T, Jiang YH, Shu Q, Wu H, Jin P. 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder. Hum Mol Genet. 2018 Sep 1;27(17):2955-2964. doi: 10.1093/hmg/ddy193. PubMed PMID: 29790956; PubMed Central PMCID: PMC6097011.


Sun X, Gao J, Jin P, Eng C, Burchard EG, Beaty TH, Ruczinski I, Mathias RA, Barnes K, Wang F, Qin ZS. Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files. Gigascience.2018 Jun 1;7(6). doi: 10.1093/gigascience/giy052. PubMed PMID: 29762754; PubMed Central PMCID: PMC6007233.


Feng H, Jin P, Wu H. Disease prediction by cell-free DNA methylation. Brief Bioinform. 2018 Apr 16;. doi: 10.1093/bib/bby029. [Epub ahead of print] PubMed PMID: 29672679.


Yao B, Jin P. A unique epigenomic landscape defines the characteristics and differentiation potentials of glioma stem cells. Genome Biol. 2018 Apr 10;19(1):51. doi: 10.1186/s13059-018-1429-x. PubMed PMID: 29636115; PubMed Central PMCID: PMC5894242.


Kim H, Wang X, Jin P. Developing DNA methylation-based diagnostic biomarkers. J Genet Genomics. 2018 Feb 20;45(2):87-97. doi: 10.1016/j.jgg.2018.02.003. Epub 2018 Feb 17. Review. PubMed PMID: 29496486; PubMed Central PMCID: PMC5857251.


Jin P. Medical genetics: Towards precision medicine. J Genet Genomics. 2018 Feb 20;45(2):55-56. doi: 10.1016/j.jgg.2018.02.005. PubMed PMID: 29548346.


Guo J, Cui Y, Liu Q, Yang Y, Li Y, Weng L, Tang B, Jin P, Li XJ, Yang S, Li S. Piperine ameliorates SCA17 neuropathology by reducing ER stress. Mol Neurodegener. 2018 Jan 30;13(1):4. doi: 10.1186/s13024-018-0236-x. PubMed PMID: 29378605; PubMed Central PMCID: PMC5789626.


Weng YL, Wang X, An R, Cassin J, Vissers C, Liu Y, Liu Y, Xu T, Wang X, Wong SZH, Joseph J, Dore LC, Dong Q, Zheng W, Jin P, Wu H, Shen B, Zhuang X, He C, Liu K, Song H, Ming GL. Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System. Neuron. 2018 Jan 17;97(2):313-325.e6. doi: 10.1016/j.neuron.2017.12.036. PubMed PMID: 29346752; PubMed Central PMCID: PMC5777326.


Yoon KJ, Ringeling FR, Vissers C, Jacob F, Pokrass M, Jimenez-Cyrus D, Su Y, Kim NS, Zhu Y, Zheng L, Kim S, Wang X, Doré LC, Jin P, Regot S, Zhuang X, Canzar S, He C, Ming GL, Song H. Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation. Cell. 2017 Nov 2;171(4):877-889.e17. doi: 10.1016/j.cell.2017.09.003. Epub 2017 Sep 28. PubMed PMID: 28965759; PubMed Central PMCID: PMC5679435.


Yao B, Cheng Y, Wang Z, Li Y, Chen L, Huang L, Zhang W, Chen D, Wu H, Tang B, Jin P. DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nat Commun. 2017 Oct 24;8(1):1122. doi: 10.1038/s41467-017-01195-y. PubMed PMID: 29066820; PubMed Central PMCID: PMC5654764.

Complete List of Published Works

bottom of page