My Bibliography

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Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J. 2022 Nov 17;41(22):e112012. doi: 10.15252/embj.2022112012. Epub 2022 Oct 10. PubMed PMID: 36215692; PubMed Central PMCID: PMC9670200.

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Zhang C, Chen R, Zhang Y. Accurate inference of genome-wide spatial expression with iSpatial. Sci Adv. 2022 Aug 26;8(34):eabq0990. doi: 10.1126/sciadv.abq0990. Epub 2022 Aug 26. PubMed PMID: 36026447; PubMed Central PMCID: PMC9417177.

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Zhao ZD, Han X, Chen R, Liu Y, Bhattacherjee A, Chen W, Zhang Y. A molecularly defined D1 medium spiny neuron subtype negatively regulates cocaine addiction. Sci Adv. 2022 Aug 12;8(32):eabn3552. doi: 10.1126/sciadv.abn3552. Epub 2022 Aug 12. PubMed PMID: 35960793; PubMed Central PMCID: PMC9374336.

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Zhang W, Zhang Y. TARSII and CARSII: Two approaches for SNP-independent identification of germline differentially methylated regions in mammals. STAR Protoc. 2022 Jun 17;3(2):101240. doi: 10.1016/j.xpro.2022.101240. eCollection 2022 Jun 17. PubMed PMID: 35310079; PubMed Central PMCID: PMC8931438.

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Chen R, Liu Y, Djekidel MN, Chen W, Bhattacherjee A, Chen Z, Scolnick E, Zhang Y. Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis. Sci Adv. 2022 Mar 4;8(9):eabm1077. doi: 10.1126/sciadv.abm1077. Epub 2022 Mar 4. PubMed PMID: 35245111; PubMed Central PMCID: PMC8896793.

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Xie Z, Zhang W, Zhang Y. Loss of Slc38a4 imprinting is a major cause of mouse placenta hyperplasia in somatic cell nuclear transferred embryos at late gestation. Cell Rep. 2022 Feb 22;38(8):110407. doi: 10.1016/j.celrep.2022.110407. PubMed PMID: 35196486; PubMed Central PMCID: PMC8919768.

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Gao Y, Duque-Wilckens N, Aljazi MB, Moeser AJ, Mias GI, Robison AJ, Zhang Y, He J. Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors. iScience. 2022 Feb 18;25(2):103742. doi: 10.1016/j.isci.2022.103742. eCollection 2022 Feb 18. PubMed PMID: 35128353; PubMed Central PMCID: PMC8800019.

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Zhang C, Wang M, Li Y, Zhang Y. Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition. Sci Adv. 2022 Feb 4;8(5):eabj3967. doi: 10.1126/sciadv.abj3967. Epub 2022 Feb 2. PubMed PMID: 35108058; PubMed Central PMCID: PMC8809684.

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Chen Z, Xie Z, Zhang Y. DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and pre-implantation development. Development. 2021 Dec 15;148(24). doi: 10.1242/dev.200178. Epub 2021 Dec 21. PubMed PMID: 34878123; PubMed Central PMCID: PMC8722388.

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Chen R, Blosser TR, Djekidel MN, Hao J, Bhattacherjee A, Chen W, Tuesta LM, Zhuang X, Zhang Y. Decoding molecular and cellular heterogeneity of mouse nucleus accumbens. Nat Neurosci. 2021 Dec;24(12):1757-1771. doi: 10.1038/s41593-021-00938-x. Epub 2021 Oct 18. PubMed PMID: 34663959; PubMed Central PMCID: PMC8639815.

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Wang Y, Wang M, Djekidel MN, Chen H, Liu D, Alt FW, Zhang Y. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature. 2021 Nov;599(7884):308-314. doi: 10.1038/s41586-021-04009-w. Epub 2021 Oct 20. PubMed PMID: 34671165; PubMed Central PMCID: PMC9295135.

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Chu C, Zhang W, Kang Y, Si C, Ji W, Niu Y, Zhang Y. Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta. Dev Cell. 2021 Oct 25;56(20):2826-2840.e7. doi: 10.1016/j.devcel.2021.09.012. Epub 2021 Oct 6. PubMed PMID: 34619096.

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Chen Z, Djekidel MN, Zhang Y. Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos. Nat Genet. 2021 Apr;53(4):551-563. doi: 10.1038/s41588-021-00821-2. Epub 2021 Apr 5. PubMed PMID: 33821005; PubMed Central PMCID: PMC8092361.

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Fu X, Zhang C, Zhang Y. Epigenetic regulation of mouse preimplantation embryo development. Curr Opin Genet Dev. 2020 Oct;64:13-20. doi: 10.1016/j.gde.2020.05.015. Epub 2020 Jun 18. Review. PubMed PMID: 32563750; PubMed Central PMCID: PMC7641911.

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Chen Z, Zhang Y. Maternal H3K27me3-dependent autosomal and X chromosome imprinting. Nat Rev Genet. 2020 Sep;21(9):555-571. doi: 10.1038/s41576-020-0245-9. Epub 2020 Jun 8. Review. PubMed PMID: 32514155; PubMed Central PMCID: PMC7717073.

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Abbott J, Ye T, Krenek K, Qin L, Kim Y, Wu W, Gertner RS, Park H, Ham D. The Design of a CMOS Nanoelectrode Array with 4096 Current-Clamp/Voltage-Clamp Amplifiers for Intracellular Recording/Stimulation of Mammalian Neurons. IEEE J Solid-State Circuits. 2020 Sep;55(9):2567-2582. doi: 10.1109/jssc.2020.3005816. Epub 2020 Jul 9. PubMed PMID: 33762776; PubMed Central PMCID: PMC7983016.

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Chen Z, Zhang Y. Role of Mammalian DNA Methyltransferases in Development. Annu Rev Biochem. 2020 Jun 20;89:135-158. doi: 10.1146/annurev-biochem-103019-102815. Epub 2019 Dec 9. Review. PubMed PMID: 31815535.

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Fu X, Djekidel MN, Zhang Y. A transcriptional roadmap for 2C-like-to-pluripotent state transition. Sci Adv. 2020 May;6(22):eaay5181. doi: 10.1126/sciadv.aay5181. eCollection 2020 May. PubMed PMID: 32523982; PubMed Central PMCID: PMC7259939.

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Zhang C, Chen Z, Yin Q, Fu X, Li Y, Stopka T, Skoultchi AI, Zhang Y. The chromatin remodeler Snf2h is essential for oocyte meiotic cell cycle progression. Genes Dev. 2020 Feb 1;34(3-4):166-178. doi: 10.1101/gad.331157.119. Epub 2020 Jan 9. PubMed PMID: 31919188; PubMed Central PMCID: PMC7000916.

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Chen Z, Yin Q, Inoue A, Zhang C, Zhang Y. Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells. Sci Adv. 2019 Dec;5(12):eaay7246. doi: 10.1126/sciadv.aay7246. eCollection 2019 Dec. PubMed PMID: 32064321; PubMed Central PMCID: PMC6989337.

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Tran NM, Shekhar K, Whitney IE, Jacobi A, Benhar I, Hong G, Yan W, Adiconis X, Arnold ME, Lee JM, Levin JZ, Lin D, Wang C, Lieber CM, Regev A, He Z, Sanes JR. Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes. Neuron. 2019 Dec 18;104(6):1039-1055.e12. doi: 10.1016/j.neuron.2019.11.006. Epub 2019 Nov 26. PubMed PMID: 31784286; PubMed Central PMCID: PMC6923571.

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Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R. Toward a Common Coordinate Framework for the Human Body. Cell. 2019 Dec 12;179(7):1455-1467. doi: 10.1016/j.cell.2019.11.019. Review. PubMed PMID: 31835027; PubMed Central PMCID: PMC6934046.

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Bhattacherjee A, Djekidel MN, Chen R, Chen W, Tuesta LM, Zhang Y. Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction. Nat Commun. 2019 Sep 13;10(1):4169. doi: 10.1038/s41467-019-12054-3. PubMed PMID: 31519873; PubMed Central PMCID: PMC6744514.

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Lu X, Chu CS, Fang T, Rayon-Estrada V, Fang F, Patke A, Qian Y, Clarke SH, Melnick AM, Zhang Y, Papavasiliou FN, Roeder RG. MTA2/NuRD Regulates B Cell Development and Cooperates with OCA-B in Controlling the Pre-B to Immature B Cell Transition. Cell Rep. 2019 Jul 9;28(2):472-485.e5. doi: 10.1016/j.celrep.2019.06.029. PubMed PMID: 31291582; PubMed Central PMCID: PMC6690613.

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Fu X, Wu X, Djekidel MN, Zhang Y. Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells. Nat Cell Biol. 2019 Jul;21(7):835-844. doi: 10.1038/s41556-019-0343-0. Epub 2019 Jun 17. PubMed PMID: 31209294; PubMed Central PMCID: PMC7137718.

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Tuesta LM, Djekidel MN, Chen R, Lu F, Wang W, Sabatini BL, Zhang Y. In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function. Nat Commun. 2019 Jun 7;10(1):2508. doi: 10.1038/s41467-019-10267-0. PubMed PMID: 31175277; PubMed Central PMCID: PMC6555850.

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Chen Z, Zhang Y. Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development. Nat Genet. 2019 Jun;51(6):947-951. doi: 10.1038/s41588-019-0418-7. Epub 2019 May 27. PubMed PMID: 31133747; PubMed Central PMCID: PMC6545155.

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Zhang W, Chen Z, Yin Q, Zhang D, Racowsky C, Zhang Y. Maternal-biased H3K27me3 correlates with paternal-specific gene expression in the human morula. Genes Dev. 2019 Apr 1;33(7-8):382-387. doi: 10.1101/gad.323105.118. Epub 2019 Feb 26. PubMed PMID: 30808660; PubMed Central PMCID: PMC6446541.

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Inoue A, Chen Z, Yin Q, Zhang Y. Maternal Eed knockout causes loss of H3K27me3 imprinting and random X inactivation in the extraembryonic cells. Genes Dev. 2018 Dec 1;32(23-24):1525-1536. doi: 10.1101/gad.318675.118. Epub 2018 Nov 21. PubMed PMID: 30463900; PubMed Central PMCID: PMC6295166.

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Kim H, Kim D, Choi SA, Kim CR, Oh SK, Pyo KE, Kim J, Lee SH, Yoon JB, Zhang Y, Baek SH. KDM3A histone demethylase functions as an essential factor for activation of JAK2-STAT3 signaling pathway. Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):11766-11771. doi: 10.1073/pnas.1805662115. Epub 2018 Oct 30. PubMed PMID: 30377265; PubMed Central PMCID: PMC6243239.

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Matoba S, Zhang Y. Somatic Cell Nuclear Transfer Reprogramming: Mechanisms and Applications. Cell Stem Cell. 2018 Oct 4;23(4):471-485. doi: 10.1016/j.stem.2018.06.018. Epub 2018 Jul 19. Review. PubMed PMID: 30033121; PubMed Central PMCID: PMC6173619.

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Matoba S, Wang H, Jiang L, Lu F, Iwabuchi KA, Wu X, Inoue K, Yang L, Press W, Lee JT, Ogura A, Shen L, Zhang Y. Loss of H3K27me3 Imprinting in Somatic Cell Nuclear Transfer Embryos Disrupts Post-Implantation Development. Cell Stem Cell. 2018 Sep 6;23(3):343-354.e5. doi: 10.1016/j.stem.2018.06.008. Epub 2018 Jul 19. PubMed PMID: 30033120; PubMed Central PMCID: PMC6326833.

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Djekidel MN, Inoue A, Matoba S, Suzuki T, Zhang C, Lu F, Jiang L, Zhang Y. Reprogramming of Chromatin Accessibility in Somatic Cell Nuclear Transfer Is DNA Replication Independent. Cell Rep. 2018 May 15;23(7):1939-1947. doi: 10.1016/j.celrep.2018.04.036. PubMed PMID: 29768195; PubMed Central PMCID: PMC5988247.

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Lee CC, Peng SH, Shen L, Lee CF, Du TH, Kang ML, Xu GL, Upadhyay AK, Cheng X, Yan YT, Zhang Y, Juan LJ. The Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell. 2017 Oct 5;68(1):89-103.e7. doi: 10.1016/j.molcel.2017.08.025. Epub 2017 Sep 21. PubMed PMID: 28943313; PubMed Central PMCID: PMC6322414.

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Inoue A, Jiang L, Lu F, Zhang Y. Genomic imprinting of Xist by maternal H3K27me3. Genes Dev. 2017 Oct 1;31(19):1927-1932. doi: 10.1101/gad.304113.117. PubMed PMID: 29089420; PubMed Central PMCID: PMC5710138.

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Wu X, Zhang Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat Rev Genet. 2017 Sep;18(9):517-534. doi: 10.1038/nrg.2017.33. Epub 2017 May 30. Review. PubMed PMID: 28555658.

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Inoue A, Jiang L, Lu F, Suzuki T, Zhang Y. Maternal H3K27me3 controls DNA methylation-independent imprinting. Nature. 2017 Jul 27;547(7664):419-424. doi: 10.1038/nature23262. Epub 2017 Jul 19. PubMed PMID: 28723896; PubMed Central PMCID: PMC9674007.

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Wu X, Inoue A, Suzuki T, Zhang Y. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes Dev. 2017 Mar 1;31(5):511-523. doi: 10.1101/gad.294843.116. Epub 2017 Mar 30. PubMed PMID: 28360182; PubMed Central PMCID: PMC5393065.

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Chen R, Wu X, Jiang L, Zhang Y. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Cell Rep. 2017 Mar 28;18(13):3227-3241. doi: 10.1016/j.celrep.2017.03.004. PubMed PMID: 28355573; PubMed Central PMCID: PMC5782816.

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Tao J, Wu H, Coronado AA, de Laittre E, Osterweil EK, Zhang Y, Bear MF. Negative Allosteric Modulation of mGluR5 Partially Corrects Pathophysiology in a Mouse Model of Rett Syndrome. J Neurosci. 2016 Nov 23;36(47):11946-11958. doi: 10.1523/JNEUROSCI.0672-16.2016. PubMed PMID: 27881780; PubMed Central PMCID: PMC5125247.

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Kim M, Lu F, Zhang Y. Loss of HDAC-Mediated Repression and Gain of NF-κB Activation Underlie Cytokine Induction in ARID1A- and PIK3CA-Mutation-Driven Ovarian Cancer. Cell Rep. 2016 Sep 27;17(1):275-288. doi: 10.1016/j.celrep.2016.09.003. PubMed PMID: 27681437; PubMed Central PMCID: PMC7734570.

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Lu F, Liu Y, Inoue A, Suzuki T, Zhao K, Zhang Y. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016 Jun 2;165(6):1375-1388. doi: 10.1016/j.cell.2016.05.050. PubMed PMID: 27259149; PubMed Central PMCID: PMC6625655.

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Wu H, Wu X, Zhang Y. Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq. Nat Protoc. 2016 Jun;11(6):1081-100. doi: 10.1038/nprot.2016.069. Epub 2016 May 12. PubMed PMID: 27172168; PubMed Central PMCID: PMC5123565.

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Jiang H, Xu Z, Zhong P, Ren Y, Liang G, Schilling HA, Hu Z, Zhang Y, Wang X, Chen S, Yan Z, Feng J. Cell cycle and p53 gate the direct conversion of human fibroblasts to dopaminergic neurons. Nat Commun. 2015 Dec 7;6:10100. doi: 10.1038/ncomms10100. PubMed PMID: 26639555; PubMed Central PMCID: PMC4672381.

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Chung YG, Matoba S, Liu Y, Eum JH, Lu F, Jiang W, Lee JE, Sepilian V, Cha KY, Lee DR, Zhang Y. Histone Demethylase Expression Enhances Human Somatic Cell Nuclear Transfer Efficiency and Promotes Derivation of Pluripotent Stem Cells. Cell Stem Cell. 2015 Dec 3;17(6):758-766. doi: 10.1016/j.stem.2015.10.001. Epub 2015 Oct 29. PubMed PMID: 26526725.

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Wu H, Zhang Y. Charting oxidized methylcytosines at base resolution. Nat Struct Mol Biol. 2015 Sep;22(9):656-61. doi: 10.1038/nsmb.3071. PubMed PMID: 26333715; PubMed Central PMCID: PMC4671372.

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Lu F, Zhang Y. Cell totipotency: molecular features, induction, and maintenance. Natl Sci Rev. 2015 Jun;2(2):217-225. doi: 10.1093/nsr/nwv009. PubMed PMID: 26114010; PubMed Central PMCID: PMC4477869.

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Jiang W, Liu Y, Liu R, Zhang K, Zhang Y. The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression. Cell Rep. 2015 Apr 7;11(1):137-48. doi: 10.1016/j.celrep.2015.03.008. Epub 2015 Apr 2. PubMed PMID: 25843708; PubMed Central PMCID: PMC7721200.

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Inoue A, Shen L, Matoba S, Zhang Y. Haploinsufficiency, but not defective paternal 5mC oxidation, accounts for the developmental defects of maternal Tet3 knockouts. Cell Rep. 2015 Feb 3;10(4):463-70. doi: 10.1016/j.celrep.2014.12.049. Epub 2015 Jan 29. PubMed PMID: 25640176; PubMed Central PMCID: PMC7717667.

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Wu H, Wu X, Shen L, Zhang Y. Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat Biotechnol. 2014 Dec;32(12):1231-40. doi: 10.1038/nbt.3073. Epub 2014 Nov 2. PubMed PMID: 25362244; PubMed Central PMCID: PMC4269366.