Adams, K.L., Riparini, G., Banerjee, P., Breur, M., Bugiani, M., Gallo, V., 2020. Endothelin-1 signaling maintains glial progenitor proliferation in the postnatal subventricular zone. Nat. Commun. 11, 2138.
|
Al-Mahdawi, S., Virmouni, S.A., Pook, M.A., 2014. The emerging role of 5-hydroxymethylcytosine in neurodegenerative diseases. Front. Neurosci. 8, 397.
|
Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F.E., Figueroa, M.E., Melnick, A., Mason, C. E., 2012. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 13, 1-9.
|
Antony, D., Becker-Heck, A., Zariwala, M.A., Schmidts, M., Onoufriadis, A., Forouhan, M., Wilson, R., Taylor-Cox, T., Dewar, A., Jackson, C., et al., 2013. Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms. Hum. Mutat. 34, 462-472.
|
Boonsawat, P., Joset, P., Steindl, K., Oneda, B., Gogoll, L., Azzarello-Burri, S., Sheth, F., Datar, C., Verma, I.C., Puri, R.D., et al., 2019. Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly. Genet. Med. 21, 2043-2058.
|
Bradley-Whitman, M.A., Lovell, M.A., 2013. Epigenetic changes in the progression of Alzheimer's disease. Mech. Ageing Dev. 134, 486-495.
|
Campbell, C.E., Piper, M., Plachez, C., Yeh, Y.T., Baizer, J.S., Osinski, J.M., Litwack, E.D., Richards, L.J., Gronostajski, R.M., 2008. The transcription factor Nfix is essential for normal brain development. BMC Dev. Biol. 8, 52.
|
Coppieters, N., Dieriks, B.V., Lill, C., Faull, R.L.M., Curtis, M.A., Dragunow, M., 2014. Global changes in DNA methylation and hydroxymethylation in Alzheimer's disease human brain. Neurobiol. Aging 35, 1334-1344.
|
Damian, J.P., Vazquez Alberdi, L., Canclini, L., Rosso, G., Bravo, S.O., Martinez, M., Uriarte, N., Ruiz, P., Calero, M., Tomaso, M.V.D., et al., 2021. Central alteration in peripheral neuropathy of Trembler-J mice: hippocampal pmp22 expression and behavioral profile in anxiety tests. Biomolecules 11, 601.
|
El Ghaleb, Y., Schneeberger, P. E., Fernandez-Quintero, M. L., Geisler, S. M., Pelizzari, S., Polstra, A. M., Hagen, J. M., Denecke, J., Campiglio, M., Liedl, K. R., et al., 2021. CACNA1I gain-of-function mutations differentially affect channel gating and cause neurodevelopmental disorders. Brain 144, 2092-2106.
|
Ghafouri-Fard, S., Fardaei, M., Gholami, M., Miryounesi, M., 2015. A case report: autosomal recessive microcephaly caused by a novel mutation in MCPH1 gene. Gene 571, 149-150.
|
Gruber, R., Zhou, Z., Sukchev, M., Joerss, T., Frappart, P.O., Wang, Z.Q., 2011. MCPH1 regulates the neuroprogenitor division mode by coupling the centrosomal cycle with mitotic entry through the Chk1-Cdc25 pathway. Nat. Cell Biol. 13, 1325-1334.
|
Gu, T., Lin, X., Cullen, S.M., Luo, M., Jeong, M., Estecio, M., Shen, J., Hardikar, S., Sun, D., Su, J., et al., 2018. DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells. Genome Biol. 19, 1-15.
|
Guo, J.U., Ma, D.K., Mo, H., Ball, M.P., Jang, M.H., Bonaguidi, M.A., Balazer, J.A., Eaves, H.L., Xie, B., Ford E., et al., 2011a. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat. Neurosci. 14, 1345-1351.
|
Guo, J.U., Su, Y., Zhong, C., Ming, G.L., Song, H., 2011b. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-434.
|
Han, Q., Kono, T.J.Y., Knutson, C.G., Parry, N.M., Seiler, C.L., Fox, J.G., Tannenbaum, S.R., Tretyakova, N.Y., 2021. Multi-omics characterization of inflammatory bowel disease-induced hyperplasia/dysplasia in the Rag2-/-/Il10-/- mouse model. Int. J. Mol. Sci. 22, 364.
|
Henderson, J.T., Georgiou, J., Jia, Z., Robertson, J., Elowe, S., Roder, J.C., Pawson, T., 2001. The receptor tyrosine kinase EphB2 regulates NMDA-dependent synaptic function. Neuron 32, 1041-1056.
|
Jiang, J., Chan, Y.S., Loh, Y.H., Cai, J., Tong, G.Q., Lim, C.A., Robson, P., Zhong, S., Ng, H.H., 2008. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat. Cell Biol. 10, 353-360.
|
Jin, S.G., Zhang, Z.M., Dunwell, T.L., Harter, M.R., Wu, X., Johnson, J., Li, Z., Liu, J., Szabo, P.E., Lu, Q., et al., 2016. Tet3 reads 5-carboxylcytosine through its CXXC domain and is a potential guardian against neurodegeneration. Cell Rep. 14, 493-505.
|
Jobe, E.M., McQuate, A.L., Zhao, X., 2012. Crosstalk among epigenetic pathways regulates neurogenesis. Front. Neurosci. 6, 59.
|
Joo, Y., Xue, Y., Wang, Y., McDevitt, R.A., Sah, N., Bossi, S., Su, S., Lee, S.K., Peng, W., Xie, A., et al., 2020. Topoisomerase 3β knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity. Nat. Commun. 11, 3143.
|
Kopparapu, P.K., Miranda, C., Fogelstrand, L., Mishra, K., Andersson, P.O., Kanduri, C., Kanduri, M., 2015. MCPH1 maintains long-term epigenetic silencing of ANGPT2 in chronic lymphocytic leukemia. FEBS J. 282, 1939-1952.
|
Kristofova, M., Ori, A., Wang, Z.Q., 2022. Multifaceted microcephaly-related gene MCPH1. Cells 11, 275.
|
Krueger, F., Andrews, S.R., 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformation. 27, 1571-1572.
|
Li, X., Liu, Y., Salz, T., Hansen, K. D., Feinberg, A., 2016. Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver. Genome Res. 26, 1730-1741.
|
Lin, I.H., Chen, Y.F., Hsu, M.T., 2017. Correlated 5-hydroxymethylcytosine (5hmC) and gene expression profiles underpin gene and organ-specific epigenetic regulation in adult mouse brain and liver. PLoS One 12. e0170779.
|
Lister, R., Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D., et al., 2013. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905.
|
Liu, X., Zong, W., Li, T., Wang, Y., Xu, X., Zhou, Z.W., Wang, Z.Q., 2017. The E3 ubiquitin ligase APC/CCdh1 degrades MCPH1 after MCPH1-βTrCP2-Cdc25A-mediated mitotic entry to ensure neurogenesis. EMBO J. 36, 3666-3681.
|
Memi, F., Killen, A.C., Barber, M., Parnavelas, J.G., Andrews, W.D., 2019. Cadherin 8 regulates proliferation of cortical interneuron progenitors. Brain Struct. Funct. 224, 277-292.
|
Mohammad, H.P., Barbash, O., Creasy, C.L., 2019. Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer. Nat. Med. 25, 403-418.
|
Park, I.H., Zhao, R., West, J.A., Yabuuchi, A., Huo, H., Ince, T.A., Lerou, P.H., Lensch, M.W., Daley, G.Q., 2008. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141-146.
|
Peng, G., Yim, E.K., Dai, H., Jackson, A.P., Burgt, I. van der, Pan, M.R., Hu, R., Li, K., Lin, S.Y., 2009. BRIT1/MCPH1 links chromatin remodelling to DNA damage response. Nat. Cell Biol. 11, 865-872.
|
Proschel, C., Hansen, J.N., Ali, A., Tuttle, E., Lacagnina, M., Buscaglia, G., Paciorkowski, A.R., 2017. Epilepsy-causing sequence variations in SIK1 disrupt synaptic activity response gene expression and affect neuronal morphology. Eur. J. Hum. Genet. 25, 216-221.
|
Qu, Q., Sun, G., Murai, K., Ye, P., Li, W., Asuelime, G., Cheung, Y.T., Shi, Y., 2013. Wnt7a regulates multiple steps of neurogenesis. Mol. Cell Biol. 33, 2551-2559.
|
Rasmussen, K.D., Berest, I., Kebler, S., Nishimura, K., Simon-Carrasco, L., Vassiliou, G.S., Pedersen, M.T., Christensen, J., Zaugg, J.B., Helin, K., 2019. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Res. 29, 564-575.
|
Reissner, C., Stahn, J., Breuer, D., Klose, M., Pohlentz, G., Mormann, M., Missler, M., 2014. Dystroglycan binding to α-neurexin competes with neurexophilin-1 and neuroligin in the brain. J. Biol. Chem. 289, 27585-27603.
|
Robinson, M.D., McCarthy, D.J., Smyth, G.K., 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
|
Rybnikova, E., Karkkainen, I., Pelto-Huikko, M., Huovila, A.P.J., 2002. Developmental regulation and neuronal expression of the cellular disintegrin ADAM11 gene in mouse nervous system. Neuroscience 112, 921-934.
|
Sansom, S.N., Livesey, F.J., 2009. Gradients in the brain: the control of the development of form and function in the cerebral cortex. Cold Spring Harbor Perspect. Biol. 1, a002519.
|
Serrano, M., Hannon, G.J., Beach, D., 1993. A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4. Nature 366, 704-707.
|
Siegfried, Z., Simon, I., 2010. DNA methylation and gene expression. WIREs Syst. Biol. Med. 2, 362-371.
|
Skvortsova, K., Iovino, N., Bogdanovic, O., 2018. Functions and mechanisms of epigenetic inheritance in animals. Nat. Rev. Mol. Cell Biol. 19, 774-790.
|
Soule, J., Messaoudi, E., Bramham, C.R., 2006. Brain-derived neurotrophic factor and control of synaptic consolidation in the adult brain. Biochem. Soc. Trans. 34, 600-604.
|
Spiers, H., Hannon, E., Schalkwyk, L.C., Bray, N.J., Mill, J., 2017. 5-hydroxymethylcytosine is highly dynamic across human fetal brain development. BMC Genom. 18, 1-14.
|
Wang, F., Yang, Y., Lin, X., Wang, J.Q., Wu, Y.S., Xie, W., Wang, D., Zhu, S., Liao, Y.Q., Sun, Q., et al., 2013. Genome-wide loss of 5-hmC is a novel epigenetic feature of Huntington's disease. Hum. Mol. Genet. 22, 3641-3653.
|
Winkler, C.W., Clancy, C.S., Rosenke, R., Peterson, K.E., 2022. Zika virus vertical transmission in interferon receptor1-antagonized Rag1-/- mice results in postnatal brain abnormalities and clinical disease. Acta. Neuropathol. Com. 10, 46.
|
Xu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A.J., Zheng, L., Zhang, H., Huang, S., et al., 2011. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell 42, 451-464.
|
Yamane, M., Ohtsuka, S., Matsuura, K., Nakamura, A., Niwa, H., 2018. Overlapping functions of Kruppel-like factor family members: targeting multiple transcription factors to maintain the naive pluripotency of mouse embryonic stem cells. Development 145, dev162404.
|
Yu, G., Wang, L.G., Han, Y., He, Q.Y., 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS A J. Integr. Biol. 16, 284-287.
|
Zeiss, C.J., 2021. Comparative milestones in rodent and human postnatal central nervous system development. Toxicol. Pathol. 49, 1368-1373.
|
Zhang, L., Li, Q., Wang, H., Wu, Y., Ye, X., Gong, Z., Li, Q., Xuan, A., 2022. Gadd45g, a novel antidepressant target, mediates metformin-induced neuronal differentiation of neural stem cells via DNA demethylation. Stem Cell. 40, 59-73.
|
Zhang, X., Huang, C.T., Chen, J., Pankratz, M.T., Xi, J., Li, J., Yang, Y., LaVaute, T.M., Li, X., Ayala, M., et al., 2010a. Pax6 is a human neuroectoderm cell fate determinant. Cell Stem Cell 7, 90-100.
|
Zhang, Y., Jurkowska, R., Soeroes, S., Rajavelu, A., Dhayalan, A., Bock, I., Rathert, P., Brandt, O., Reinhardt, R., Fischle, W., et al., 2010b. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res. 38, 4246-4253.
|
Zhang, Y., Zhang, Y., Chen, D., Wang, C., Chen, L., Gao, C., Fan, W., Shi, J., Zhang, J., Li, B., 2019. Genome-wide alteration of 5-hydroxymethylcytosine in hypoxic-ischemic neonatal rat model of cerebral palsy. Front. Mol. Neurosci. 12, 214.
|
Zito, A., Cartelli, D., Cappelletti, G., Cariboni, A., Andrews, W., Parnavelas, J., Poletti, A., Galbiati, M., 2014. Neuritin 1 promotes neuronal migration. Brain Struct. Funct. 219, 105-118.
|
Zullo, K.M., Douglas, B., Maloney, N.M., Ji, Y., Wei, Y., Herbine, K., Cohen, R., Pastore, C., Cramer, Z., Wang, X., et al., 2021. LINGO3 regulates mucosal tissue regeneration and promotes TFF2 dependent recovery from colitis. Scand. J. Gastroenterol. 56, 791-805.
|
[1] | Lei Gao, Haifang Jiang, Minze Li, Danfeng Wang, Hongtao Xiang, Rong Zeng, Limei Chen, Xiaoyan Zhang, Jianru Zuo, Shuhua Yang, Yiting Shi. Genetic and lipidomic analyses reveal the key role of lipid metabolism for cold tolerance in maize[J]. Journal of Genetics and Genomics, 2024, 51(3): 326-337. doi: 10.1016/j.jgg.2023.07.004 |
[2] | Ludong Yang, Xinxin Zhang, Fan Wang, Li Zhang, Jing Li, Jia-Xing Yue. NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with nanopore direct RNA sequencing[J]. Journal of Genetics and Genomics, 2024, 51(11): 1300-1309. doi: 10.1016/j.jgg.2024.07.007 |
[3] | Weizhi Ouyang, Zhilin Cao, Dan Xiong, Guoliang Li, Xingwang Li. Decoding the plant genome: From epigenome to 3D organization[J]. Journal of Genetics and Genomics, 2020, 47(8): 425-435. doi: 10.1016/j.jgg.2020.06.007 |
[4] | Hong Li, Zhen Wang, Shumei Chai, Xiong Bai, Guohui Ding, Yuanyuan Li, Junyi Li, Qingyu Xiao, Benpeng Miao, Weili Lin, Jie Feng, Mingyue Huang, Cheng Gao, Bin Li, Wei Hu, Jiaojiao Lin, Zhiqiang Fu, Jianyun Xie, Yixue Li. Genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis[J]. Journal of Genetics and Genomics, 2020, 47(12): 743-755. doi: 10.1016/j.jgg.2020.11.009 |
[5] | Zhixiong Chen, Wen Zhao, Xiaobo Zhu, Chengdong Zou, Junjie Yin, Mawsheng Chern, Xiaogang Zhou, Heng Ying, Xin Jiang, Yongzhen Li, Haicheng Liao, Mengping Cheng, Weitao Li, Min He, Jing Wang, Jichun Wang, Bingtian Ma, Jirui Wang, Shigui Li, Lihuang Zhu, Xuewei Chen. Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis[J]. Journal of Genetics and Genomics, 2018, 45(12): 663-672. doi: 10.1016/j.jgg.2018.10.007 |
[6] | Jing Yuan, Perry Bateman, Jose Gutierrez-Marcos. Genetic and epigenetic control of transfer cell development in plants[J]. Journal of Genetics and Genomics, 2016, 43(9): 533-539. doi: 10.1016/j.jgg.2016.08.002 |
[7] | Ofer Isakov, Dorit Lev, Lubov Blumkin, Gershon Celniker, Esther Leshinsky-Silver, Noam Shomron. Crowdfunding Effort Identifies the Causative Mutation in a Patient with Nystagmus, Microcephaly, Dystonia and Hypomyelination[J]. Journal of Genetics and Genomics, 2015, 42(2): 79-81. doi: 10.1016/j.jgg.2014.12.004 |
[8] | Jialong Liang, Wanshi Cai, Zhongsheng Sun. Single-Cell Sequencing Technologies: Current and Future[J]. Journal of Genetics and Genomics, 2014, 41(10): 513-528. doi: 10.1016/j.jgg.2014.09.005 |
[9] | Stefanie Dukowic-Schulze, Anthony Harris, Junhua Li, Anitha Sundararajan, Joann Mudge, Ernest F. Retzel, Wojciech P. Pawlowski, Changbin Chen. Comparative Transcriptomics of Early Meiosis in Arabidopsis and Maize[J]. Journal of Genetics and Genomics, 2014, 41(3): 139-152. doi: 10.1016/j.jgg.2013.11.007 |
[10] | Jingwen Lv, Yongjuan Xin, Wenhao Zhou, Zilong Qiu. The Epigenetic Switches for Neural Development and Psychiatric Disorders[J]. Journal of Genetics and Genomics, 2013, 40(7): 339-346. doi: 10.1016/j.jgg.2013.04.007 |
[11] | Jian Yan, Yan Jiao, Hong Chen, Feng Jiao, Karen A. Hasty, John M. Stuart, Weikuan Gu. Dual Effects of IL-1 Overactivity on the Immune System in a Mouse Model of Arthritis due to Deficiency of IL-1 Receptor Antagonist[J]. Journal of Genetics and Genomics, 2013, 40(2): 83-91. doi: 10.1016/j.jgg.2013.01.001 |
[12] | Zengxiang Pan, Jinbi Zhang, Qifa Li, Yinxia Li, Fangxiong Shi, Zhuang Xie, Honglin Liu. Current Advances in Epigenetic Modification and Alteration during Mammalian Ovarian Folliculogenesis[J]. Journal of Genetics and Genomics, 2012, 39(3): 111-123. doi: 10.1016/j.jgg.2012.02.004 |
[13] | Yu Zhao, Dao-Xiu Zhou. Epigenomic Modification and Epigenetic Regulation in Rice[J]. Journal of Genetics and Genomics, 2012, 39(7): 307-315. doi: 10.1016/j.jgg.2012.02.009 |
[14] | Elina Jacobs, James D. Mills, Michael Janitz. The Role of RNA Structure in Posttranscriptional Regulation of Gene Expression[J]. Journal of Genetics and Genomics, 2012, 39(10): 535-543. doi: 10.1016/j.jgg.2012.08.002 |
[15] | Xueling Huang, Xianming Chen, Tristan Coram, Meinan Wang, Zhensheng Kang. Gene expression profiling of Puccinia striiformis f. sp. tritici during development reveals a highly dynamic transcriptome[J]. Journal of Genetics and Genomics, 2011, 38(8): 357-371. doi: 10.1016/j.jgg.2011.07.004 |
[16] | Hao Yan, Zhonghai Yan, Qingwen Ma, Fei Jiao, Shuzhen Huang, Fanyi Zeng, Yitao Zeng. Association between mitochondrial DNA haplotype compatibility and increased efficiency of bovine intersubspecies cloning[J]. Journal of Genetics and Genomics, 2011, 38(1): 21-28. doi: 10.1016/j.jcg.2010.12.003 |
[17] | Meishan Zhang, Josphert N. Kimatu, Kezhang Xu, Bao Liu. DNA cytosine methylation in plant development[J]. Journal of Genetics and Genomics, 2010, 37(1): 1-12. doi: 10.1016/S1673-8527(09)60020-5 |
[18] | Tin-Lap Lee, Yunmin Li, Diana Alba, Queenie P. Vong, Shao-Ming Wu, Vanessa Baxendale, Owen M. Rennert, Yun-Fai Chris Lau, Wai-Yee Chan. Developmental staging of male murine embryonic gonad by SAGE analysis[J]. Journal of Genetics and Genomics, 2009, 36(4): 215-227. doi: 10.1016/S1673-8527(08)60109-5 |
[19] | Dasari Vasanthi, Rakesh K Mishra. Epigenetic regulation of genes during development: A conserved theme from flies to mammals[J]. Journal of Genetics and Genomics, 2008, 35(7): 413-429. doi: 10.1016/S1673-8527(08)60059-4 |
[20] | Aidong Zhou, Jianlin Zhou, Liping Yang, Mingjun Liu, Hong Li, Su Xu, Mei Han, Jian Zhang. A nuclear localized protein ZCCHC9 is expressed in cerebral cortex and suppresses the MAPK signal pathway[J]. Journal of Genetics and Genomics, 2008, 35(8): 467-472. doi: 10.1016/S1673-8527(08)60064-8 |