遗传 ›› 2022, Vol. 44 ›› Issue (3): 208-215.doi: 10.16288/j.yczz.21-299
崔浩亮(), 史佩华, 高锦春, 张新博, 赵顺然, 陶晨雨()
收稿日期:
2021-08-13
修回日期:
2022-01-07
出版日期:
2022-03-20
发布日期:
2022-02-24
通讯作者:
陶晨雨
E-mail:1522942442@qq.com;taochenyuty@163.com
作者简介:
崔浩亮,在读硕士研究生,专业方向:动物遗传育种与繁殖。E-mail: 基金资助:
Haoliang Cui(), Peihua Shi, Jinchun Gao, Xinbo Zhang, Shunran Zhao, Chenyu Tao()
Received:
2021-08-13
Revised:
2022-01-07
Online:
2022-03-20
Published:
2022-02-24
Contact:
Tao Chenyu
E-mail:1522942442@qq.com;taochenyuty@163.com
Supported by:
摘要:
细胞重编程是指在精卵结合或核移植过程中,核遗传物质的表观遗传标记发生删除和重塑,从而使已分化的细胞成为具有全能性的过程。发生细胞重编程的方法主要有细胞融合、体细胞核移植以及诱导多能干细胞等。核小体是染色质的基本结构及功能单位,是染色质的一级结构,核小体定位对基因的表达及细胞的状态有着重要的调控作用。细胞重编程过程中核小体的含量和位置也会发生剧烈的变化,同时在相关基因启动子位置的核小体含量也会降低从而促进多能性基因的表达。本文综述了核小体定位在基因激活与抑制、染色质重塑以及转录因子识别中的作用,旨在为深入解析细胞重编程机制提供重要依据。
崔浩亮, 史佩华, 高锦春, 张新博, 赵顺然, 陶晨雨. 细胞重编程过程中核小体定位改变研究进展[J]. 遗传, 2022, 44(3): 208-215.
Haoliang Cui, Peihua Shi, Jinchun Gao, Xinbo Zhang, Shunran Zhao, Chenyu Tao. Progress on the study of nucleosome reorganization during cellular reprogramming[J]. Hereditas(Beijing), 2022, 44(3): 208-215.
[1] | Baldi S. Nucleosome positioning and spacing: from genome-wide maps to single arrays. Essays Biochem, 2019,63(1):5-14. |
[2] | Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet, 2019,20(4):207-220. |
[3] | Jullien J, Pasque V, Halley-Stott RP, Miyamoto K, Gurdon JB. Mechanisms of nuclear reprogramming by eggs and oocytes: a deterministic process? Nat Rev Mol Cell Biol, 2011,12(7):453-459. |
[4] | Kwon D, Kim JS, Cha BH, Park KS, Han I, Park KS, Bae H, Han MK, Kim KS, Lee SH. The effect of fetal bovine serum (FBS) on efficacy of cellular reprogramming for induced pluripotent stem cell (iPSC) generation. Cell Transplant, 2016,25(6):1025-1042. |
[5] | Huang KM, Zhang XB, Shi JJ, Yao MZ, Lin JN, Li J, Liu H, Li HH, Shi G, Wang ZB, Zhang BL, Chen JK, Pan GJ, Jiang CZ, Pei DQ, Yao HJ. Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells. Sci Rep, 2015,5:17691. |
[6] | Tao CY, Li J, Zhang X, Chen BB, Chi DM, Zeng YQ, Niu YJ, Wang CF, Cheng W, Wu WJ, Pan ZX, Lian JM, Liu HL, Miao YL. Dynamic reorganization of nucleosome positioning in somatic cells after transfer into porcine enucleated oocytes. Stem Cell Reports, 2017,9(2):642-653. |
[7] | Silva J, Barrandon O, Nichols J, Kawaguchi J, Theunissen TW, Smith A. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol, 2008,6(10):e253. |
[8] | Kim JB, Zaehres H, Wu GM, Gentile L, Ko K, Sebastiano V, Araúzo-Bravo MJ, Ruau D, Han DW, Zenke M, Schöler HR. Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature, 2008,454(7204):646-650. |
[9] | Luo M, Ling T, Xie WB, Sun H, Zhou YG, Zhu QY, Shen ML, Zong L, Lyu GL, Zhao Y, Ye T, Gu J, Tao W, Lu ZG, Grummt I. NuRD blocks reprogramming of mouse somatic cells into pluripotent stem cells. Stem Cells, 2013,31(7):1278-1286. |
[10] | Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res, 2014,24(9):1421-1432. |
[11] | Tao Y, Zheng WS, Jiang YH, Ding GT, Hou XF, Tang YT, Li YY, Gao S, Chang GC, Zhang XB, Liu WQ, Kou XC, Wang H, Jiang CZ, Gao SR. Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers. BMC Biol, 2014,12:109. |
[12] | Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol, 2012,19(11):1185-1192. |
[13] | Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet, 2012,13(4):233-245. |
[14] | Iwafuchi-Doi M, Zaret KS. Cell fate control by pioneer transcription factors. Development, 2016,143(11):1833-1837. |
[15] | Duan JL, Li BX, Bhakta M, Xie SQ, Zhou P, Munshi NV, Hon GC. Rational reprogramming of cellular states by combinatorial perturbation. Cell Rep, 2019, 27(12): 3486- 3499.e6. |
[16] | Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Structural features of transcription factors associating with nucleosome binding. Mol Cell, 2019, 75(5): 921-932.e6. |
[17] | Boller S, Ramamoorthy S, Akbas D, Nechanitzky R, Burger L, Murr R, Schübeler D, Grosschedl R. Pioneering activity of the C-terminal domain of EBF1 shapes the chromatin landscape for B cell programming. Immunity, 2016,44(3):527-541. |
[18] | Li R, Cauchy P, Ramamoorthy S, Boller S, Chavez L, Grosschedl R. Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming. Genes Dev, 2018,32(2):96-111. |
[19] | Dodonova SO, Zhu FJ, Dienemann C, Taipale J, Cramer P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature, 2020,580(7805):669-672. |
[20] | Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science, 2020,368(6498):1460-1465. |
[21] | Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell, 2015,161(3):555-568. |
[22] | Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell, 2012,151(5):994-1004. |
[23] | Jin R, Klasfeld S, Zhu Y, Fernandez Garcia M, Xiao J, Han SK, Konkol A, Wagner D. LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate. Nat Commun, 2021,12(1):626. |
[24] | Tanaka H, Takizawa Y, Takaku M, Kato D, Kumagawa Y, Grimm SA, Wade PA, Kurumizaka H. Interaction of the pioneer transcription factor GATA3 with nucleosomes. Nat Commun, 2020,11(1):4136. |
[25] | Zaret KS. Pioneer transcription factors initiating gene network changes. Annu Rev Genet, 2020,54:367-385. |
[26] | Smolle MM. Chd1 bends over backward to remodel. Nat Struct Mol Biol, 2018,25(1):2-3. |
[27] | Kingston RE, Tamkun JW. Transcriptional regulation by trithorax-group proteins. Cold Spring Harb Perspect Biol, 2014,6(10):a019349. |
[28] | Rawal Y, Chereji RV, Qiu HF, Ananthakrishnan S, Govind CK, Clark DJ, Hinnebusch AG. SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast. Genes Dev, 2018,32(9-10):695-710. |
[29] | Li ZY, Gadue P, Chen KF, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell, 2012,151(7):1608-1616. |
[30] | Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR. Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome- depleted regions at promoters. Mol Biol Cell, 2011,22(12):2106-2118. |
[31] | Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol, 2017,18(7):407-422. |
[32] | Cao ZB, Gao D, Yin HQ, Li H, Xu TT, Zhang MY, Wang X, Liu QC, Yan YL, Ma YY, Yu T, Li YS, Zhang YH. Chromatin remodeler INO80 mediates trophectoderm permeability barrier to modulate morula-to-blastocyst transition. Zool Res, 2021,42(5):562-573. |
[33] | Beckwith SL, Schwartz EK, García-Nieto PE, King DA, Gowans GJ, Wong KM, Eckley TL, Paraschuk AP, Peltan EL, Lee LR, Yao W, Morrison AJ. The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation. PLoS Genet, 2018,14(2):e1007216. |
[34] | Scacchetti A, Brueckner L, Jain D, Schauer T, Zhang X, Schnorrer F, van Steensel B, Straub T, Becker PB. CHRAC/ACF contribute to the repressive ground state of chromatin. Life Sci Alliance, 2018,1(1):e201800024. |
[35] | Börner K, Jain D, Vazquez-Pianzola P, Vengadasalam S, Steffen N, Fyodorov DV, Tomancak P, Konev A, Suter B, Becker PB. A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis. Dev Biol, 2016,411(2):217-230. |
[36] | Shao SM, Cao HW, Wang ZK, Zhou DM, Wu CS, Wang S, Xia D, Zhang DY. CHD4/NuRD complex regulates complement gene expression and correlates with CD8 T cell infiltration in human hepatocellular carcinoma. Clin Epigenetics, 2020,12(1):31. |
[37] | Kloet SL, Karemaker ID, van Voorthuijsen L, Lindeboom RGH, Baltissen MP, Edupuganti RR, Poramba-Liyanage DW, Jansen PWTC, Vermeulen M. NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells. Nat Commun, 2018,9(1):4588. |
[38] | de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Bou Dargham D, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, Gut M, Gut I, Werner M, Deleuze JF, Olaso R, Aude JC, Chantalat S, Pugh BF, Gérard M. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature, 2016,530(7588):113-116. |
[39] | Ohhata T, Wutz A. Reactivation of the inactive X chromosome in development and reprogramming. Cell Mol Life Sci, 2013,70(14):2443-2461. |
[40] | Banaszynski LA, Wen DC, Dewell S, Whitcomb SJ, Lin MY, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng DY, Allis CD. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell, 2013,155(1):107-120. |
[41] | Cao KX, Lailler N, Zhang YZ, Kumar A, Uppal K, Liu Z, Lee EK, Wu HW, Medrzycki M, Pan CY, Ho PY, Cooper GP Jr, Dong X, Bock C, Bouhassira EE, Fan YH. High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genet, 2013,9(4):e1003417. |
[42] | Dahl JA, Jung I, Aanes H, Greggains GD, Manaf A, Lerdrup M, Li GQ, Kuan S, Li B, Lee AY, Preissl S, Jermstad I, Haugen MH, Suganthan R, Bjørås M, Hansen K, Dalen KT, Fedorcsak P, Ren B, Klungland A. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature, 2016,537(7621):548-552. |
[43] | Shaytan AK, Landsman D, Panchenko AR. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Curr Opin Struct Biol, 2015,32:48-57. |
[44] | Huh NE, Hwang IW, Lim K, You KH, Chae CB. Presence of a bi-directional S phase-specific transcription regulatory element in the promoter shared by testis-specific TH2A and TH2B histone genes. Nucleic Acids Res, 1991,19(1):93-98. |
[45] | Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T. Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b. Biophys Chem, 2017,221:41-48. |
[46] | Shinagawa T, Takagi T, Tsukamoto D, Tomaru C, Huynh LM, Sivaraman P, Kumarevel T, Inoue K, Nakato R, Katou Y, Sado T, Takahashi S, Ogura A, Shirahige K, Ishii S. Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell, 2014,14(2):217-227. |
[47] | Bagchi DN, Battenhouse AM, Park D, Iyer VR. The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription. Nucleic Acids Res, 2020,48(1):157-170. |
[48] | Dong FL, Song ZW, Yu JL, Zhang BL, Jiang BC, Shen Y, Lu YD, Song CL, Cong PQ, Liu HL. Dynamic changes in occupancy of histone variant H2A.Z during induced somatic cell reprogramming. Stem Cells Int, 2016,2016:3162363. |
[1] | 邓玮杭, 李鑫辉. MNase-seq与核小体定占位研究[J]. 遗传, 2020, 42(12): 1143-1155. |
[2] | 张競文,续倩,李国亮. 癌症发生发展中的表观遗传学研究[J]. 遗传, 2019, 41(7): 567-581. |
[3] | 宋红卫, 安铁洙, 朴善花, 王春生. 哺乳动物DNA甲基化及其在体细胞诱导重编程中的作用[J]. 遗传, 2014, 36(5): 431-438. |
[4] | 侯志伟 王赟 高宏 侯圣伟. dRNA-seq原理及其在原核生物转录组学研究中的应用[J]. 遗传, 2013, 35(8): 983-991. |
[5] | 郭晓强,张巧霞,黄卫人,段相林,蔡志明. 染色质重塑因子ARID1A的肿瘤抑制作用[J]. 遗传, 2013, 35(3): 255-261. |
[6] | 王春生,张志人,朴善花,安铁洙. microRNA在诱导体细胞重编程中的作用[J]. 遗传, 2012, 34(12): 1545-1550. |
[7] | 肖遥,张华林,白莉雅,王晓民,李文功,杨利国. 哺乳动物中的DNA主动去甲基化[J]. 遗传, 2011, 33(4): 298-306. |
[8] | 王蕊,曾宪录. ATP依赖的染色质改构复合物及其作用机制[J]. 遗传, 2010, 32(4): 301-306. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||
www.chinagene.cn
备案号:京ICP备09063187号-4
总访问:,今日访问:,当前在线: