转录因子及其动态成像分析技术的研究进展
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摘要
转录因子是通过直接或间接的方式与顺式作用元件相互作用,从而对靶基因进行调控的一组蛋白。由于转录因子在植物生长发育、响应外界刺激等方面发挥着重要作用,其结构和动态特征一直作为研究的重点。转录因子的基本特征被逐渐揭示,然而关于它们之间是如何响应特定的信号而表现出不同的动态特征,在很大程度上仍是未知的。近年来,随着活细胞单分子成像技术的发展,为学者深入了解转录因子间的动态调控提供了新的契机。本文主要介绍了转录因子的结构特征和研究方法,重点叙述了单分子动态成像技术在分析转录因子动态调控中的应用,以期为后续研究转录因子的动态调控过程提供参考。
Transcription factor is a group of proteins that interact with a cis-acting element, either directly or indirectly, to regulate a target gene. Due to the important role of transcription factor in plant growth and development in response to the external environment, the basic properties of transcription factor have been largely reported. However, how they respond to specific signals and exhibit different dynamic characteristics to a large extent is still unknown. With the development of single-molecule techniques, these new approaches provide great opportunity for us to understand the dynamics and regulation of transcription factor. This paper mainly introduces the structural characteristics and research methods of transcription factor, and specially focuses on the application of single-molecule techniques in the analysis of dynamic regulation of transcription factor, in order to provide reference for the subsequent study of functions of transcription factor.
Transcription factor is a group of proteins that interact with a cis-acting element, either directly or indirectly, to regulate a target gene. Due to the important role of transcription factor in plant growth and development in response to the external environment, the basic properties of transcription factor have been largely reported. However, how they respond to specific signals and exhibit different dynamic characteristics to a large extent is still unknown. With the development of single-molecule techniques, these new approaches provide great opportunity for us to understand the dynamics and regulation of transcription factor. This paper mainly introduces the structural characteristics and research methods of transcription factor, and specially focuses on the application of single-molecule techniques in the analysis of dynamic regulation of transcription factor, in order to provide reference for the subsequent study of functions of transcription factor.
引文
[1] 刘相莲,乔芳,黄德玉,等. 转录因子研究方法进展 [J]. 生理科学进展,2017,48(1): 73-76.
[2] XU Z H,YOSHIDA T,WU L J,et al. Transcription factor MEF2C suppresses endothelial cell inflammation via regulation of NF-kappa B and KLF2 [J]. J Cell Physiol,2015,230(6): 1310-1320.
[3] SHU Y,TAO Y,WANG S,et al. GmSBH1, a homeobox transcription factor gene, relates to growth and development and involves in response to high temperature and humidity stress in soybean [J]. Plant Cell Rep,2015,34(11): 1927-1937.
[4] ZHANG J, LIU B, LI M S, et al. The bHLH transcription factor bHLH104 interacts with IAA-LEUCINE RESISTANT3 and modulates iron homeostasis in Arabidopsis [J]. Plant Cell,2015, 27(3): 787-805.
[5] WANG H Y,WANG H L,SHAO H B,et al. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology [J]. Front Plant Sci,2016,7(248): 67.
[6] 陈晔光,张传茂. 分子细胞生物学 [M]. 北京:清华大学出版社,2011.
[7] 杨致荣,王兴春,李西明,等. 高等植物转录因子的研究进展 [J]. 遗传,2004, 26(3): 403-408.
[8] EHRENSBERGER K M, CORKINS M E, CHOI S Y, et al. The double zinc finger domain and adjacent accessory domain from the transcription factor loss of zinc sensing 1 (Loz1) are necessary for DNA binding and zinc sensing [J]. J Biol Chem,2014, 289(26): 18087-18096.
[9] 李洁. 植物转录因子与基因调控 [J]. 生物学通报,2004,39(3): 9-11.
[10] SUN H X,XU Y,YANG X R,et al. Hypoxia inducible factor 2 alpha inhibits hepatocellular carcinoma growth through the transcription factor dimerization partner 3/E2F transcription factor 1-dependent apoptotic pathway [J]. Hepatology,2013,57(3): 1088-1097.
[11] KLINGE B,UBERLACKER B,KORFHAGE C,et al. ZmHox: a novel class of maize homeobox genes [J]. Plant Mol Biol, 1996, 30(3): 439-453.
[12] PURANIK S,ACAJJAOUI S,CONN S,et al. Structural basis for the oligomerization of the MADS domain transcription factor SEPALLATA3 in Arabidopsis [J]. Plant Cell,2014,26(9): 3603-3615.
[13] 王传琦, 孔稳稳, 李晶. 植物转录因子最新研究方法 [J]. 生物技术通讯,2013,1: 118-123.
[14] FANG Z H,WANG X M,LI J,et al. Cloning and expression analyses of NAC transcription factor gene in Bothriochloa ischaemum [J]. Acta Agrestia Sinica,2013,21(3):590-597.
[15] CHEN X J, ZHAO J. Establishment of Maize transcription factor ABP9 transient expression system[J]. J Agr Sci, 2014,9: 2554-2558.
[16] 黄泽军, 黄荣峰, 黄大昉. 植物转录因子功能分析方法 [J]. 农业生物技术学报,2002,10(3): 295-300.
[17] CAMARGORAMIREZ R, VALTORREGROSA B, SAN B S. MiR858-mediated regulation of flavonoid-specific MYB transcription factor genes controls resistance to pathogen infection in Arabidopsis [J]. Plant Cell Physiol,2018,59(1): 190-204.
[18] RENAK D, DUPL'AKOVA N, HONYS D. Wide-scale screening of T-DNA lines for transcription factor genes affecting male gametophyte development in Arabidopsis [J]. Sex Plant Reprod, 2012, 25(1): 39-60.
[19] LIN Y, ZHANG Q, ZHANG H M, et al. Transcription factor and miRNA co-regulatory network reveals shared and specific regulators in the development of B cell and T cell [J]. Sci Rep,2015,5:15215.
[20] 钱乾. 响应纹枯病菌的水稻基因及其miRNA的表达分析与功能研究 [D]. 武汉:武汉大学,2017.
[21] DEVI S J S R,MADHAV M S,KUMAR G R,et al. Identification of abiotic stress miRNA transcription factor binding motifs (TFBMs) in rice [J]. Gene, 2013, 531(1): 15-22.
[22] CHEN M, ZHAO Y J, ZHUO C L, et al. Overexpression of a NF-YC transcription factor from bermudagrass confers tolerance to drought and salinity in transgenic rice [J]. Plant Biotechnol J, 2015, 13(4): 482-491.
[23] RAVIKUMAR G, MANIMARAN P, VOLETI S R, et al. Stress-inducible expression of AtDREB1A transcription factor greatly improves drought stress tolerance in transgenic indica rice [J]. Transgenic Res, 2014, 23(3): 421-439.
[24] XIONG H Y, LI J J, LIU P L, et al. Overexpression of OsMYB48-1, a novel MYB-related transcription factor, enhances drought and salinity tolerance in Rice [J]. PloS One, 2014, 9(3): e92913.
[25] KELEMEN Z, SEBASTIAN A, XU W, et al. Analysis of the DNA-binding activities of the Arabidopsis R2R3-MYB transcription factor family by One-Hybrid experiments in Yeast [J]. PloS One, 2015, 10(10): e0141044.
[26] KELEMEN Z, SEBASTIAN A, XU W J, et al. Analysis of the DNA-binding activities of the Arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in Yeast [J]. PloS One, 2015, 10(10): e0141044.
[27] JOHNSON K D, BRESNICK E H. Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation [J]. Methods, 2002, 26(1): 27-36.
[28] LI W,LIN Y C,LI Q,et al. A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue [J]. Nat Protoc,2014,9(9): 2180-2193.
[29] SAMBROCK J,RUSSELL D W. Molecular cloning: a laboratory manual,3rd Edition[M]. Cold Spring Harbor Laboratory Press,2001. Chapter 17: Analysis of Gene Expression in Cultured Mammalian Cell.
[30] 张娜, 尹继刚, 孙高超, 等. 真核生物转录因子及其研究方法进展 [J]. 动物医学进展,2009,30(1): 75-79.
[31] MIAO Z,XU D,CUI M,et al. High mobility group protein DSP1 negatively regulates HSP70 transcription in Crassostrea hongkongensis [J]. Biochem Biophys Res Commun,2016,474(4): 634-639.
[32] 耿德玉,原媛,郭华荣. 双荧光素酶报告基因系统的应用研究进展 [J]. 科技资讯,2012(21): 1.
[33] LU Z P, XIAO Z L, ZHE Y, et al. Hepatitis B virus X protein promotes human hepatoma cell growth via upregulation of transcription factor AP2α and sphingosine kinase 1 [J]. Acta Pharmacol Sin, 2015, 36(10): 1228-1236.
[34] BUENROSTRO J D, GIRESI P G, ZABA L C, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position [J]. Nat Methods, 2013, 10(12): 1213.
[35] DUNHAM I, KUNDAJE A, ALDRED S F, et al. An integrated encyclopedia of DNA elements in the human genome [J]. Nature, 2012, 489(7414): 57-74.
[36] LIU Z, TJIAN R. Visualizing transcription factor dynamics in living cells [J]. J Cell Biol, 2018, 217(4): 1181-1191.
[37] 隋鑫, 满奕, 张越,等. 荧光漂白恢复技术及其在生物膜系统研究中的应用[J]. 电子显微学报, 2017, 36(6):601-609.
[38] GROENEWEG F L, Van ROYEN M E, FENZ S, et al. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP [J]. PloS One, 2014, 9(3): e90532.
[39] SPRAGUE B L, PEGO R L, STAVREVA D A, et al. Analysis of binding reactions by fluorescence recovery after photobleaching [J]. Biophys J, 2004, 86(6): 3473-3495.
[40] MCNALLY J G, MULLER W G, WALKER D, et al. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells [J]. Science, 2000, 287(5456): 1262-1265.
[41] 曲绍峰, 林金星, 李晓娟. FCS/FCCS技术及其在植物细胞生物学中的应用[J]. 电子显微学报, 2014, 33(5), 461-468.
[42] WHITE M D, ANGIOLINI J F, ALVAREZ Y D, et al. Long-lived binding of Sox2 to DNA predicts cell fate in the four-cell mouse embryo [J]. Cell,2016,165(1): 75-87.
[43] STASEVICH T J, MUELLER F, MICHELMAN-RIBEIRO A, et al. Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates [J]. Biophys J,2010,99(9): 3093-3101.
[44] PAAKINAHO V, PRESMAN D M, BALL D A, et al. Single-molecule analysis of steroid receptor and cofactor action in living cells [J]. Nat Commun,2017,8:15896.
[45] CHEN J J,ZHANG Z J,LI L,et al. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells [J]. Cell,2014, 156(6): 1274-1285.
[46] Van de CORPUT M P C, DE BOER E, KNOCH T A, et al. Super-resolution imaging reveals three-dimensional folding dynamics of the beta-globin locus upon gene activation [J]. J Cell Sci,2012,125(19): 4630-4639.
[47] 范路生,薛轶群,王晓华,等. 隐失波荧光显微镜及其在植物细胞生物学中的应用[J]. 电子显微学报,2011,30(1):48-56.
[48] SUGO N, MORIMATSU M, ARAI Y, et al. Single-molecule imaging reveals dynamics of CREB transcription factor bound to its target sequence [J]. Sci Rep,2015,5:10662.
[49] LIU Z, LEGANT W R, CHEN B C, et al. 3D imaging of Sox2 enhancer clusters in embryonic stem cells [J]. eLife, 2014, 3:e04236.
[50] RIECKHER M. Light sheet microscopy to measure protein dynamics [J]. J Cell Physiol, 2017, 232(1): 27-35.
[2] XU Z H,YOSHIDA T,WU L J,et al. Transcription factor MEF2C suppresses endothelial cell inflammation via regulation of NF-kappa B and KLF2 [J]. J Cell Physiol,2015,230(6): 1310-1320.
[3] SHU Y,TAO Y,WANG S,et al. GmSBH1, a homeobox transcription factor gene, relates to growth and development and involves in response to high temperature and humidity stress in soybean [J]. Plant Cell Rep,2015,34(11): 1927-1937.
[4] ZHANG J, LIU B, LI M S, et al. The bHLH transcription factor bHLH104 interacts with IAA-LEUCINE RESISTANT3 and modulates iron homeostasis in Arabidopsis [J]. Plant Cell,2015, 27(3): 787-805.
[5] WANG H Y,WANG H L,SHAO H B,et al. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology [J]. Front Plant Sci,2016,7(248): 67.
[6] 陈晔光,张传茂. 分子细胞生物学 [M]. 北京:清华大学出版社,2011.
[7] 杨致荣,王兴春,李西明,等. 高等植物转录因子的研究进展 [J]. 遗传,2004, 26(3): 403-408.
[8] EHRENSBERGER K M, CORKINS M E, CHOI S Y, et al. The double zinc finger domain and adjacent accessory domain from the transcription factor loss of zinc sensing 1 (Loz1) are necessary for DNA binding and zinc sensing [J]. J Biol Chem,2014, 289(26): 18087-18096.
[9] 李洁. 植物转录因子与基因调控 [J]. 生物学通报,2004,39(3): 9-11.
[10] SUN H X,XU Y,YANG X R,et al. Hypoxia inducible factor 2 alpha inhibits hepatocellular carcinoma growth through the transcription factor dimerization partner 3/E2F transcription factor 1-dependent apoptotic pathway [J]. Hepatology,2013,57(3): 1088-1097.
[11] KLINGE B,UBERLACKER B,KORFHAGE C,et al. ZmHox: a novel class of maize homeobox genes [J]. Plant Mol Biol, 1996, 30(3): 439-453.
[12] PURANIK S,ACAJJAOUI S,CONN S,et al. Structural basis for the oligomerization of the MADS domain transcription factor SEPALLATA3 in Arabidopsis [J]. Plant Cell,2014,26(9): 3603-3615.
[13] 王传琦, 孔稳稳, 李晶. 植物转录因子最新研究方法 [J]. 生物技术通讯,2013,1: 118-123.
[14] FANG Z H,WANG X M,LI J,et al. Cloning and expression analyses of NAC transcription factor gene in Bothriochloa ischaemum [J]. Acta Agrestia Sinica,2013,21(3):590-597.
[15] CHEN X J, ZHAO J. Establishment of Maize transcription factor ABP9 transient expression system[J]. J Agr Sci, 2014,9: 2554-2558.
[16] 黄泽军, 黄荣峰, 黄大昉. 植物转录因子功能分析方法 [J]. 农业生物技术学报,2002,10(3): 295-300.
[17] CAMARGORAMIREZ R, VALTORREGROSA B, SAN B S. MiR858-mediated regulation of flavonoid-specific MYB transcription factor genes controls resistance to pathogen infection in Arabidopsis [J]. Plant Cell Physiol,2018,59(1): 190-204.
[18] RENAK D, DUPL'AKOVA N, HONYS D. Wide-scale screening of T-DNA lines for transcription factor genes affecting male gametophyte development in Arabidopsis [J]. Sex Plant Reprod, 2012, 25(1): 39-60.
[19] LIN Y, ZHANG Q, ZHANG H M, et al. Transcription factor and miRNA co-regulatory network reveals shared and specific regulators in the development of B cell and T cell [J]. Sci Rep,2015,5:15215.
[20] 钱乾. 响应纹枯病菌的水稻基因及其miRNA的表达分析与功能研究 [D]. 武汉:武汉大学,2017.
[21] DEVI S J S R,MADHAV M S,KUMAR G R,et al. Identification of abiotic stress miRNA transcription factor binding motifs (TFBMs) in rice [J]. Gene, 2013, 531(1): 15-22.
[22] CHEN M, ZHAO Y J, ZHUO C L, et al. Overexpression of a NF-YC transcription factor from bermudagrass confers tolerance to drought and salinity in transgenic rice [J]. Plant Biotechnol J, 2015, 13(4): 482-491.
[23] RAVIKUMAR G, MANIMARAN P, VOLETI S R, et al. Stress-inducible expression of AtDREB1A transcription factor greatly improves drought stress tolerance in transgenic indica rice [J]. Transgenic Res, 2014, 23(3): 421-439.
[24] XIONG H Y, LI J J, LIU P L, et al. Overexpression of OsMYB48-1, a novel MYB-related transcription factor, enhances drought and salinity tolerance in Rice [J]. PloS One, 2014, 9(3): e92913.
[25] KELEMEN Z, SEBASTIAN A, XU W, et al. Analysis of the DNA-binding activities of the Arabidopsis R2R3-MYB transcription factor family by One-Hybrid experiments in Yeast [J]. PloS One, 2015, 10(10): e0141044.
[26] KELEMEN Z, SEBASTIAN A, XU W J, et al. Analysis of the DNA-binding activities of the Arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in Yeast [J]. PloS One, 2015, 10(10): e0141044.
[27] JOHNSON K D, BRESNICK E H. Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation [J]. Methods, 2002, 26(1): 27-36.
[28] LI W,LIN Y C,LI Q,et al. A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue [J]. Nat Protoc,2014,9(9): 2180-2193.
[29] SAMBROCK J,RUSSELL D W. Molecular cloning: a laboratory manual,3rd Edition[M]. Cold Spring Harbor Laboratory Press,2001. Chapter 17: Analysis of Gene Expression in Cultured Mammalian Cell.
[30] 张娜, 尹继刚, 孙高超, 等. 真核生物转录因子及其研究方法进展 [J]. 动物医学进展,2009,30(1): 75-79.
[31] MIAO Z,XU D,CUI M,et al. High mobility group protein DSP1 negatively regulates HSP70 transcription in Crassostrea hongkongensis [J]. Biochem Biophys Res Commun,2016,474(4): 634-639.
[32] 耿德玉,原媛,郭华荣. 双荧光素酶报告基因系统的应用研究进展 [J]. 科技资讯,2012(21): 1.
[33] LU Z P, XIAO Z L, ZHE Y, et al. Hepatitis B virus X protein promotes human hepatoma cell growth via upregulation of transcription factor AP2α and sphingosine kinase 1 [J]. Acta Pharmacol Sin, 2015, 36(10): 1228-1236.
[34] BUENROSTRO J D, GIRESI P G, ZABA L C, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position [J]. Nat Methods, 2013, 10(12): 1213.
[35] DUNHAM I, KUNDAJE A, ALDRED S F, et al. An integrated encyclopedia of DNA elements in the human genome [J]. Nature, 2012, 489(7414): 57-74.
[36] LIU Z, TJIAN R. Visualizing transcription factor dynamics in living cells [J]. J Cell Biol, 2018, 217(4): 1181-1191.
[37] 隋鑫, 满奕, 张越,等. 荧光漂白恢复技术及其在生物膜系统研究中的应用[J]. 电子显微学报, 2017, 36(6):601-609.
[38] GROENEWEG F L, Van ROYEN M E, FENZ S, et al. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP [J]. PloS One, 2014, 9(3): e90532.
[39] SPRAGUE B L, PEGO R L, STAVREVA D A, et al. Analysis of binding reactions by fluorescence recovery after photobleaching [J]. Biophys J, 2004, 86(6): 3473-3495.
[40] MCNALLY J G, MULLER W G, WALKER D, et al. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells [J]. Science, 2000, 287(5456): 1262-1265.
[41] 曲绍峰, 林金星, 李晓娟. FCS/FCCS技术及其在植物细胞生物学中的应用[J]. 电子显微学报, 2014, 33(5), 461-468.
[42] WHITE M D, ANGIOLINI J F, ALVAREZ Y D, et al. Long-lived binding of Sox2 to DNA predicts cell fate in the four-cell mouse embryo [J]. Cell,2016,165(1): 75-87.
[43] STASEVICH T J, MUELLER F, MICHELMAN-RIBEIRO A, et al. Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates [J]. Biophys J,2010,99(9): 3093-3101.
[44] PAAKINAHO V, PRESMAN D M, BALL D A, et al. Single-molecule analysis of steroid receptor and cofactor action in living cells [J]. Nat Commun,2017,8:15896.
[45] CHEN J J,ZHANG Z J,LI L,et al. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells [J]. Cell,2014, 156(6): 1274-1285.
[46] Van de CORPUT M P C, DE BOER E, KNOCH T A, et al. Super-resolution imaging reveals three-dimensional folding dynamics of the beta-globin locus upon gene activation [J]. J Cell Sci,2012,125(19): 4630-4639.
[47] 范路生,薛轶群,王晓华,等. 隐失波荧光显微镜及其在植物细胞生物学中的应用[J]. 电子显微学报,2011,30(1):48-56.
[48] SUGO N, MORIMATSU M, ARAI Y, et al. Single-molecule imaging reveals dynamics of CREB transcription factor bound to its target sequence [J]. Sci Rep,2015,5:10662.
[49] LIU Z, LEGANT W R, CHEN B C, et al. 3D imaging of Sox2 enhancer clusters in embryonic stem cells [J]. eLife, 2014, 3:e04236.
[50] RIECKHER M. Light sheet microscopy to measure protein dynamics [J]. J Cell Physiol, 2017, 232(1): 27-35.