细胞凋亡反应中NOXA基因启动子发挥增强子功能调节BCL2基因表达

doi:10.16288/j.yczz.20-213

[an error occurred while processing this directive]

Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (11): 1110-1121.doi: 10.16288/j.yczz.20-213

• Research Article • Previous Articles Next Articles

The NOXA promoter could function as an active enhancer to regulate the expression of BCL2 in the apoptosis response

Zhongyong Qin^1,², Xiao Shi^1,², Pingping Cao^1,², Ying Chu^1,², Wei Guan⁴, Nan Yang^1,³, He Cheng^1,²(), Yujie Sun^1,²()

^1. Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China
^2. Department of Cell Biology, Nanjing Medical University, Nanjing 211166, China
^3. Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 211166, China
^4. The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029,China

Received:2020-07-07 Revised:2020-10-04 Online:2020-11-20 Published:2020-11-06
Contact: Cheng He,Sun Yujie E-mail:chenghe@njmu.edu.cn;yujiesun@njmu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China Nos(81172091);Supported by the National Natural Science Foundation of China Nos(81572789)

Abstract

Abstract:

The transcription of eukaryotic genes is regulated by both proximal promoters and distal enhancers. Some promoters also have enhancer activity. NOXA and BCL2 are pro-apoptotic and anti-apoptotic members of the BCL2 family of protein, respectively. Our previous study has found that the NOXA gene promoter and the BCL2 gene promoter interact at the level of three-dimensional chromatin structure. Moreover, the NOXA gene promoter region displays histone modifications characteristic of both promoters and enhancers. This study aimed to explore whether and when the NOXA promoter could act as an active enhancer to regulate BCL2 expression. Based on the apoptosis model of MCF-7 cells induced by camptothecin, we used chromosome conformation capture (3C), quantitative real-time PCR (qRT-PCR) and the luciferase reporter gene technology to demonstrate that the NOXA promoter could function as an active enhancer and physically interact with the BCL2 promoter through chromatin looping. The regulatory properties of the NOXA promoter were closely related to the strength of the apoptosis stimulation. Under weak apoptotic stimulation (1 μmol/L camptothecin treatment), the NOXA promoter mainly functioned as an enhancer; with the enhancement of apoptotic stimulation (10 μmol/L camptothecin treatment), the NOXA promoter activity increased and mainly regulated the expression of the gene itself to promote apoptosis. Chromatin immunoprecipitation (ChIP) confirmed that the dynamic changes of the promoter activity and enhancer activity in the NOXA promoter region are consistent with its histone modification marks. This study provides new clues for further exploring the mechanism underlying cooperative response of BCL2 family member to apoptosis stimuli.

Key words: NOXA promoter, enhancer, dual transcription regulation function, BCL2 gene, apoptosis

Zhongyong Qin, Xiao Shi, Pingping Cao, Ying Chu, Wei Guan, Nan Yang, He Cheng, Yujie Sun. The NOXA promoter could function as an active enhancer to regulate the expression of BCL2 in the apoptosis response[J]. Hereditas(Beijing), 2020, 42(11): 1110-1121.

Figures/Tables 4

References 48

[1]	Kim TK, Shiekhattar R . Architectural and functional commonalities between enhancers and promoters. Cell, 2015,162(5):948-959. doi: 10.1016/j.cell.2015.08.008 pmid: 26317464
[2]	Khoury G, Gruss P . Enhancer elements. Cell, 1983,33(2):313-314. doi: 10.1016/0092-8674(83)90410-5 pmid: 6305503
[3]	Butler JEF, Kadonaga JT . Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev, 2001,15(19):2515-2519. doi: 10.1101/gad.924301 pmid: 11581157
[4]	Qi HY, Zhang ZJ, Li YJ, Fang XD . Role of chromatin conformation in eukaryotic gene regulation. Hereditas (Beijing), 2011,33(12):1291-1299. doi: 10.3724/SP.J.1005.2011.01291
	亓合媛, 张昭军, 李雅娟, 方向东 . 染色质构象调控真核基因的表达. 遗传, 2011,33(12):1291-1299. doi: 10.3724/SP.J.1005.2011.01291
[5]	Fromm M, Berg P . Deletion mapping of DNA regions required for SV40 early region promoter function in vivo. J Mol Appl Genet, 1982,1(5):457-481. pmid: 6296253
[6]	Smale ST, Kadonaga JT . The RNA polymerase II core promoter. Annu Rev Biochem, 2003,72:449-479. doi: 10.1146/annurev.biochem.72.121801.161520 pmid: 12651739
[7]	Atchison ML . Enhancers: mechanisms of action and cell specificity. Annu Rev Cell Biol, 1988,4:127-153. doi: 10.1146/annurev.cb.04.110188.001015 pmid: 2848550
[8]	Morris JR, Petrov, DA, Lee AM, Wu CT, . Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics, 2004,167(4):1739-1747. doi: 10.1534/genetics.104.026955 pmid: 15342512
[9]	He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang QB, Zhang Y, Xu KX, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao KJ, Brown M, Liu XS . Nucleosome dynamics define transcriptional enhancers. Nat Genet, 2010,42(4):343-347. doi: 10.1038/ng.545 pmid: 20208536
[10]	Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM . The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev, 2018,32(1):42-57. doi: 10.1101/gad.308619.117 pmid: 29378788
[11]	Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao XB, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A . An atlas of active enhancers across human cell types and tissues. Nature, 2014,507(7493):455-461. doi: 10.1038/nature12787
[12]	Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang XM, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B . Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 2009,459(7243):108-112. doi: 10.1038/nature07829 pmid: 19295514
[13]	Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, JaenischS R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA, 2010,107(50):21931-21936. doi: 10.1073/pnas.1016071107 pmid: 21106759
[14]	Charlet J, Duymich CE, Lay FD, Mundbjerg K, Dalsgaard Sorensen K, Liang GN, Jones PA . Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol Cell, 2016,62(3):422-431. doi: 10.1016/j.molcel.2016.03.033 pmid: 27153539
[15]	Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, Wang CC, Hsia JE, Shiau AK, Ge K, Corbett KD, Wang D, Zhou HL, Ren B . Identification of H3K4me1- associated proteins at mammalian enhancers. Nat Genet, 2018,50(1):73-82. doi: 10.1038/s41588-017-0015-6 pmid: 29255264
[16]	Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S, . Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet, 2017,49(7):1073-1081. doi: 10.1038/ng.3884 pmid: 28581502
[17]	Hua JT, Ahmed M, Guo HY, Zhang YZ, Chen SJ, Soares F, Lu J, Zhou S, Wang M, Li H, Larson NB, McDonnell SK, Patel PS, Liang Y, Yao CQ, van der Kwast T, Lupien M, Feng FY, Zoubeidi A, Tsao MS, Thibodeau SN, Boutros PC, He HH. Risk SNP-Mediated promoter-enhancer switching drives prostate cancer through lncRNA PCAT19. Cell, 2018, 174(3): 564-575.e518. doi: 10.1016/j.cell.2018.06.014 pmid: 30033362
[18]	Medina-Rivera A, Santiago-Algarra D, Puthier D, Spicuglia S . Widespread enhancer activity from core promoters. Trends Biochem Sci, 2018,43(6):452-468. doi: 10.1016/j.tibs.2018.03.004 pmid: 29673772
[19]	Zinkel S, Gross A, Yang E . BCL2 family in DNA damage and cell cycle control. Cell Death Differ, 2006,13(8):1351-1359. doi: 10.1038/sj.cdd.4401987 pmid: 16763616
[20]	Hwang KT, Kim K, Chang JH, Oh S, Kim YA, Lee JY, Jung SH, Choi IS . BCL2 regulation according to molecular subtype of breast cancer by analysis of the cancer genome atlas database. Cancer Res Treat, 2018,50(3):658-669. doi: 10.4143/crt.2017.134 pmid: 28701032
[21]	Radha G, Raghavan SC . BCL2: A promising cancer therapeutic target. Biochim Biophys Acta Rev Cancer, 2017,1868(1):309-314. doi: 10.1016/j.bbcan.2017.06.004 pmid: 28647470
[22]	Lisachev PD, Pustyl'nyak VO, Shtark MB, . Expression of Bcl2 family genes in the early phase of long-term potentiation. Bull Exp Biol Med, 2014,158(1):77-79. doi: 10.1007/s10517-014-2696-5 pmid: 25403402
[23]	Moldoveanu T, Follis AV, Kriwacki RW, Green DR . Many players in BCL-2 family affairs. Trends Biochem Sci, 2014,39(3):101-111. doi: 10.1016/j.tibs.2013.12.006 pmid: 24503222
[24]	Kim JY, Ahn HJ, Ryu JH, Suk K, Park JH . BH3-only protein Noxa is a mediator of hypoxic cell death induced by hypoxia-inducible factor 1α. J Exp Med, 2004,199(1):113-124. doi: 10.1084/jem.20030613 pmid: 14699081
[25]	Chen L, Willis SN, Wei A, Smith BJ, Fletcher JI, Hinds MG, Colman PM, Day CL, Adams JM, Huang DC . Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function. Mol Cell, 2005,17(3):393-403. doi: 10.1016/j.molcel.2004.12.030 pmid: 15694340
[26]	Yang Y, Wang ZD, Sun L, Shao LP, Yang N, Yu DW, Zhang X, Han X, Sun YJ . SATB1 mediates long-range chromatin interactions: a dual regulator of anti-apoptotic BCL2 and Pro-apoptotic NOXA genes. PLoS One, 2015,10(9):e0139170. doi: 10.1371/journal.pone.0139170 pmid: 26422397
[27]	Zhang JJ, Ma CY, Han X, Durrin LK, Sun YJ . The bcl-2 major breakpoint region (mbr) possesses transcriptional regulatory function. Gene, 2006,379:127-131. doi: 10.1016/j.gene.2006.05.002 pmid: 16777355
[28]	Ma C, Zhang J, Durrin LK, Lv J, Zhu D, Han X, Sun Y . The BCL2 major breakpoint region (mbr) regulates gene expression. Oncogene, 2007,26(18):2649-2657. doi: 10.1038/sj.onc.1210069 pmid: 17057736
[29]	Gong FR, Sun L, Wang ZD, Shi JF, Li W, Wang SM, Han X, Sun YJ . The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR. Nucleic Acids Res, 2011,39(11):4640-4652. doi: 10.1093/nar/gkr023 pmid: 21310710
[30]	Hu WJ, Sun YJ . The mbr-FPGS efficient expression plasmid enhances the sensitivity of Jurkat cells to methotrexate. Hereditas(Beijing), 2012,34(6):705-710.
	胡文佳, 孙玉洁 . mbr-FPGS高效表达质粒增强Jurkat细胞对甲氨蝶呤的敏感性. 遗传, 2012,34(6):705-710.
[31]	Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ . UCSC genome browser tutorial. Genomics, 2008,92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003
[32]	Zhao JC, Chai Z, Guo SM, Liu ZH . Analysis of SOX2 gene promoter activity in porcine early embryonic development. Hereditas(Beijing), 2019,41(10):950-961.
	赵剑超, 柴壮, 郭诗萌, 刘忠华 . 猪早期胚胎发育中SOX2基因启动子活性分析. 遗传, 2019,41(10):950-961.
[33]	Li GL, Ruan XN, Auerbach RK, Sandhu KS, Zheng MZ, Wang P, Poh HM, Goh Y, Lim J, Zhang JY, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong SZ, Zhang ZZ, Landt S, Raha D, Euskirchen G, Wei CL, Ge WH, Wang HE, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan YJ . Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 2012,148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014
[34]	Dekker J, Rippe K, Dekker M, Kleckner N . Capturing chromosome conformation. Science, 2002,295(5558):1306-1311. doi: 10.1126/science.1067799 pmid: 11847345
[35]	Cope NF, Fraser P, . Chromosome conformation capture. Cold Spring Harb Protoc, 2009, 2009(2): pdb.prot5137. doi: 10.1101/pdb.top098210 pmid: 29438064
[36]	Sati S, Cavalli G . Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma, 2017,126(1):33-44. doi: 10.1007/s00412-016-0593-6 pmid: 27130552
[37]	Orekhova AS, Rubtsov PM . Bidirectional promoters in the transcription of mammalian genomes. Biochemistry (Mosc), 2013,78(4):335-341. doi: 10.1134/S0006297913040020
[38]	Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K . Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin. Mol Cell, 2015,58(6):1101-1112. doi: 10.1016/j.molcel.2015.04.006 pmid: 26028540
[39]	Nejepinska J, Malik R, Moravec M, Svoboda P . Deep sequencing reveals complex spurious transcription from transiently transfected plasmids. PLoS One, 2012,7(8):e43283. doi: 10.1371/journal.pone.0043283 pmid: 22916237
[40]	Li QY, Zu YG, Shi RZ, Yao LP . Review camptothecin: current perspectives. Curr Med Chem, 2006,13(17):2021-2039. doi: 10.2174/092986706777585004 pmid: 16842195
[41]	Sriram D, Yogeeswari P, Thirumurugan R, Bal TR . Camptothecin and its analogues: a review on their chemotherapeutic potential. Nat Prod Res, 2005,19(4):393-412. doi: 10.1080/14786410412331299005 pmid: 15938148
[42]	Pommier Y . Topoisomerase I inhibitors: camptothecins and beyond. Nat Rev Cancer, 2006,6(10):789-802. doi: 10.1038/nrc1977 pmid: 16990856
[43]	Ding N, Qu HZ, Fang XD . The ENCODE project and functional genomics studies. Hereditas(Beijing), 2014,36(3):237-247.
	丁楠, 渠鸿竹, 方向东 . ENCODE计划和功能基因组研究. 遗传, 2014,36(3):237-247.
[44]	Campbell KJ, Tait SWG . Targeting BCL-2 regulated apoptosis in cancer. Open Biol, 2018,8(5):180002. doi: 10.1098/rsob.180002 pmid: 29769323
[45]	Oing C, Tennstedt P, Simon R, Volquardsen J, Borgmann K, Bokemeyer C, Petersen C, Dikomey E, Rothkamm K, Mansour WY . BCL2-overexpressing prostate cancer cells rely on PARP1-dependent end-joining and are sensitive to combined PARP inhibitor and radiation therapy. Cancer Lett, 2018,423:60-70. doi: 10.1016/j.canlet.2018.03.007 pmid: 29526801
[46]	Diao YR, Fang RX, Li B, Meng ZP, Yu JT, Qiu YJ, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B . A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods, 2017,14(6):629-635. pmid: 28417999
[47]	Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei YN, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY . Enhancer connectome in primary human cells identifies target genes of disease- associated DNA elements. Nat Genet, 2017,49(11):1602-1612.
[48]	Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA . YY1 Is a structural regulator of enhancer- promoter loops. Cell, 2017, 171(7): 1573-1588.e1528. pmid: 29224777

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

The NOXA promoter could function as an active enhancer to regulate the expression of BCL2 in the apoptosis response

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 4

References 48

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Mengting An, Guanlin Guo, Jie Wu, Wenjing Sun, Xueyuan Jia. Analysis of regulatory mechanisms of enhancers in gastric cancer with double minute chromosomes based on bioinformatics [J]. Hereditas(Beijing), 2025, 47(5): 558-572.
[2]	Rui He, Xiujuan Zheng, Ningning Wang, Xuying Li, Mingqi Li, Shijing Nian, Kewei Wang. Identification of PANoptosis-related lncRNAs in hepatocellular carcinoma based on bioinformatics and construction of a prognostic model [J]. Hereditas(Beijing), 2025, 47(4): 456-475.
[3]	Gulimire·Abudureyimu , Ying Chen, Shuhong Tang, Hong Dong, Liqin Wang, Yangsheng Wu, Juncheng Huang, Jiapeng Lin. Molecular mechanism of Mfn2 alleviating endoplasmic reticulum stress and inhibiting apoptosis of sheep follicular granulosa cells [J]. Hereditas(Beijing), 2025, 47(3): 342-350.
[4]	Ke Li, Xiaorong Zhou, Dongli Zhu, Xiaofeng Chen, Yan Guo. Exploration of the regulatory function of genetic variants at FAM167A-BLK locus in systemic lupus erythematosus [J]. Hereditas(Beijing), 2025, 47(11): 1244-1255.
[5]	Run Li, Hong Shi. Function of Bcl-2 gene and its mechanism on body size adaptive evolution in primates [J]. Hereditas(Beijing), 2025, 47(11): 1231-1243.
[6]	Min Yang, Siyuan Lin, Changqi Yang, Yaosheng Chen, Zuyong He. Progress on SOX9 and its enhancers in mammalian sex determination [J]. Hereditas(Beijing), 2024, 46(9): 677-689.
[7]	Jilong Wang, Qing Li, Tingzheng Zhan. Principle and application of self-transcribing active regulatory region sequencing in enhancer discovery research [J]. Hereditas(Beijing), 2024, 46(8): 589-602.
[8]	Yang Jian, Shi Guojuan, Peng Anghui, Xu Qingbo, Wang Ruiqi, Xue Lei, Yu Xinyang, Sun Yihao. Tip60-FOXO regulates JNK signaling mediated apoptosis in Drosophila [J]. Hereditas(Beijing), 2024, 46(6): 490-501.
[9]	Jinyi Zhang, Yumo He, Jingyu Zhou, Shufeng Weng, Huixia Ma, Taiyue Lin, Ying Xu. Hsa_circ_0007460 affects the survival of intracellular Mycobacterium tuberculosis by regulating autophagy and apoptosis of macrophages [J]. Hereditas(Beijing), 2023, 45(11): 1039-1051.
[10]	Xiuli Chen, Haiyan Huang, Qiang Wu. Targeted deletion of 5′HS2 enhancer of β-globin locus control region in K562 cells [J]. Hereditas(Beijing), 2022, 44(9): 783-797.
[11]	Siyuan Xu, Jia Shou, Qiang Wu. Additional evidence of HS5-1 enhancer eRNA PEARL for protocadherin alpha gene regulation [J]. Hereditas(Beijing), 2022, 44(8): 695-764.
[12]	Sihan Qi, Qilin Wang, Junyou Zhang, Qian Liu, Chunyan Li. The regulatory mechanisms by enhancers during cancer initiation and progression [J]. Hereditas(Beijing), 2022, 44(4): 275-288.
[13]	Cuiling Wang, Xinyi Liu, Yahui Wang, Zheng Zhang, Zhidong Wang, Gangqiao Zhou. MCM2 promotes the proliferation, migration and invasion of cholangiocarcinoma cells by reducing the p53 signaling pathway [J]. Hereditas(Beijing), 2022, 44(3): 230-244.
[14]	Xingqi Wan, Wanzhen Wei, Shengliang Guo, Yixiao Cui, Xueying Jing, Lujie Huang, Jie Ma. Functional analysis of the long-range regulatory element of BMP2 gene [J]. Hereditas(Beijing), 2022, 44(12): 1141-1147.
[15]	Ling Wang, Jinhuan Li, Haiyan Huang, Qiang Wu. Serial deletions of tandem reverse CTCF sites reveal balanced HOXD regulatory landscape of enhancers [J]. Hereditas(Beijing), 2021, 43(8): 775-791.