lncRNA DLEU2转录调控因子的生物信息学分析

曾薇; 刘翼; 李文婷; 李怡; 朱金峰

doi:10.16766/j.cnki.issn.1674-4152.001998

lncRNA DLEU2转录调控因子的生物信息学分析

doi: 10.16766/j.cnki.issn.1674-4152.001998

曾薇^{1, 2},
刘翼³,
李文婷⁴,
李怡²,
朱金峰^{5, 6, ,}

1.
新疆医科大学附属肿瘤医院肺内科, 新疆乌鲁木齐 830011
2.
深圳大学总医院血液肿瘤科, 广东深圳 518055
3.
深圳大学总医院胸心外科, 广东深圳 518055
4.
深圳大学总医院病理科, 广东深圳 518055
5.
新疆医科大学附属肿瘤医院胃肠外科, 广东深圳 518055
6.
深圳大学总医院普外科, 广东深圳 518055

基金项目:

新疆维吾尔自治区自然科学基金面上项目 2018D01C255

详细信息

通讯作者:
朱金峰, E-mail: zjf122@hotmail.com

中图分类号: R393 R730.43
计量
- 文章访问数: 229
- HTML全文浏览量: 55
- PDF下载量: 2
- 被引次数: 0
出版历程
- 收稿日期: 2020-06-09
- 网络出版日期: 2022-02-16

Bioinformatics analysis of lncRNA DLEU2 transcriptional regulatory factors

ZENG Wei^{1, 2},
LIU Yi³,
LI Wen-ting⁴,
LI Yi²,
ZHU Jin-feng^{5, 6
, ,}

1.
First Department of Lung Cancer Chemotherapy, the Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China

摘要

摘要: 目的探讨lncRNA DLEU2转录调控因子的结构特征及其与lncRNA DLEU2结合位点。方法利用生物信息学工具分析lncRNA DLEU2转录调控因子的理化性质、结构、跨膜区、信号肽和亚细胞定位，预测转录因子与lncRNA DLEU2的结合位点。结果等电点分析表明转录调控因子CTCF、MAX、ELF1、YY1、USF1等电点小于7.0，POLR2A、FOXA1、BHLHE40、CEBPB、ATF3等电点大于7.0；脂溶指数分析显示，上述10个转录调控因子的脂溶指数均小于100，均为疏水性蛋白；不稳定指数分析结果显示，本研究中10个转录调控因子的不稳定指数大于40，均为不稳定蛋白；上述所有转录调控因子二级结构均由α-螺旋、无规则卷曲和扩展链结构3种形式组成；上述转录调控因子中并未发现跨膜蛋白和信号肽结构；亚细胞定位分析发现，除YY1定位为细胞质中，其他转录因子均位于细胞核；同时预测出上述10个转录调控因子与lncRNA DLEU2的结合位点。结论 lncRNA DLEU2转录调控因子呈现多样性特征，可能有助于对lncRNA DLEU2转录表达调控机制的深入研究，研究结果将有助于开展基于lncRNA DLEU2相关癌症治疗药物的筛选。
- lncRNA DLEU2 /
- 转录调控因子 /
- 生物信息学分析 /
- 结合位点
Abstract: Objective To investigate the structural characteristics of lncRNA DLEU2 transcription factor and its transcriptional binding sites with lncRNA DLEU2. Methods Bioinformatics tools were used to analyse the physical and chemical properties, structure, transmembrane region, signal peptide and subcellular localisation of lncRNA DLEU2 transcriptional regulatory factors and to predict the transcriptional binding sites between transcriptional factors and lncRNA DLEU2. Results Isoelectric point analysis showed that the isoelectric points of transcriptional regulatory factors CTCF, MAX, ELF1, YY1 and USF1 were less than 7.0. The isoelectric points of POLR2A, FOXA1, BHLHE40, CEBPB and ATF3 were more than 7.0. Lipolysis index analysis showed that the liposolubility index of the above 10 transcriptional regulatory factors were less than 100, indicating that they were hydrophobic proteins. The results of instability index analysis showed that the instability index of 10 transcriptional regulatory factors in this study were greater than 40, indicating that they were unstable proteins. All the secondary structures of the above transcriptional regulatory factors were composed of α-helix, irregular coiling and extended chain structure, and no transmembrane protein and signal peptide structures were found in the above transcriptional factors. Subcellular localisation analysis showed that YY1 was located in the cytoplasm, and other transcription factors were located in the nucleus. At the same time, the 10 transcriptional regulatory factors and lncRNA DLEU2 transcriptional binding sites were predicted. Conclusion The diversity of lncRNA DLEU2 transcriptional regulatory factors may contribute to the further study of the regulation of lncRNA DLEU2 transcriptional expression, and the results will be helpful for the screening of lncRNA DLEU2 related cancer therapeutic drugs.
- LncRNA DLEU2 /
- Transcriptional regulatory factor /
- Bioinformatics analysis /
- Binding site

HTML全文

表 1 ENCODE中转录调控因子信息

转录因子	实验数量	实验对应的细胞系或组织
POLR2A	12	MCF 10A，K562，HCT116，HeLa-S3，MCF-7，GM12878，Ishikawa，Raji，A549
CTCF	8	GM23338，spleen，LNCaP clone FGC，neutrophil，DOHH2，SU-DHL-6，kidney epithelial cell，hepatocyte
FOXA1	7	MCF-7，T47D，liver，A549，HepG2
MAX	7	liver，GM12878，HepG2，H1，K562
BHLHE40	6	GM12878，HepG2，IMR-90，K562
CEBPB	6	IMR-90，K562，HepG2
ELF1	6	HepG2，GM12878，K562，MCF-7
YY1	6	liver，HepG2，H1，SK-N-SH，HEK293
ATF3	5	K562，liver，HepG2，H1，K562
USF1	5	K562，HepG2，GM12878，H1，SK-N-SH

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表 2 lncRNA DLEU2转录调控因子的理化性质

转录因子	单向转运体	氨基酸数量	分子量	等电点	分子式	脂溶指数	不稳定指数	α-螺旋
POLR2A	P24928	1 970	217 176.17	7.02	C9591H15009N2609O2984S80	67.88	63.18	575
CTCF	P49711	727	82 785.40	6.51	C3549H5660N1058O1127S50	55.36	61.68	199
FOXA1	P55317	472	49 147.83	8.93	C2127H3279N607O679S29	50.61	55.56	95
MAX	P61244	159	18 143.64	5.88	C760H1220N244O269S2	55.97	79.78	75
BHLHE40	O14503	412	45 510.03	8.30	C2007H3206N564O606S18	75.78	58.73	139
CEBPB	P17676	345	36 105.82	8.55	C1603H2495N449O481S11	59.97	63.21	108
ELF1	P32519	619	67 497.94	5.09	C2942H4738N806O968S19	77.58	57.12	136
YY1	P25490	414	44 712.57	5.80	C1929H3013N573O623S16	61.23	48.56	71
ATF3	P18847	181	20 575.62	8.80	C889H1472N266O275S9	81.38	68.53	75
USF1	P22415	310	33 538.08	5.36	C1431H2303N427O487S8	69.23	51.37	86

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表 3 转录调控因子二级结构分析

转录因子	蛋白质数据库识别码	跨膜区	信号肽	α-螺旋	扩展链	无规则卷曲
POLR2A	5IY6_A	0	No	575	239	1 156
CTCF	6QNX_C	0	No	199	85	443
FOXA1	5A5U_B	0	No	95	26	350
MAX	1AN2_A	0	No	75	11	74
BHLHE40	2MH3_A	0	No	139	21	252
CEBPB	1HJB_A	0	No	108	11	226
ELF1	1DUX_C	0	No	136	151	332
YY1	1UBD_C	0	No	71	73	270
ATF3	2WT7_A	0	No	75	28	78
USF1	1AN4_A	0	No	86	51	173

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表 4 转录调控因子亚细胞定位分析

蛋白识别码	细胞核	线粒体基质空间	微体(过氧化物酶体)	细胞质	细胞骨架	液泡	质膜
POLR2A	73.90	-	-	17.40	4.30	4.30	-
CTCF	100.00	-	-		-	-	-
FOXA1	95.70	-	-	4.30	-	-	-
MAX	69.60	17.40	-	8.70	4.30	-	-
BHLHE40	82.60	4.30	-	13.00	-	-	-
CEBPB	73.90	13.00	-	13.00	-	-	-
ELF1	91.30	-	4.30	4.30	-	-	-
YY1	21.70	17.40	4.30	52.20	-	-	4.30
ATF3	95.70	-	4.30	-	-	-	-
USF1	69.60	13.00	-	13.00	-	4.30	-
注：“-”为表格中的项目不存在。

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