基于转录组测序对GULP1下游靶基因筛选及分析

doi:10.16288/j.yczz.24-221

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Hereditas(Beijing) ›› 2024, Vol. 46 ›› Issue (10): 860-870.doi: 10.16288/j.yczz.24-221

• Research Article • Previous Articles Next Articles

Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing

Xin Wen(), Jin Mei, Meiyu Qian, Yidan Jiang, Juan Wang, Shibo Xu, Cuizhe Wang, Jun Zhang()

Key laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine，Shihezi University, Shihezi 832000, China

Received:2024-08-02 Revised:2024-09-01 Online:2024-09-02 Published:2024-09-02
Contact: Jun Zhang E-mail:1391476108@qq.com;zhangjunyc@.163.com
Supported by:
National Natural Science Foundation of China Project(82260162);Xinjiang Uyghur Autonomous Region “Tianshan Talent” Project(2023TSYCCX0116);Xinjiang Uyghur Autonomous Region “Tianshan Talent” Project(2023TSYCQNTJ0032);Xinjiang Production and Construction Corps Guided Science and Technology Plan Project(2022ZD001);Xinjiang Production and Construction Corps Guided Science and Technology Plan Project(2023ZD037)

Abstract

Abstract:

GULP1 is an engulfment adaptor protein containing a phosphotyrosine-binding (PTB) domain, and existing studies have shown that it can promote glucose uptake in 3T3-L1 adipocytes. To further explore key metabolically related differential genes downstream of GULP1, this study conducted transcriptome analysis on adipocytes and skeletal muscle cells overexpressing GULP1. Subsequently, abnormally expressed genes were subjected to bioinformatic analysis, and real-time fluorescent quantitative PCR (qRT-PCR) was used for mutual validation with transcriptome sequencing. The results indicated that, with a threshold of P < 0.05 and |Log₂FoldChange| ≥ 1 for screening differentially expressed genes, compared with control cells, there were 278 upregulated and 263 downregulated genes in adipocytes overexpressing GULP1. Metabolism-related GO (Gene Ontology) terms included cholesterol biosynthetic process, cholesterol metabolic process, response to lipopolysaccharide, lipid metabolic process, etc. A total of 52 metabolically related differentially expressed genes were enriched in 10 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, with lipid metabolism being highly enriched. In skeletal muscle cells overexpressing GULP1, there were 280 upregulated and 302 downregulated genes, with metabolism-related GO terms including hormone metabolic process, response to lipopolysaccharide, one-carbon metabolic process, etc. A total of 86 metabolically related differentially expressed genes were enriched in 10 KEGG pathways, with amino acid metabolism, lipid metabolism, and carbohydrate metabolism being highly enriched. GULP1's biological functions are extensive, including lipid metabolism and oncology. This study, through transcriptomics and bioinformatic analysis, identified key metabolically related differential genes downstream of GULP1, obtained metabolically related differential genes and signaling pathways after GULP1 overexpression, providing important theoretical basis for future research on GULP1 downstream target genes.

Key words: GULP1, transcriptome, differentially expressed gene, metabolism, bioinformatic

Xin Wen, Jin Mei, Meiyu Qian, Yidan Jiang, Juan Wang, Shibo Xu, Cuizhe Wang, Jun Zhang. Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing[J]. Hereditas(Beijing), 2024, 46(10): 860-870.

Figures/Tables 9

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样本	原始 reads 数目	原始测序量	过滤后的Reads数目	过滤后的测序量	有效碱基百分比	Q30(%)	GC(%)
3T3-NC1	48.75	7.18	47.51	7	97.45	95.13	51.88
3T3-NC2	48.84	7.18	47.45	6.97	97.15	95.18	52.55
3T3-NC3	47.86	7.06	46.7	6.89	97.57	95.11	52.56
3T3-OE1	47.87	7.06	46.71	6.89	97.56	95.19	52.25
3T3-OE2	49.11	7.2	47.63	6.99	96.99	95.08	51.98
3T3-OE3	48.65	7.18	47.49	7.01	97.6	95.34	52.52
C2C12-NC1	48.39	7.12	47.06	6.93	97.26	95.17	52.9
C2C12-NC2	48.7	7.2	47.52	7.02	97.56	95.1	52.87
C2C12-NC3	48.5	7.12	47.11	6.92	97.13	95.23	52.53
C2C12-OE1	48.42	7.1	46.95	6.89	96.96	95.08	52.42
C2C12-OE2	48.21	7.1	46.91	6.91	97.3	95.11	53.01
C2C12-OE3	48.32	7.14	47.25	6.99	97.79	95.05	52.3

基因	上游引物序列(5′→3′)	下游引物序列(5′→3′)
Abca1	GCTTGTTGGCCTCAGTTAAGG	GTAGCTCAGGCGTACAGAGAT
Ccl3	TTCTCTGTACCATGACACTCTGC	CGTGGAATCTTCCGGCTGTAG
Ccl5	GCTGCTTTGCCTACCTCTCC	TCGAGTGACAAACACGACTGC
Fos	CGGGTTTCAACGCCGACTA	TTGGCACTAGAGACGGACAGA
Il6	TAGTCCTTCCTACCCCAATTTCC	TTGGTCCTTAGCCACTCCTTC
Lbp	GATCACCGACAAGGGCCTG	GGCTATGAAACTCGTACTGCC
Map2k6	ATGTCTCAGTCGAAAGGCAAG	TTGGAGTCTAAATCCCGAGGC
Map3k8	ATGGAGTACATGAGCACTGGA	GGCTCTTCACTTGCATAAAGGTT
Tlr7	ATGTGGACACGGAAGAGACAA	GGTAAGGGTAAGATTGGTGGTG
Angpt4	CAGCCAGCTATGCTACTAGATGG	CCTCTGGAGGCTATTGGAGC
Gngt2	CAGGACCTCAGTGAGAAGGAG	CCTGCTTGGGCCTCTACATAAT
Il2rb	TGGAGCCTGTCCCTCTACG	TCCACATGCAAGAGACATTGG
Ret	TTTCTCAAGGGATGCTTACTGGG	CCCGTAGGGCATGGACATAGA
Adora2a	GCCATCCCATTCGCCATCA	GCAATAGCCAAGAGGCTGAAGA
Atp1b2	GGCAGGTGGTTGAGGAGTG	GGGGTATGGTCAGAGACGGT
Calml4	TCTTCTGGTGTCCATGAGGTG	GAAGTCCAGCTCTCCGTTCTT
Npr1	GCTTGTGCTCTATGCAGATCG	TCGACGAACTCCTGGTGATTTA
Npy1r	GCTTGTGCTCTATGCAGATCG	TCGACGAACTCCTGGTGATTTA

Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing

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