The integration of various omics information such as DNA, RNA, protein, epigenetic regulation brings new opportunities for the mining of important genes and the analysis of molecular genetic mechanisms. It is possible to mine and screen functional genes (including circRNA, lincRNA miRNA and mRNA) from different levels and perspectives by obtaining information of genome, transcriptome, proteome, epigenome, and metagenomics. In this way, gene networks and regulatory pathways can be studied more efficiently, which will lay a solid foundation for analyzing the mechanism of functional genes.

The current special issue will focus on gene regulation and its molecular mechanism in humans and animals. We welcome investigators in relevant fields to contribute original research, review and methods articles. Potential topics include but are not limited to the followings:

• Research and application of genetic basis of important traits in humans and animals

• breeding theory and new breed cultivation

• Research on the mining and function of excellent genetic resources of humans and animals

• Epigenetic research of genes

• High-throughput sequencing research

• Construction of gene (including circRNA, lincRNA miRNA and mRNA) expression regulation network map

Keywords

Economic Traits, Gene Expression, Epigenetic, Gene Regulation Network Construction

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ARTICLE

miR-103-3p regulates the differentiation of bone marrow mesenchymal stem cells in myelodysplastic syndrome
NINGYU LI, XIAOFANG CHEN, SUXIA GENG, PEILONG LAI, LISI HUANG, MINMING LI, XIN HUANG, CHENGXIN DENG, YULIAN WANG, JIANYU WENG, XIN DU
BIOCELL, Vol.47, No.1, pp. 133-141, 2023, DOI:10.32604/biocell.2022.022021
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract The pathogenesis of myelodysplastic syndrome (MDS) may be related to the abnormal expression of microRNAs (miRNAs), which could influence the differentiation capacity of mesenchymal stem cells (MSCs) towards adipogenic and osteogenic lineages. In this study, exosomes from bone marrow plasma were successfully extracted and identified. Assessment of miR-103-3p expression in exosomes isolated from BM in 34 MDS patients and 10 controls revealed its 0.52-fold downregulation in patients with MDS compared with controls (NOR) and was downregulated 0.55-fold in MDS-MSCs compared with NOR-MSCs. Transfection of MDS-MSCs with the miR-103-3p mimic improved osteogenic differentiation and decreased adipogenic differentiation More >

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ARTICLE

Exosomal miR-218 regulates the development of endometritis in dairy cows by targeting TGIF2/TGF-β pathway
CHANG CHEN, LIMIN QIAO, KAIJUN GUO, YINGQIU WANG, MENGYI YUAN, BOFAN FU, XIAOBO GAO, HEMIN NI, LONGFEI XIAO, XIANGGUO WANG
BIOCELL, Vol.46, No.11, pp. 2415-2423, 2022, DOI:10.32604/biocell.2022.021510
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Endometritis affects the reproductive capacity of dairy cows and leads to serious economic losses in dairy farming. Clarification of the pathogenesis of endometritis is necessary to improve the reproductive efficiency of dairy cows. Exosomes and their miRNAs have been proven to play an important role in inflammatory regulation. Exosomal miR-218 is a differentially expressed miRNA found in endometrial epithelial cells (EECs) under endometrial inflammation. Therefore, we investigated the expression of miR-218 in the uterine tissue of dairy cows, lipopolysaccharide (LPS) treated EECs, exosomal vesicles, and regulation of exosomal miR-218 by targeting TGIF-2 inducible factor homology… More >

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ARTICLE

Metformin alleviates LTA-induced inflammatory response through PPARγ/MAPK/NF-κB signaling pathway in bovine mammary epithelial cells
ABDELAZIZ ADAM IDRISS ARBAB, CHUNQING YIN, XUBIN LU, YAN LIANG, ISMAIL MOHAMED ABDALLA, AMER ADAM IDRIS, TIANLE XU, YONGJIANG MAO, ZHANGPING YANG
BIOCELL, Vol.46, No.11, pp. 2443-2454, 2022, DOI:10.32604/biocell.2022.020865
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Mastitis is a common inflammatory cow mammary infection; that causes significant economic loss in dairy industry. Given the interesting connection between metformin’s anti-inflammatory function and mastitis model induced by LTA in pbMECs, our objective was to prove that metformin was beneficial in suppressing proinflammatory response induced by LTA through modulation of mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) signaling pathways and activation of peroxisome proliferator-activated receptor-γ (PPARγ) in pbMECs. The proliferation of cells and mRNA expression were measured using EdU assay and quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Immunoblotting and immunofluorescence analysis… More >

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ARTICLE

Immune-related DNA methylation signature associated with APLN expression predicts prognostic of hepatocellular carcinoma
FEIFEI TIAN, HUAN HU, DI WANG, HUAN DING, QINGJIA CHI, HUAPING LIANG, WENLI ZENG
BIOCELL, Vol.46, No.10, pp. 2291-2301, 2022, DOI:10.32604/biocell.2022.020198
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract This study used transcriptome and epigenetic data to predict the prognosis of immune-related genes (IRGs) Apelin (APLN) in patients with hepatocellular carcinoma (HCC). The TCGA database has gene expression and clinical data for HCC. And DNA methylation 450 k data for HCC was download from the University of California Santa Cruz (UCSC) Xena browser. Performing clinical and prognostic analysis of APLN expression, results show that APLN is highly expressed in tumor samples. And it has an increasing trend with the development of clinical stage and T stage. To explore the prognostic role of APLN, the… More >

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ARTICLE

BET protein inhibitor apabetalone represses Porphyromonas gingivalis LPS-induced macrophage M1 polarization via regulating miR-130a/STAT3 axis
MEIHUA CHEN, HUIHUI WANG, XIAOFENG CHEN, YAN CHEN, TIANYING BIAN
BIOCELL, Vol.46, No.10, pp. 2281-2289, 2022, DOI:10.32604/biocell.2022.020697
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Periodontitis is a frequent chronic inflammatory disorder destroying periodontium. Recent studies have revealed the role of bromodomain and extraterminal domain inhibitor (BETi) and microRNA (miR)-130a in regulating macrophage polarization and pro-inflammatory response. However, little is known about whether apabetalone (a novel BETi) and miR-130a are correlated with chronic inflammatory state in periodontitis by regulating macrophage polarization. Here murine RAW264.7 macrophages were applied as an in vitro inflammatory model. After treatment with Porphyromonas gingivalis-derived lipopolysaccharide (Pg LPS) and apabetalone, the expression of macrophage M1 polarization markers and inflammatory cytokines was assessed using real-time PCR, western blot, and enzyme-linked… More >

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ARTICLE

An integrated bioinformatics analysis and experimental study identified key biomarkers CD300A or CXCL1, pathways and immune infiltration in diabetic nephropathy mice
WEI LIANG, QIANG LUO, ZONGWEI ZHANG, KEJU YANG, ANKANG YANG, QINGJIA CHI, HUAN HU
BIOCELL, Vol.46, No.8, pp. 1989-2002, 2022, DOI:10.32604/biocell.2022.019300
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Diabetic nephropathy (DN) is a common microvascular complication that easily leads to end-stage renal disease. It is important to explore the key biomarkers and molecular mechanisms relevant to diabetic nephropathy (DN). We used highthroughput RNA sequencing to obtain the genes related to DN glomerular tissues and healthy glomerular tissues of mice. Then we used LIMMA to analyze differentially expressed genes (DEGs) between DN and non-diabetic glomerular samples. And we performed KEGG, gene ontology functional (GO) enrichment, and gene set enrichment analysis to reveal the signaling pathway of the disease. The CIBERSORT algorithm based on support… More >

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ARTICLE

Genome-wide analysis of microRNAs induced and regulated by colchicine in mulberry
MENGMENG WU, PENG GUO, YISU SHI, DANYAN ZHENG, QIAONAN ZHANG, XIN JIN, YUHUA WANG, QIANG LIN, RONGJUN FANG, WEIGUO ZHAO
BIOCELL, Vol.46, No.8, pp. 1935-1945, 2022, DOI:10.32604/biocell.2022.019223
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract A variety of plants were colchicine treated to double their chromosome number. Chromosomes are genetic carriers that determine the individual traits of organisms. The doubling of chromosomes will lead to modifications in plant morphology, physiology and genetics. To determine the response of mulberry trees induced by colchicine, using mulberry variety Yu-711 leaves as research materials, two small RNA libraries (control and experimental groups) were constructed. It was found that 45 known miRNA genes and 78 predicted novel miRNA genes in the sequence results. A comparison of data between the control group and the experimental group… More >

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ARTICLE

Weighted gene co-expression network analysis identifies a novel immune-related gene signature and nomogram to predict the survival and immune infiltration status of breast cancer
JUNXIA LIU, KE PANG, FEI HE
BIOCELL, Vol.46, No.7, pp. 1661-1673, 2022, DOI:10.32604/biocell.2022.018023
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Breast cancer is one of the most common cancers in the world and seriously threatens the health of women worldwide. Prognostic models based on immune-related genes help to improve the prognosis prediction and clinical treatment of breast cancer patients. In the study, we used weighted gene co-expression network analysis to construct a co-expression network to screen out highly prognostic immune-related genes. Subsequently, the prognostic immune-related gene signature was successfully constructed from highly immune-related genes through COX regression and LASSO COX analysis. Survival analysis and time receiver operating characteristic curves indicate that the prognostic signature has More >

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ARTICLE

Identification of differential mRNA and lncRNA expression in AcMNPV-infected Sf9 cells
TIEJUN ZHAO, RIQIANG DENG, MENGQIU CHEN, XUNZHANG WANG
BIOCELL, Vol.46, No.7, pp. 1675-1686, 2022, DOI:10.32604/biocell.2022.018166
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Sf9Sf9 are the ovarian cells of Spodoptera frugiperda that is the host of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), and hence can serve as an effective test vehicle to understand the AcMNPV infection mechanism. In this study, through high-throughput sequencing technology using samples collected from Sf9 cells at different time points after AcMNPV infection, 3463 pieces of time-series differentially expressed RNA (1,200 mRNA and 2,263 lncRNA) are identified and justified by experimental verification of randomly selected samples from them, proving the validity of the bioinformatical analysis on this topic. Functional enrichment analysis and target prediction are performed on… More >

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ARTICLE

Gene expression profile analysis reveals the effect of metformin treatment on HepG2 cells
YI HUANG, CHUNFENG DOU, XUMING HU, HENGMI CUI
BIOCELL, Vol.46, No.4, pp. 961-967, 2022, DOI:10.32604/biocell.2022.018131
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Metformin is a first-line drug in the fight against type 2 diabetes. In recent years, studies have shown that metformin has some preventive and therapeutic effects on liver cancer, but the effects of metformin on the gene expression of liver cancer cells are not fully known. This study focused on the differences in the gene expression profiles in liver cancer cells treated with or without metformin. A total of 153 differentially expressed genes (DEGs) (FC > 2 and q-values < 0.001) were found, including 77 upregulated genes and 76 downregulated genes. These DEGs are involved in More >

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ARTICLE

Effect of RBM10 on regulating the proliferation and metastasis activity of human hepatocellular carcinoma cells by affecting the stability of miR-21
LI JIANG, KE ZHANG, CHONG HU, HONGWEI ZHANG, DANPU WANG, WEIWEI ZHAI
BIOCELL, Vol.46, No.4, pp. 969-978, 2022, DOI:10.32604/biocell.2022.017765
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract In recent decades, RNA binding motif (RBM) proteins have been widespread concerned by researchers. Among them, RBM5 is considered as a potential tumor suppressor gene in HCC. RBM10, also belonging to the RBM family, have similar structure and high homology with RBM5, indicating its potential as potential tumor suppressor genes. However, the role of RBM10 in tumors is controversial. The purpose of this study was to analyze the expression correlation and functional relationship of miR-21 and RBM10 in human hepatocellular carcinoma (HCC) tissues and corresponding tumor cells. Bioinformatics analysis showed that miR-21 and RBM10 were… More >

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ARTICLE

Phylogenetic analysis and target gene prediction of miR477 gene family in grape
HUI-YING JIN, MAO-SONG PEI, DA-LONG GUO
BIOCELL, Vol.46, No.4, pp. 941-949, 2022, DOI:10.32604/biocell.2022.016718
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract To understand the molecular characteristics of the miR477 gene family of grape (Vvi-miR477) and to predict its target genes, the Vvi-miR477 genes were identified from previous small RNA sequencing data, then phylogenetic analysis and prediction of target gene were conducted. The Vvi-miR477 family consists of two precursor sequences and three mature sequences. The miR477 family members were mostly 19-22nt in length. The sequence is relatively conservative. Vvi-MIR477a and Vvi-MIR477b are located on chromosomes 1 and 2, respectively. These precursor sequences can form the typical stable stem-loop structure. Their minimum folding free energy is −39.10 kcal/mol and −50.90 kcal/mol, More >

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963
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ARTICLE

BDLR: lncRNA identification using ensemble learning
LEJUN GONG, SHEHAI ZHOU, JINGMEI CHEN, YONGMIN LI, LI ZHANG, ZHIHONG GAO
BIOCELL, Vol.46, No.4, pp. 951-960, 2022, DOI:10.32604/biocell.2022.016625
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Long non-coding RNAs (lncRNAs) play an important role in many life activities such as epigenetic material regulation, cell cycle regulation, dosage compensation and cell differentiation regulation, and are associated with many human diseases. There are many limitations in identifying and annotating lncRNAs using traditional biological experimental methods. With the development of high-throughput sequencing technology, it is of great practical significance to identify the lncRNAs from massive RNA sequence data using machine learning method. Based on the Bagging method and Decision Tree algorithm in ensemble learning, this paper proposes a method of lncRNAs gene sequence identification More >

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ARTICLE

Immune prognostic implications of PSMD14 and its associated genes signatures in hepatocellular carcinoma
CHUAN TIAN, MUBALAKE ABUDOUREYIMU, XINRONG LIN, HAO ZHOU, XIAOYUAN CHU, RUI WANG
BIOCELL, Vol.45, No.6, pp. 1527-1541, 2021, DOI:10.32604/biocell.2021.016203
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract PSMD14 played a vital role in initiation and progression of hepatocellular carcinoma (HCC). However, PSMD14 and its-related genes for the immune prognostic implications of HCC patients have rarely been analyzed. Messenger RNA expression profiles and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database-Liver Hepatocellular Carcinoma (LIHC). Additionally, we used multi-dimensional bioinformatics analysis to construct and validate a PSMD14-based immune prognostic signature (including RBM45, PSMD1, OLA1, CCT6A, LCAT and IVD) for HCC prognosis prediction. Patients in the high-risk group shown significantly poorer survival than patients in the More >

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REVIEW

Advances in molecular regulation of goat lipid metabolism and FAS structure and function regulation
JIAHE GUO, XIAOGUANG JI, YONGJIANG MAO, ZHANGPING YANG, ZHI CHEN, YUAN YUAN
BIOCELL, Vol.45, No.4, pp. 835-847, 2021, DOI:10.32604/biocell.2021.015652
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Goat milk is widely recognized for its nutritional value. Fatty acid synthase (FAS) is the crucial enzyme of fatty acid de novo synthesis. It plays an important role in the formation of goat milk fat. In this paper, we first introduced the molecular regulation process of goat milk fat metabolism based on the structure research of FAS. Secondly, we reviewed some key factors in FAS transcription and post-transcriptional regulation of the goat mammary gland and preliminarily constructed the expression network of the goat mammary gland FAS gene. The purpose of this paper is to systematically introduce More >

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ARTICLE

Long intergenic noncoding RNAs differentially expressed in Staphylococcus aureus-induced inflammation in bovine mammary epithelial cells
JINGPENG ZHOU, XIAOGUANG JI, YUHAO WANG, XIAOLONG WANG, YONGJIANG MAO, ZHANGPING YANG
BIOCELL, Vol.45, No.4, pp. 1033-1044, 2021, DOI:10.32604/biocell.2021.015586
（This article belongs to the Special Issue: Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression)
Abstract Cow mastitis is the most common disease that affects the dairy farming industry and causes serious harm to dairy cows and humans, and Staphylococcus (S.) aureus is one of the main pathogens that cause mastitis in dairy cows. In this study, a mastitis model was established through the infection of bovine mammary epithelial cells (BMECs) with S. aureus (bacterial concentration of 1 × 10⁹/mL), and these cells and a blank group (untreated) were analyzed by flow cytometry (10000 cells, 200 cells collected per second), hematoxylin and eosin (H&E) staining and immunohistochemistry. In addition, the lncRNAs (long non-coding RNAs)… More >

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Decoding Gene (including circRNA, lincRNA miRNA and mRNA) Expression

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