Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis

Zhang, Jinwei; Ma, Jideng; Zhou, Xiankun; Hu, Silu; Ge, Liangpeng; Sun, Jing; Li, Penghao; Long, Keren; Jin, Long; Tang, Qianzi; Liu, Lingyan; Li, Xuewei; Shuai, Surong; Li, Mingzhou

doi:10.3389/fgene.2020.00845

Cited by 3 publications

(4 citation statements)

References 76 publications

(95 reference statements)

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“…The significant upregulation of lncRNA DQ786243 in the intestines of patients with Crohn’s disease suggests that it may play an important role in pathogenesis [ 38 ]. Consistent with previous studies, intestinal lncRNAs showed low expression but high tissue specificity [ 20 ]. Therefore, when evaluating the expression of lncRNAs, we have adopted a lower standard (TPM > 0.1 in at least three samples) than PCGs (TPM > 1 in at least three samples), and we have finally retained 66% (11969/18095) of PCGs and 64% (1701/2634) of lncRNAs.…”

Section: Discussionsupporting

confidence: 91%

“…The transcripts per kilobase million (TPM) of PCGs and lncRNAs were calculated by Kallisto (v0.44.0), the parameters of Kallisto use default values. We considering the expression characteristics of different transcripts, the PCGs with TPM > 1 in at least three samples were defined as expressed PCGs (lncRNAs with TPM > 0.1 in at least three samples) [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

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The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

Tang

Kong

et al. 2022

Animals

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The intestine is a tubular organ with multiple functions such as digestion absorption and immunity, but the functions of each intestinal segments are different. Intestinal regionalization is necessary for normal physiological function, but it also means the research results obtained at specific sites may not be applicable to other intestinal segments. In order to comprehensively describe the functional changes in the intestine, different intestinal segments and their contents (duodenum, jejunum, ileum, cecum, colon, and rectum) of guinea pigs were collected for RNA seq and 16S rRNA seq, respectively. The results showed differential genes of each intestinal segment mainly involve mucosa, digestion, absorption, and immunity. The gene sets related to fat, bill salts, vitamins, aggregates, amino acids, and water absorption were highly expressed in the small intestine, and the gene sets related to metal ions, nucleotides, and SCFAs were highly expressed in the large intestine. In terms of immunity, the CD8+ T, Th1, eosinophils, pDCs, and natural killer (NK) T cells in the small intestine showed higher scores than those in the large intestine, while the pattern-recognition receptor signaling pathway-related genes are highly expressed in the large intestine. In terms of microbial composition, Proteobacteria and Actinobacteria are abundant in the small intestine, while Firmicutes and Spirochaete are abundant in large intestine. The correlation analysis showed a high correlation between intestinal microorganisms and gene modules related to digestion and absorption. In addition, cross-species analysis showed the SCFA metabolism gene expression trends in human and rodent intestine were different. In conclusion, we analyzed the changes in substance transport, immune and microbial composition between different intestinal segments of guinea pigs, and explored the relationship between intestinal transcriptome and microorganisms, our research will provides a reference for subsequent intestinal-related research.

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Section: Discussionsupporting

confidence: 91%

Section: Methodsmentioning

confidence: 99%

The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

Tang

Kong

et al. 2022

Animals

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“…was applied to calculate the Pearson correlations between lncRNAs and mRNAs; mRNAs with high correlations (| r | > 0.90 and p < 0.05) were collected ( trans analysis). Finally, the results of cis and trans analysis were integrated to identify one-to-one lncRNA–mRNA pairs ( Zhang et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Commensal microbiota modulates phenotypic characteristics and gene expression in piglet Peyer’s patches

et al. 2023

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The gastrointestinal tract contains a complex microbial community. Peyer’s patches (PPs) play an important role in inducing mucosal immune responses in the gastrointestinal tract. However, little is known about the effect of commensal microbiota on the host’s PPs. Here, we analyzed the phenotypic-to-transcriptome changes in the intestine PPs of specific pathogen-free (SPF) and germ-free (GF) piglets (fed in an environment with and without commensal microbiota, respectively) to elucidate the role of commensal microbiota in host intestine mucosal immunity. Analyses of anatomical and histological characteristics showed that commensal microbiota deficiency led to PP hypoplasia, especially regarding B and T cells. A total of 12,444 mRNAs were expressed in 12 libraries; 2,156 and 425 differentially expressed (DE) mRNAs were detected in the jejunal PP (JPP) and ileal PP (IPP), respectively (SPF vs. GF). The shared DE mRNAs of the JPP and IPP were mainly involved in basic physiological and metabolic processes, while the specific DE mRNAs were enriched in regulating immune cells in the JPP and microbial responses and cellular immunity in the IPP. Commensal microbiota significantly modulated the expression of genes related to B-cell functions, including activation, proliferation, differentiation, apoptosis, receptor signaling, germinal center formation, and IgA isotype class switching, particularly in the JPP. TLR4 pathway-related genes were induced in response to microbial colonization and in LPS/SCFA-treated B cells. We also detected 69 and 21 DE lncRNAs in the JPP and IPP, respectively, and four one-to-one lncRNA-mRNA pairs were identified. These findings might represent key regulatory axes for host intestine mucosal immunity development during microbial colonization. Overall, the findings of this study revealed that commensal microbiota modulated phenotypic characteristics and gene expression in the piglet intestine PPs and underscored the importance of early microbial colonization for host mucosal immunity development.

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“…Because lncRNAs occupy a large part of the human genome in lation of pyruvate to oxaloacetate in order to regulate lipid metabolism (Figure 1C). As adipocytes can be easily isolated and cultured, there are several screening studies to find lncRNAs associated with adipogenesis identifying hundreds of differentially expressed lncRNAs [41][42][43][44][45][46]. Thus, further functional and mechanistic studies are needed to elucidate the functional importance of these adipose-related lncRNAs.…”

Section: Introductionmentioning

confidence: 99%

Potential Involvement of LncRNAs in Cardiometabolic Diseases

Ilieva

Uchida

2023

Genes

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Characterized by cardiovascular disease and diabetes, cardiometabolic diseases are a major cause of mortality around the world. As such, there is an urgent need to understand the pathogenesis of cardiometabolic diseases. Increasing evidence suggests that most of the mammalian genome are transcribed as RNA, but only a few percent of them encode for proteins. All of the RNAs that do not encode for proteins are collectively called non-protein-coding RNAs (ncRNAs). Among these ncRNAs, long ncRNAs (lncRNAs) are considered as missing keys to understand the pathogeneses of various diseases, including cardiometabolic diseases. Given the increased interest in lncRNAs, in this study, we will summarize the latest trend in the lncRNA research from the perspective of cardiometabolism and disease by focusing on the major risk factors of cardiometabolic diseases: obesity, cholesterol, diabetes, and hypertension. Because genetic inheritance is unavoidable in cardiometabolic diseases, we paid special attention to the genetic factors of lncRNAs that may influence cardiometabolic diseases.

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Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis

Cited by 3 publications

References 76 publications

The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

Commensal microbiota modulates phenotypic characteristics and gene expression in piglet Peyer’s patches

Potential Involvement of LncRNAs in Cardiometabolic Diseases

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