RNA-Seq reveals the potential molecular mechanisms of bovine KLF6 gene in the regulation of adipogenesis

Raza, Sayed Haidar Abbas; Khan, Rajwali; Chen, Gong; Long, Feng; Sun, Bing; Easa, Ahmed A.; Schreurs, Nicola M.; Pant, Sameer D.; Wenzhen, Zhang; Li, Anning; Zan, Linsen

doi:10.1016/j.ijbiomac.2021.11.202

Cited by 51 publications

(24 citation statements)

References 43 publications

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“…M6A-seq technology employs a co-immunoprecipitation approach in which m6A-specific antibodies are incubated with RNA fragments that are randomly interrupted (IP) and fragments that grasp the m6A methylation modification are sequenced. One control group (input) was simultaneously sequenced in parallel and used to eliminate background during grasping with methylated fragments ( 20 ). So we performed m6A-seq in concert with RNA-seq.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens

Jiang

Chen³

et al. 2022

Front. Vet. Sci.

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N6-Methyladenosine (m6A) modification has been shown to play important role in skeletal muscle development. Wenchang chickens are commonly used as a high-quality animal model in researching meat quality. However, there have been no previous reports regarding the profile of m6A and its function in the embryonic breast muscle development of Wenchang chickens. In this paper, we identified different developmental stages of breast muscle in Wenchang chickens and performed m6A sequencing and miRNA sequencing in the breast muscle of embryos. Embryo breast muscles were weighed and stained with hematoxylin–eosin after hatching. We found that myofibers grew fast on the 10th day after hatching (E10) and seldom proliferated beyond the 19th day after hatching (E19). A total of 6,774 differentially methylated genes (DMGs) were identified between E10 and E19. For RNA-seq data, we found 5,586 differentially expressed genes (DEGs). After overlapping DEGs and DMGs, we recorded 651 shared genes (DEMGs). Subsequently, we performed miRNA-seq analysis and obtained 495 differentially expressed miRNAs (DEMs). Then, we overlapped DEMGs and the target genes of DEMs and obtained 72 overlapped genes (called miRNA-m6A-genes in this study). GO and KEGG results showed DEMGs enriched in many muscle development-related pathways. Furthermore, we chose WNT7B, a key regulator of skeletal muscle development, to perform IGV visualization analysis and found that the m6A levels on the WNT7B gene between E10 and E19 were significantly different. In conclusion, we found that miRNAs, in conjunction with m6A modification, played a key role in the embryonic breast muscle development of Wenchang chickens. The results of this paper offer a theoretical basis for the study of m6A function in muscle development and fat deposition of Wenchang chickens.

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Section: Methodsmentioning

confidence: 99%

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens

Jiang

Chen³

et al. 2022

Front. Vet. Sci.

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“…KLF6 activates the PPARG gene, which increases the amount of TG in the body [ 51 , 54 ]. The PPARG gene is a marker gene that plays an important role in early fat differentiation [ 52 , 55 ]. So, the previous research validates that PPARG is a key pathway that governs lipogenesis.…”

Section: Discussionmentioning

confidence: 99%

Deciphering the Key Regulatory Roles of KLF6 and Bta-miR-148a on Milk Fat Metabolism in Bovine Mammary Epithelial Cells

Iqbal

Ping

et al. 2022

Genes

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MicroRNAs (miRNAs) are non-coding RNAs that regulate the expression of their target genes involved in many cellular functions at the post-transcriptional level. Previously, bta-miR-148a showed significantly high expression in bovine mammary epithelial cells (BMECs) of Chinese Holstein cows producing high milk fat compared to those with low milk fat content. Here, we investigated the role of bta-miR-148a through targeting Krüppel-like factor 6 (KLF6) and further analyzed the role of KLF6 in regulating fat metabolism through targeting PPARA, AMPK/mTOR/PPARG, and other fat marker genes in BMECs of Chinese Holstein. The bioinformatics analysis showed that the 3’ UTR of KLF6 mRNA possesses the binding sites for bta-miR-148a, which was further verified through dual-luciferase reporter assay. The BMECs were transfected with bta-miR-148a-mimic, inhibitor, and shNC, and the expression of KLF6 was found to be negatively regulated by bta-miR-148a. Moreover, the contents of triglyceride (TG), and cholesterol (CHO) in BMECs transfected with bta-miR-148a-mimic were significantly lower than the contents in BMECs transfected with bta-miR-148a-shNC. Meanwhile, the TG and CHO contents were significantly increased in BMECs transfected with bta-miR-148a-inhibitor than in BMECs transfected with bta-miR-148a-shNC. In addition, the TG and CHO contents were significantly decreased in BMECs upon the down-regulation of KLF6 through transfection with pb7sk-KLF6-siRNA1 compared to the control group. Contrarily, when KLF6 was overexpressed in BMECs through transfection with pBI-CMV3-KLF6, the TG and CHO contents were significantly increased compared to the control group. Whereas, the qPCR and Western blot evaluation of PPARA, AMPK/mTOR/PPARG, and other fat marker genes revealed that all of the genes were considerably down-regulated in the KLF6-KO-BMECs compared to the normal BMECs. Taking advantage of deploying new molecular markers and regulators for increasing the production of better-quality milk with tailored fat contents would be the hallmark in dairy sector. Hence, bta-miR-148a and KLF6 are potential candidates for increased milk synthesis and the production of valuable milk components in dairy cattle through marker-assisted selection in molecular breeding. Furthermore, this study hints at the extrapolation of a myriad of functions of other KLF family members in milk fat synthesis.

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“…Transcriptome analysis of tissues or cells at different conditions is pivotal for fully understanding the relevant gene regulatory networks. For example, Raza et al have demonstrated that KLF6 has a role in regulating lipid metabolism ( 11 ). Also, Sandford et al and Sun et al separately used microarray and RNAseq to identify the gene expression profile of different immune tissues infected by APEC, screening a large number of immune genes and signal pathways against APEC infection ( 12 – 17 ).…”

Section: Introductionmentioning

confidence: 99%

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

Sun

Yang

et al. 2022

Front. Vet. Sci.

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Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD cells. A total of di erentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD cells vs. wild type HD cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP CB, BCL L , RAB A, and TSC ) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB A-gga-miR-b-p, circRAB A-gga-miR-, and circTSC -gga-miR--p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.

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RNA-Seq reveals the potential molecular mechanisms of bovine KLF6 gene in the regulation of adipogenesis

Cited by 51 publications

References 43 publications

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens

Deciphering the Key Regulatory Roles of KLF6 and Bta-miR-148a on Milk Fat Metabolism in Bovine Mammary Epithelial Cells

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

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