Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages

Xuan, Rong; Chao, Tianle; Wang, Aili; Zhang, Fuhong; Sun, Ping; Liu, Shuang; Guo, Maosen; Wang, Guizhi; Ji, Zhibin; Wang, Jianmin; Cheng, Ming

doi:10.1371/journal.pone.0234427

Cited by 25 publications

(23 citation statements)

References 80 publications

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“…Besides, proteins encoded by phosphoserine phosphatase (PSPH) are engaged in serine synthesis [46,47]. miR-146b was upregulated in the mammary glands of the HP group, which was reported to be involved mainly in leukemia, epidermal growth factor receptor (EGFR) signaling, MAPK, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathways [48][49][50].…”

Section: Discussionmentioning

confidence: 99%

Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle

Cai

et al. 2021

Preprint

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BackgroundMilk protein is one of the most important economic traits in the milk industry. Our previous study has revealed some functional genes responsible for milk protein synthesis in mammals. Yet, the miRNA-mediated gene regulatory network for the synthesis of milk protein in mammary is poorly understood. Results12 samples from Chinese Holstein Cows with three too high and three low phenotypic values for milk protein percentage in lactation and non-lactating were examined through deep small RNA sequencing. By bioinformatics analysis, we characterized 387 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. Using genome-wide association signal (GWAS) enrichment analysis among five milk production traits, we found the differentially expressed targets were significantly related to milk protein traits.ConclusionsThis integrated study on the transcriptional and post-transcriptional regulatory profiles between significantly differential phenotype of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.

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Section: Discussionmentioning

confidence: 99%

Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle

Cai

et al. 2021

Preprint

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“…To further understand the expression pattern of the DE miRNAs with TPM ≥ 50 in the SMGs of goats at three different developmental stages, expression pattern analysis of the DE miRNAs was performed with TCseq software (1.14.0) ( http://bioconductor.org/packages/release/bioc/html/TCseq.html ) (Xuan et al, 2020 ) using the c-means method with the parameter dist = “Euclidean,” algo = “cm,” k = 5. Line graphs were drawn with the expression levels of the DE miRNAs of the goats in three different developmental stages.…”

Section: Methodsmentioning

confidence: 99%

Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions

Wang

Xuan

et al. 2021

Front. Genet.

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Submandibular glands (SMGs) are one of the primary components of salivary glands in goats. The proteins and biologically active substances secreted by the SMGs change with growth and development. Our previous studies showed that most of the differentially expressed genes in the SMGs of goats at different developmental stages are involved in immune-related signaling pathways, but the miRNA expression patterns in the same tissues are unknown. The aim of this study was to reveal the expression profile of miRNAs at three different developmental stages, detect differentially expressed miRNAs (DE miRNAs) and predict disease-related DE miRNAs. SMG tissue samples were collected from groups of 1-month-old kids, 12-month-old maiden goats and 24-month-old adult goats (three samples from each group), and high-throughout transcriptome sequencing was conducted. A total of 178, 241 and 7 DE miRNAs were discovered between 1-month-old kids and 12-month-old maiden goats, between 1-month-old kids and 24-month-old adult goats, and between 12-month-old maiden goats and 24-month-old adult goats, respectively. Among these DE miRNAs, 88 DE miRNAs with medium or high expression levels (TPM ≥50) were classified into five expression pattern clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that some of the predicted target genes of the DE miRNAs in the five clusters were enriched in disease-related GO terms and pathways. MiRNA target genes in significant pathways were significantly enriched in Hepatitis B (FDR = 9.03E-10) and Pathways in cancer (FDR = 4.2E-10). Further analysis was performed with a PPI network, and 10 miRNAs were predicted to play an important role in the occurrence and prevention of diseases during the growth and development of goats.

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“…In cluster 2, cluster of differentiation 109 (CD109), regulator of G protein signaling 4 (RGS4), IGFBP5, B cell lymphoma 2 like 11 (BCL2L11), amphiregulin (AREG), and sulfatase 2 (SULF2) were highly expressed in the LL and DP stages but were expressed at lower levels in the LG stage. In our previous study, BCL2L11 was shown to have potential function in promoting the apoptosis of mammary gland epithelial cells [17]. In cluster 3, Wnt family member 5A (WNT5A), reticulon 4 (RTN4), cysteine dioxygenase type 1 (CDO1), and glycerol-3-phosphate acyltransferase 4 (GPAT4) were highly expressed in the LL and LG stages and were expressed at low levels in the DP stage.…”

Section: Functional Network Analysis Of Degsmentioning

confidence: 98%

“…Moreover, mammary epithelial cells already begin to synthesize and secrete milk, and milk is stored in the acinus [17,18].…”

Section: Introductionmentioning

confidence: 99%

Identification of regulatory networks and hub genes controlling mammary gland development and lactation in dairy goats during the late lactation, dry period, and late gestation stages

Xuan

Chao

Zhao

et al. 2020

Preprint

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Background From the late lactation to late gestation stages, the mammary gland tissue of goats undergoes a process from involution to remodeling and then to high differentiation of mammary gland tissue. From the perspective of lactation, this is a continuous development process of the goat mammary gland from the termination of lactation to the restoration of lactation. We performed transcriptome sequencing on goat mammary gland tissues at three mammary gland developmental stages to screen for differentially expressed genes that affect mammary gland development and the physiological process of lactation and mapped their expression profiles in three stages. The objective of this study is to reveal the expression characteristics of these genes and their potential function during mammary gland development and lactation. Results We identified 1,381 differentially expressed genes in the mammary gland during three stages and found that the expression level of genes encoding casein, such as alpha-s1-casein (CSN1S1), alpha-s2-casein (CSN1S2), beta-casein (CSN2), and kappa-casein (CSN3), and alpha-lactalbumin (LALBA) were higher in mammary gland tissues during the late lactation stage and late gestation stage than those during the dry period. In addition, we constructed six functional networks related to differentially expressed genes and found that these genes are closely related to mammary gland growth and development, apoptosis, immunity, substance transport, biosynthesis, and metabolism. Finally, we identified 35 differentially expressed transcription factors, which were classified into 16 families, and predicted that transcription factors of the basic leucine zipper domain (bZIP) family and basic helix-loop-helix (bHLH) family regulated the expression levels of genes related to mammary gland development and lactation. Conclusions Among the late lactation, dry period, and late gestation stages, there are differences in the expression levels of genes related to mammary gland growth and development, apoptosis, immunity, basic substance transport, biosynthesis, and metabolism in mammary gland tissues. Some genes in the same family or with similar functions have similar expression patterns. These differentially expressed genes or transcription factors work synergistically to participate in the regulation of mammary gland development and the physiological process of lactation.

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Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages

Cited by 25 publications

References 80 publications

Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle

Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle

Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions

Identification of regulatory networks and hub genes controlling mammary gland development and lactation in dairy goats during the late lactation, dry period, and late gestation stages

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