Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period

Yang, Bing; Jiao, Beilei; Ge, Wei; Zhang, Xiaolan; Wang, Shanhe; Zhao, Hang; Wang, Xin

doi:10.1186/s12864-018-4974-5

Cited by 40 publications

(44 citation statements)

References 69 publications

(80 reference statements)

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“…These characteristics indicate the functional diversity of lncRNAs, which may perform different important physiological regulatory roles in mammary gland development and lactation. Other studies, such as those conducted on bovines, have attempted to identify and characterize the expression of lncRNAs in peak, late and dry lactation stages [23,24], and lncRNAs, as an important posttranscriptional regulators, participate widely in the regulation pathways related to the development and lactation of mammary glands. Therefore, an extensive investigation of the functions of lncRNAs will provideus with a clear understanding of the lncRNA word in various biological processes.…”

Section: Discussionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

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Section: Discussionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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“…lncRNAs can be either single-exonic or multi-exonic, while it is a challenge to distinguish true lncRNAs from the abundant one exon, low expression fragments and expression noise assembled from RNA-Seq data (Cabili et al 2011;Derrien et al 2012). Thus, we only chose multi-exonic lncRNAs for further analysis, as was done in other studies (Tong et al 2017;Kern et al 2018;Yang et al 2018;Yue et al 2019), and depends on a highly stringent filtering pipeline to minimise the number of false-positive lncRNAs. Consequently, 4155 non-protein coding transcripts were considered as highly reliable lncRNAs, which was less than previous studies due to our stringent criteria (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…With the development of genetic array and high throughput sequencing technology, more and more lncRNAs have been discovered in human, rat and mouse (Zhao et al 2016). Recently, lncRNAs have also been identified in pig (Yang et al 2017;Jin et al 2018;Kern et al 2018), chicken (Muret et al 2017;Kern et al 2018;Li et al 2019), sheep (Ren et al 2016;Ling et al 2017;Bush et al 2018;Sulayman et al 2019) and cattle (Billerey et al 2014;Koufariotis et al 2015;Tong et al 2017;Bush et al 2018;Kern et al 2018;Weikard et al 2018;Yang et al 2018;Choi et al 2019;Wang et al 2019;Yue et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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Long non-coding RNAs (lncRNAs) have been essentially involved in all kinds of important biological processes, such as cell differentiation and development. In this study, we comprehensively profiled genome-wide lncRNAs of bovine skeletal muscle in two Chinese cattle breeds using RNAseq approach. The longissimus dorsi samples were collected from three Charolais (CH) and three Tongjiang (TJ) adult cattle, respectively. Approximately 80 million reads were obtained per library, and by which we assembled 31,009 unique transcripts. We successfully identified a total of 4155 different lncRNAs in six muscle samples, consisting of 3204 intronic lncRNAs, 737 intergenic lncRNAs, 113 sense lncRNAs and 101 antisense lncRNAs. Among them, 32 lncRNAs were differentially expressed (Fold Change >1.0, FDR < 0.05) between CH and TJ. Among these lncRNAs, 1744 identified bovine lncRNAs were located adjacent to 1146 protein-coding genes (<100 kb upstream and downstream) and functionally enriched in organ development, gene regulation and signal transduction. Our results provide a catalogue of bovine skeletal muscle-related lncRNAs, which will complement the list of bovine lncRNAs and contribute to understanding of the molecular mechanism of underpinning muscle development in cattle. HIGHLIGHTS The first study to compare specialised beef cattle breed with Chinese local beef cattle breed on long non-coding RNA (lncRNA). The 4155 different lncRNAs in beef cattle genome were identified to complement the list of bovine lncRNAs. The 1146 protein-coding genes were found maybe in cis-regulatory relationships with lncRNAs to understand the molecular mechanism underpinning muscle development in cattle.

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“…A third study investigated the transcriptomes of goat somatic cells, milk fat globules and blood cells via using microarrays [6]. This situation contrasts strongly with that of cattle, in which several studies outlining how the gene expression profile of the mammary gland changes in response to different experimental conditions have been published so far [7][8][9][10]. Indeed, RNA-Seq studies performed in dairy cattle [11] and also in sheep [12] have revealed that hundreds of genes are differentially expressed (DE) in the mammary gland when lactating vs. non-lactating individuals are compared.…”

Section: Introductionmentioning

confidence: 99%

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

Guan

Landi

Luigi-Sierra

et al. 2020

J Animal Sci Biotechnol

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Background: In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats. Results: The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins. Conclusions: The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.

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Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period

Cited by 40 publications

References 69 publications

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

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