Long non-coding RNAs and mRNAs profiling of liver tissue during four developmental stages in chickens
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ABSTRACT:
PROVIDER: PRJNA574932 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10202388_1.fastq.gz | Fastqsanger.gz | |||
| SRR10202388_2.fastq.gz | Fastqsanger.gz | |||
| SRR10202389_1.fastq.gz | Fastqsanger.gz | |||
| SRR10202389_2.fastq.gz | Fastqsanger.gz | |||
| SRR10202390_1.fastq.gz | Fastqsanger.gz |
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Project description:Liver is the major organ of lipid biosynthesis in chicken. In laying hens, the liver synthesizes most of yolk precursors and transports to the developing follicles to produce eggs. However, a systematic and comprehensive investigation of long non-coding RNAs (lncRNAs) and mRNAs transcriptome in chicken liver across different developmental stages remain clearly unknown. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages, including juvenile period (JP, day 60), sexual maturity period (SM, day 133), peak laying period (PL, day 220) and broodiness period (BP, day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified among these samples. More than half of identified lncRNAs were intergenic lncRNAs (lincRNAs), accounting for 53.70%. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs (DE lncRNA) and mRNAs (DEGs) by pairwise comparisons between the four developmental stages and found that vitellogenin 2 (VTG2), riboflavin binding protein (RBP), and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the module with up-regulated genes were enriched in related to lipid metabolism process. Co-expression networks suggested the functional relatedness between mRNAs and lncRNAs and the results showed the DE-lncRNAs also mainly involve in lipid biosynthesis and metabolism process. These results suggest the transcriptome variation of liver in different developmental stages and improve the comparative understandings of molecular mechanisms of liver development in chickens.
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Project description:Introduction: As a valuable genetic resource, native birds can contribute to the sustainable development of animal production. Tibetan chickens, known for their special flavor, are one of the important local poultry breeds in the Qinghai-Tibet Plateau. However, Tibetan chickens have a slow growth rate and poor carcass traits compared with broilers. Although most of the research on Tibetan chickens focused on their hypoxic adaptation, there were fewer studies related to skeletal muscle development. Methods: Here, we performed the transcriptional sequencing of leg muscles from Tibetan chicken embryos at E (embryonic)10, E14, and E18. Results: In total, 1,600, 4,610, and 2,166 DE (differentially expressed) mRNAs, 210, 573, and 234 DE lncRNAs (long non-coding RNAs), and 52, 137, and 33 DE miRNAs (microRNAs) were detected between E10 and E14, E10 and E18, and E14 and E18, respectively. Functional prediction showed several DE mRNAs and the target mRNAs of DE lncRNAs and DE miRNAs were significantly enriched in sarcomere organization, actin cytoskeleton organization, myofibril, muscle fiber development, and other terms and pathways related to muscle growth and development. Finally, a lncRNA-miRNA-mRNA ceRNA (competing endogenous RNA) network associated with muscle growth and development, which contained 6 DE lncRNAs, 13 DE miRNAs, and 50 DE mRNAs, was constructed based on the screened DE RNAs by Gene Ontology (GO) enrichment. These DE RNAs may play a critical regulatory role in the skeletal muscle development of chickens. Discussion: The results provide a genomic resource for mRNAs, lncRNAs, and miRNAs potentially involved in the skeletal muscle development of chickens, which lay the foundation for further studies of the molecular mechanisms underlying skeletal muscle growth and development in Tibetan chickens.
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Project description:The liver is the major organ of lipid biosynthesis in the chicken. In laying hens, the liver synthesizes most of the yolk precursors and transports them to developing follicles to produce eggs. However, a systematic investigation of the long non-coding RNA (lncRNA) and mRNA transcriptome in liver across developmental stages is needed. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages: juvenile (day 60), sexual maturity (day 133), peak laying (day 220), and broodiness (day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified. More than half (53.70%) of the lncRNAs were intergenic lncRNAs. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs and mRNAs by pairwise comparison between the four developmental stages and found that VTG2, RBP, and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the modules with upregulated genes were involved in lipid metabolism processes. Co-expression networks suggested functional relatedness between mRNAs and lncRNAs; the DE-lncRNAs were mainly involved in lipid biosynthesis and metabolism processes. We showed that the liver transcriptome varies across different developmental stages. Our results improve our understanding of the molecular mechanisms underlying liver development in chickens.
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Project description:Leishmaniasis is a worldwide public health problem caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the most important species responsible for tegumentary leishmaniases in Brazil. An understanding of the molecular mechanisms underlying the success of this parasite is urgently needed. An in-depth study on the modulation of gene expression across the life cycle stages of L. braziliensis covering coding and noncoding RNAs (ncRNAs) was missing and is presented herein. Analyses of differentially expressed (DE) genes revealed that most prominent differences were observed between the transcriptomes of insect and mammalian proliferative forms (6,576 genes). Gene ontology (GO) analysis indicated stage-specific enriched biological processes. A computational pipeline and 5 ncRNA predictors allowed the identification of 11,372 putative ncRNAs. Most of the DE ncRNAs were found between the transcriptomes of insect and mammalian proliferative stages (38%). Of the DE ncRNAs, 295 were DE in all three stages and displayed a wide range of lengths, chromosomal distributions and locations; many of them had a distinct expression profile compared to that of their protein-coding neighbors. Thirty-five putative ncRNAs were submitted to northern blotting analysis, and one or more hybridization-positive signals were observed in 22 of these ncRNAs. This work presents an overview of the L. braziliensis transcriptome and its adjustments throughout development. In addition to determining the general features of the transcriptome at each life stage and the profile of protein-coding transcripts, we identified and characterized a variety of noncoding transcripts. The novel putative ncRNAs uncovered in L. braziliensis might be regulatory elements to be further investigated.
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