Transcriptome analyses of differential gene expression in the bursa of Fabricius between Silky Fowl and White Leghorn

Han, Deguo; Zhang, Yuanyuan; Chen, Jianfei; Hua, Guoying; Li, Junying; Deng, Xuegong; Deng, Xuemei

doi:10.1038/srep45959

Cited by 18 publications

(10 citation statements)

References 49 publications

(69 reference statements)

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“…While in cattle the GC content were 48.79% and 51.38%, respectively ( Fig 3D). The present results that are in accordance with those of previous studies [33][34][35].…”

Section: A Boxplot Of Average Expression Level Histogram Of Lengthssupporting

confidence: 94%

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Wang¹,

Chai²,

Zhong³

et al. 2019

Preprint

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Background: the yak (Bos grunniens) is one of the major livestock that can survive the extremely cold, harsh and oxygen-poor conditions and provide meat, milk and transportation for Tibetans living in the Qinghai-Tibetan Plateau, and there are some cattle migrate to yak habitat but cannot survive the extremely conditions well. However, the regulatory mechanisms that drive hypoxic adaptation of yak remain elusive. Results: Thus, we collected heart tissues from Leiwuqi (LWQ) yak and their relatives, the migration cattle in LWQ yak habitat (HAC) and low-altitude cattle (LAC), respectively, for RNA sequencing, 178 co-differentially expressed protein-coding transcripts (CETs) including 6 down-regulated and 172 up-regulated CETs were discovered in both LAC-vs-LWQY and LAC-vs-HAC comparison groups. There were 133, 11 and 3 lncRNA transcripts were specific expressed in LWQY, HAC, and LAC groups, respectively. 2 and 230 lncRNA transcripts differentially expressed in LAC-vs-LWQY and LAC-vs-HAC，respectively, but no lncRNA transcripts co-differentially expressed in those two comparison groups. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and 1 down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiply CETs which are the target genes for miRNAs/lncRNAs were significantly enriched in high-altitude adaptation related processes, for instance, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network by integrating competing relationships among CETs, miRNAs, lncRNAs and circRNAs were constructed. Furthermore, we constructed a hypoxic adaptation related ceRNA network to identified that 8 miRNAs and 15 circRNAs were predicted to regulated MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1 and F2R genes. Conclusion: In conclusion, our data reinforce the view that the molecular network of high-altitude adaptation is composed of several protein-coding transcripts and non-coding transcripts that involved in multiply hypoxic adaptation regulatory pathways. The detailed mechanism for how this network crosstalk each other in heart of Bovidae are worthy of future research efforts.

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“…While in cattle the GC content were 48.79% and 51.38%, respectively ( Fig 3D). The present results that are in accordance with those of previous studies [33][34][35].…”

Section: A Boxplot Of Average Expression Level Histogram Of Lengthssupporting

confidence: 94%

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Wang¹,

Chai²,

Zhong³

et al. 2019

Preprint

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“…To maximise the co-expression signal, we chose datasets to represent the greatest possible diversity of tissues and organ systems. Not all studies contain links to a publicly archived dataset, such as a study of induced ochratoxicosis in the kidney cortex [ 55 ] and two studies of the bursa of Fabricius [ 56 , 57 ]. Samples containing less than 10 million reads were not used, such as those from a study of the follicular transcriptome throughout the ovulation cycle [ 58 ].…”

Section: Resultsmentioning

confidence: 99%

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

et al. 2018

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BackgroundThe domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.ResultsRandomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.ConclusionExpression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4972-7) contains supplementary material, which is available to authorized users.

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“…For example, a novel high-throughput RNA sequencing (RNA-seq) method identified the ASB2 gene as a gene candidate for pectoralis muscle tenderness in broiler chickens [ 6 ]. Moreover, Han et al [ 7 ] using an RNA-seq method concluded that B-cell development could be affected by noncoding RNAs expressed in the bursa of Fabricius in Silky Fowl chicken strain. Han et al [ 8 ] evaluating the hypothalamic transcriptome provided new insight into miRNA functions involved in timing the rapid development of chicken gonads.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Changes in Broiler Chicken Hypothalamus during Growth and Development

Piórkowska

Żukowski

Połtowicz

et al. 2018

International Journal of Genomics

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The hypothalamus plays an overarching role that is reflected in the physiological processes observed in the entire organism. The hypothalamus regulates selected metabolic processes and activities of the autonomic nervous system. The avian hypothalamus due to the structural complexity is not well described and has a slightly different function than the mammalian hypothalamus that is the subject of numerous studies. The present study evaluated activities of hypothalamic genes in fast-growing chickens during development (at the 1st day and 3rd and 6th weeks after hatching). The hypothalamic transcriptomes for 3- and 6-week-old cockerels were analysed using an RNA sequencing method in next-generation sequencing (NGS) technology. The differentially expressed gene analysis was conducted using DESeq2 software. In younger 22-day-old cockerels, 389 genes showed higher expression (fold change > 1.5) than that in 45-day-old birds. These genes played a role in several biological processes because they encoded proteins involved in integrin signalling, regulation of hormone levels, camera-type eye development, and blood vessel development. Moreover, surprisingly in the hypothalamus of 3-week-old cockerels, transcripts were identified for proteins involved in both anorexigenic (POMC, NMU) and orexigenic (PMCH, ALDH1A1, LPL, and GHRH) pathways. The RNA-seq results were confirmed by qPCR methods. In summary, the intensive growth of 3-week-old chickens was reflected in hypothalamic activities because the genes associated with the somatotropin axis and regulation of satiety centre showed increased expression.

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Transcriptome analyses of differential gene expression in the bursa of Fabricius between Silky Fowl and White Leghorn

Cited by 18 publications

References 49 publications

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Transcriptomic Changes in Broiler Chicken Hypothalamus during Growth and Development

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