Dataset Information

Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus).

ABSTRACT: Long noncoding RNAs (lncRNAs) play roles in almost all biological processes; however, their function and profile in skin development and pigmentation is less understood. In addition, because lncRNAs are species-specific, their function in goats has not been established.We systematically identified lncRNAs in 100-day-old fetal skin by deep RNA-sequencing using the Youzhou dark goat (dark skin) and Yudong white goat (white skin) as a model of skin pigmentation. A total of 841,895,634 clean reads were obtained from six libraries (samples). We identified 1336 specific lncRNAs in fetal skin that belonged to three subtypes, including 999 intergenic lncRNAs (lincRNAs), 218 anti-sense lncRNAs, and 119 intronic lncRNAs. Our results demonstrated significant differences in gene architecture and expression among the three lncRNA subtypes, particularly in terms of density and position bias of transpose elements near the transcription start site. We also investigated the impact of lncRNAs on its target genes in cis and trans, indicating that these lncRNAs have a strict tissue specificity and functional conservation during skin development and pigmentation.The present study provides a resource for lncRNA studies in diseases involved in pigmentation and skin development. It expands our knowledge about lncRNA biology as well as contributes to the annotation of the goat genome.

SUBMITTER: Ren H

PROVIDER: S-EPMC4719336 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus).

Ren Hangxing H Wang Gaofu G Chen Lei L Jiang Jing J Liu Liangjia L Li Nianfu N Zhao Jinhong J Sun Xiaoyan X Zhou Peng P

BMC genomics 20160119

<h4>Background</h4>Long noncoding RNAs (lncRNAs) play roles in almost all biological processes; however, their function and profile in skin development and pigmentation is less understood. In addition, because lncRNAs are species-specific, their function in goats has not been established.<h4>Result</h4>We systematically identified lncRNAs in 100-day-old fetal skin by deep RNA-sequencing using the Youzhou dark goat (dark skin) and Yudong white goat (white skin) as a model of skin pigmentation. A ...[more]

PMID: 26785828

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Project description:Animal emotional states can be investigated by evaluating their impact on cognitive processes. In this study, we used a judgement bias paradigm to determine if short-term positive human-animal interaction (grooming) induced a positive affective state in goats. We tested two groups of goats and trained them to discriminate between a rewarded and a non-rewarded location over nine training days. During training, the experimental group (n = 9) was gently groomed by brushing their heads and backs for five min over 11 days (nine training days, plus two testing days, total time 55 min). During training, the control group (n = 10) did not experience any direct interaction with the experimenter, but was kept unconstrained next to him for the same period of time. After successful completion of the training, the responses (latency time) of the two groups to reach ambiguous locations situated between the two reference locations (i.e., rewarded/non-rewarded) were compared over two days of testing. There was not a positive bias effect after the animals had been groomed. In a second experiment, 10 goats were tested to investigate whether grooming induced changes in physiological activation (i.e., heart rate and heart rate variability). Heart rate increased when goats were groomed compared to the baseline condition, when the same goats did not receive any contact with the experimenter. Also, subjects did not move away from the experimenter, suggesting that the grooming was positively accepted. The very good care and the regular positive contacts that goats received from humans at the study site could potentially account for the results obtained. Good husbandry outcomes are influenced by animals' perception of the events and this is based on current circumstances, past experiences and individual variables. Taking into account animals' individual characteristics and identifying effective strategies to induce positive emotions could increase the understanding and reliability of using cognitive biases paradigms to investigate and promote animal welfare.

Project description:BackgroundIn quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat (Capra hircus) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology.ResultsBased on the transcriptome dataset of 39 goat skin tissue samples, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3 + SDHA + PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released.ConclusionThis study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3 + SDHA + PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

Dataset Information

Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus).

Publications

Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus).

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