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

BMC Genomics
Hangxing RenPeng Zhou

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 pigm...Continue Reading

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Citations

Sep 13, 2016·Animal Genetics·R WeikardC Kuehn
Feb 16, 2017·BMC Genomics·Xiaoxiao GaoYunhai Zhang
Feb 2, 2017·BMC Genomics·Chih-Kuan ChenWen-Hsiung Li
Feb 16, 2018·Genome Génome / Conseil National De Recherches Canada·Tuanhui RenXiangtao Kang
Jan 24, 2018·BioMed Research International·Dongyun LeiLi He
Jul 8, 2018·Reproduction in Domestic Animals = Zuchthygiene·Chen YangYinghui Ling
Jun 5, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Bolin WuWen Cheng
Aug 15, 2018·International Journal of Molecular Sciences·Hyosun HongJin-Wu Nam
Aug 4, 2018·Frontiers in Genetics·Bahareldin A AbdallaXiquan Zhang
Oct 20, 2018·Journal of Animal Science and Biotechnology·Monika RuszkowskaRenata E Ciereszko

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Datasets Mentioned

BETA
GSE69812

Methods Mentioned

BETA
PCR
RNA-seq
RNA Assay
Assay

Software Mentioned

DAVID
R
RepeatMasker
CNCI
Pfam
scan
Phast
custom scripts
Scripture
ggplot2

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