+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Genes 10(3):

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log₂ fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA⁻miRNA⁻gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA⁻miRNA⁻gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA⁻miRNA⁻gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 066585362

Download citation: RISBibTeXText

PMID: 30866582

DOI: 10.3390/genes10030201

Related references

Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development. Genes 8(10):, 2017

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Research 45(D1): D43-D50, 2017

Transcriptome analysis of coding and long non-coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs. Bmc Genomics 18(1): 148-148, 2017

A Catalogue of Putative cis -Regulatory Interactions Between Long Non-coding RNAs and Proximal Coding Genes Based on Correlative Analysis Across Diverse Human Tumors. G3 8(6): 2019-2025, 2018

Identification of crucial regulatory relationships between long non-coding RNAs and protein-coding genes in lung squamous cell carcinoma. Molecular and Cellular Probes 30(3): 146-152, 2016

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. Bmc Genomics 17(1): 841, 2016

Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs. Frontiers in Genetics 9: 102, 2018

Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development 140(13): 2828-2834, 2013

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. Plos Genetics 13(2): E1006563, 2017

Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus). Bmc Genomics 18(1): 767, 2017

Integrative analysis reveals enhanced regulatory effects of human long intergenic non-coding RNAs in lung adenocarcinoma. Journal of Genetics and Genomics 42(8): 423-436, 2015

Long non-coding RNAs expression profile in HepG2 cells reveals the potential role of long non-coding RNAs in the cholesterol metabolism. Chinese Medical Journal 128(1): 91-97, 2015

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. Plos one 9(10): E109443, 2014

Comprehensive analysis of differentially expressed profiles of non‑coding RNAs in peripheral blood and ceRNA regulatory networks in non‑syndromic orofacial clefts. Molecular Medicine Reports 20(1): 513-528, 2019

Integrating non-coding RNAs in JAK-STAT regulatory networks. Jak-Stat3(1):E28055, 2014