Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

Journal of Pineal Research

et al. 2019

Self Cite

The interaction of granulosa cells (GCs) with oocytes is important to regulate follicle development. The exogenous melatonin promoting the maturation of oocytes by GCs has been approved in pig, however, the transcriptome profile and the functions of the genes regulated by melatonin in GCs have not yet to be fully characterized. In this study, we found melatonin could stimulate the synthesis of estradiol in pig GCs. The RNA‐seq was used to explore the effects of melatonin on gene expression, a total of 89 differentially expressed genes (DEGs) were identified. Gene ontology analysis showed DEGs which associated with regulation of cell proliferation, cell cycle, and anti‐apoptosis were significantly enriched. The functions of two DEGs, NOTCH2 and FILIP1L, were studied in pig GCs. The results showed that NOTCH2 inhibited the synthesis of estradiol, but FILIP1L promoted the synthesis of estradiol. Furthermore, inhibiting NOTCH2 in granulosa cells cocultured with cumulus‐oocyte‐complexes had no obvious effect on the maturation of pig oocyte, but could upregulate the cleavage rate of oocyte. We proved that FILIP1L had no effect on the maturation and cleavage of pig oocytes. Our work deepens the understanding of melatonin's effects on GCs and oocyte. The DEGs we found will be beneficial to reveal mechanisms of melatonin acting on GCs and oocytes and design the pharmacological interventions.

Section: Methodsmentioning

confidence: 99%

Effects of melatonin on the synthesis of estradiol and gene expression in pig granulosa cells

Liu

Journal of Pineal Research

et al. 2019

Self Cite

“…The microRNAs (miRNAs) and small nuclear RNAs (snRNAs) were detected by searching against the Rfam database (release 12.0) [33] with INFERNAL (version 1.1.1) [34]. Long non-coding RNAs (LncRNAs) and Circular RNAs (circRNAs) were predicted by methods described previously [4, 35, 36].…”

Section: Methodsmentioning

confidence: 99%

Chromosome-scalede novoassembly and phasing of a Chinese indigenous pig genome

Lian²,

Xie³

et al. 2019

Preprint

Self Cite

21Chinese indigenous pigs differ significantly from Western commercial pig breeds in 22 phenotypic and genomic characteristics. Thus, building a high-quality reference 23 genome for Chinese indigenous pigs is pivotal to exploring gene function, genome 24 evolution and improving genetic breeding in pigs. Here, we report an ultrahigh-quality 25 phased chromosome-scale genome assembly for a male Luchuan pig, a representative 26 Chinese domestic breed, by generating and combining data from PacBio Sequel reads, 27 Illumina paired-end reads, high-throughput chromatin conformation capture and 28 BioNano optical map. The primary assembly is ~ 2.58 Gb in size with contig and 29 scaffold N50s of 18.03 Mb and 140.09 Mb, respectively. Comparison between primary 30 assembly and alternative haplotig reveals numerous haplotype-specific alleles, which 31 provide a rich resource to study the allele-specific expression, epigenetic regulation, 32 genome structure and evolution of pigs. Gene enrichment analysis indicates that the 33 Luchuan-specific genes are predominantly enriched in Gene Ontology terms for 34 phosphoprotein phosphatase activity, signaling receptor activity and 35 phosphatidylinositol binding. We provide clear molecular evolutionary evidence that 36 the divergence time between Luchuan and Duroc pigs is dated back to about 1.7 million 37 years ago. Meanwhile, Luchuan exhibits fewer events of gene family expansion and 38 stronger gene family contraction than Duroc. The positively selected genes (PSGs) in 39 Luchuan pig significantly enrich for protein tyrosine kinase activity, microtubule motor 40 activity, GTPase activator activity and ubiquitin-protein transferase activity, whereas 41 the PSGs in Duroc pig enrich for G-protein coupled receptor activity. Overall, our 42 findings not only provide key benchmark data for the pig genetics community, but also 43 pave a new avenue for utilizing porcine biomedical models to study human health and 44 diseases.45 46 48 value in food supply and biomedical research. Plenty of archaeological and molecular 49 evidence suggests that pigs were independently domesticated in the Near East and 50

“…; Yang et al . ). To make lncRNAnet more comprehensive, we added 23 293 pig lncRNAs from NONCODEV4 (Xie et al .…”

mentioning

confidence: 97%

“…We also enabled browsing of S. scrofa lncRNAs by their tissue‐specific expression described by Yang et al . (). This should help users understand the potential regulatory roles of lncRNAs in specific tissues.…”

mentioning

confidence: 97%

See 1 more Smart Citation

LncRNAnet: a comprehensive Sus scrofa lncRNA database

Liang

et al. 2018

Animal Genetics

Long noncoding RNAs (lncRNAs) constitute a large class of functional non-coding RNAs that play important roles in many biological processes. Thousands of lncRNAs have been identified in mammals. Pig is an important farm animal and biomedical model. It is essential to create a Sus scrofa lncRNA database to enable further study of the function and evolution of lncRNAs. In this study, we built a systematic S. scrofa lncRNA database named lncRNAnet that contains 53 468 S. scrofa lncRNAs with their sequence characteristics, genomic locations, conservation, overlapping SNPs and QTLs, and transcript abundance across nine tissues in pigs. We also integrated 212 922 human and mouse lncRNAs sequences into lncRNAnet. This database will provide for a systematic S. scrofa lncRNA classification and help investigators browse, search for and analyze lncRNAs as well as do BLAST searches among human, mouse and pig lncRNAs. Thus, lncRNAnet should improve the understanding of the biological functions of lncRNA. The database is freely accessible at http://lnc.rnanet.org/.