Long intergenic non-coding RNA GALMD3 in chicken Marek\u2019s disease

Bo Han,Chunfang Zhao,Li Zhang,Yi Ding,Ling Lian,Ning Yang,Jiuzhou Song,Yanghua He

doi:10.1038/s41598-017-10900-2

Abstract

Long intergenic non-coding RNAs (lincRNAs) are transcribed from non-coding DNA sequences. Studies have revealed that aberrant expressions of lincRNAs are associated with various types of cancers and neurological disorders. Marek’s disease (MD) is a highly contagious T-cell lymphoid neoplasia of chicken induced by Marek’s disease virus (MDV). In this study, we first identified and validated linc-GALMD3 highly expressed in MDV-infected CD4+ T cells by RNA-Seq and qRT-PCR. By RNA-Seq analysis in MDCC-MSB1 cells after loss of function of linc-GALMD3 by shRNA, we found that linc-GALMD3 could positively cis-regulate its downstream gga-miR-223 gene expression. In contrast, it could trans-regulate the 748 differentially expressed genes (FDR < 0.01) that were mainly enriched into mitochondrial structure and cell cycle processes using GO analysis. Of these, the most significantly expressed gene EPYC might cause iris lesion in MD. The other eight genes, NDUFA4, NDUFB6, NDUFV1, NDUFS8, SDHB, UQCRC1, UQCRC2, and COX7A2, actively participated in oxidative phosphorylation in mitochondrial dysfunction and cell death. Most importantly, we found that the MDV replication was repressed when linc-GALMD3 was knocked down in CEF cells. Our results suggested that linc-GALMD3 might be a critical regulator in chicken MD and could be used as a candidate-promising mark for MD prevention, diagnosis, and treatment.

Highlights

93% human genome can be transcribed into RNAs, only 2% of these RNAs can be translated to proteins
We identified that linc-GALMD3 has the significantly higher expression in Marek’s disease virus (MDV)-infected CD4+ T cells for two reciprocal cross chicken lines (63 × 72: fold change = 3.95, false discovery rate (FDR) = 0.0013; and 72 × 63: fold change = 4.26, FDR = 0.0014)
We detected the expression of linc-GALMD3 in CD4+ T cells in these two lines by qRT-PCR, and we found that the qRT-PCR result was consistent to that of RNA sequencing (RNA-Seq) (Fig. 1A)

Summary

Introduction

93% human genome can be transcribed into RNAs, only 2% of these RNAs can be translated to proteins. The ncRNAs are divided into small and long non-coding RNAs (lncRNAs) depending on the length of the RNAs3. LncRNAs generally expressed low in organism, but have a tissue and cell-specific expression compared with the protein coding RNAs7, 8. Long intergenic non-coding RNAs (lincRNAs) are a kind of lncRNAs that transcribed from DNA sequences between coding genes[9]. MD is characterized by CD4+ T cell lymphoma formation, and MDV infection can be generally divided into four phases: early cytolysis (3–6 days post infection [dpi.]), latency (7–10 dpi.), late cytolysis (10–14 dpi.), and neoplastic lymphoma transformation (after 21 dpi.)[32]. The mean value of log[2] FC (Infected/Non-infected) was compared in the bar chart for CD4+ T cells from two reciprocal cross lines (63 × 72 and 72 × 63), respectively; FC means fold change; and the qRT-PCR data was normalized by GAPDH expression. We have already identified more than 1,000 lincRNAs in chicken bursa, but the detailed study on lincRNA function is missing[36]

Methods

Results

Discussion

Conclusion