Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene.

Zhongjing Su,Bin Zhang,Ze Lin,Dongyang Huang,Guangyu Liu

doi:10.3390/genes12050759

Zhongjing Su, Bin Zhang + Show 3 more

Open Access

https://doi.org/10.3390/genes12050759

Copy DOI

Journal: Genes	Publication Date: May 17, 2021
Citations: 3	License type: CC BY 4.0

Affiliation: Shantou University, Shantou University Medical College

Abstract

The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.

Highlights

CD45, known as protein tyrosine phosphatase receptor type C (PTPRC), is mainly expressed on immune cells to initiate cross-membrane signal transduction [1,2]
The genotype-tissue expression (GTEx) data indicated that CD45 and its natural antisense RNA PEBP1P3 were highly expressed in lymphoid-associated tissues, and the RNA levels of PEBP1P3 were positively correlated with the expression of CD45 in multiple human tissues except for the testis
To detect whether there was a regulatory effect of PEBP1P3 on the expression of the sense gene

Summary

Introduction

CD45, known as protein tyrosine phosphatase receptor type C (PTPRC), is mainly expressed on immune cells to initiate cross-membrane signal transduction [1,2]. Distinct CD45 isoforms are expressed on lymphocyte subsets at different developmental stages and regulate different functional statuses of lymphocytes [3,4]. Regarding the regulation of CD45 splicing, previous studies found that nucleotide polymorphisms at the splicing site of CD45 alternative exons influenced the expression of CD45 isoforms and the function of immune cells [6,7,8], and heterogeneous ribonucleoprotein hnRNPs were identified as critical regulators of CD45 alternative splicing [9,10,11].

Methods

Results

Conclusion