RBM25 binds to and regulates alternative splicing levels of Slc38a9, Csf1, and Coro6 to affect immune and inflammatory processes in H9c2 cells

PeerJ. 2023 Nov 7:11:e16312. doi: 10.7717/peerj.16312. eCollection 2023.

Abstract

Background: Alternative splicing (AS) is a biological process that allows genes to be translated into diverse proteins. However, aberrant AS can predispose cells to aberrations in biological mechanisms. RNA binding proteins (RBPs), closely affiliated with AS, have gained increased attention in recent years. Among these RBPs, RBM25 has been reported to participate in the cardiac pathological mechanism through regulating AS; however, the involvement of RBM25 as a splicing factor in heart failure remains unclarified.

Methods: RBM25 was overexpressed in H9c2 cells to explore the target genes bound and regulated by RBM25 during heart failure. RNA sequencing (RNA-seq) was used to scrutinize the comprehensive transcriptional level before identifying AS events influenced by RBM25. Further, improved RNA immunoprecipitation sequencing (iRIP-seq) was employed to pinpoint RBM25-binding sites, and RT-qPCR was used to validate specific genes modulated by RBM25.

Results: RBM25 was found to upregulate the expression of genes pertinent to the inflammatory response and viral processes, as well as to mediate the AS of genes associated with cellular apoptosis and inflammation. Overlap analysis between RNA-seq and iRIP-seq suggested that RBM25 bound to and manipulated the AS of genes associated with inflammation in H9c2 cells. Moreover, qRT-PCR confirmed Slc38a9, Csf1, and Coro6 as the binding and AS regulatory targets of RBM25.

Conclusion: Our research implies that RBM25 plays a contributory role in cardiac inflammatory responses via its ability to bind to and regulate the AS of related genes. This study offers preliminary evidence of the influence of RBM25 on inflammation in H9c2 cells.

Keywords: Alternative splicing; H9c2 cell; Heart failure; Improved RNA immunoprecipitation sequencing; Inflammation; RBM25; RNA-seq.

MeSH terms

  • Alternative Splicing* / genetics
  • Animals
  • Heart Failure* / genetics
  • Inflammation / genetics
  • Nuclear Proteins / genetics
  • RNA Recognition Motif Proteins* / genetics
  • RNA Splicing Factors* / genetics
  • RNA-Binding Proteins / genetics
  • Rats

Substances

  • Nuclear Proteins
  • RNA-Binding Proteins
  • RNA Splicing Factors
  • RNA Recognition Motif Proteins

Grants and funding

This work was supported by the National Natural Science Foundation of China under grant [82360082] and [81760074]; the Special Foundation Projects of Joint Applied Basic Research of Yunnan Provincial Department of Science and Technology with Kunming Medical University under grant [202201AY070001-064] and [2017FE468(-043)]; the Yunnan Health Training Project of High-Level Talents under grant [D-2018020]; the Clinical Medical Center for Cardiovascular and Cerebrovascular Disease of Yunnan Province under grant [ZX2019-03-01]; the Foundation Projects of young and middle-aged academic and technical leaders reserve talent of Yunnan province under grant [202305AC160048]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.