The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells

Abstract

Chimeric RNAs are often associated with chromosomal rearrangements in cancer. In addition, they are also widely detected in normal tissues, contributing to transcriptomic complexity. Despite their prevalence, little is known about the characteristics and functions of chimeric RNAs. Here, we examine the genetic structure and biological roles of CLEC12A-MIR223HG, a novel chimeric transcript produced by the fusion of the cell surface receptor CLEC12A and the miRNA-223 host gene (MIR223HG), first identified in chronic myeloid leukemia (CML) patients. Surprisingly, we observed that CLEC12A-MIR223HG is not just expressed in CML, but also in a variety of normal tissues and cell lines. CLEC12A-MIR223HG expression is elevated in pro-monocytic cells resistant to chemotherapy and during monocyte-to-macrophage differentiation. We observed that CLEC12A-MIR223HG is a product of trans-splicing rather than a chromosomal rearrangement and that transcriptional activation of CLEC12A with the CRISPR/Cas9 Synergistic Activation Mediator (SAM) system increases CLEC12A-MIR223HG expression. CLEC12A-MIR223HG translates into a chimeric protein, which largely resembles CLEC12A but harbours an altered C-type lectin domain altering key disulphide bonds. These alterations result in differences in post-translational modifications, cellular localization, and protein–protein interactions. Taken together, our observations support a possible involvement of CLEC12A-MIR223HG in the regulation of CLEC12A function. Our workflow also serves as a template to study other uncharacterized chimeric RNAs.

Transcriptional Regulation and Its Misregulation in Human Diseases

“…Consequently, differences in post-translational modifications, cellular localization, and protein-protein interactions occur. These findings not only support a possible involvement of CLEC12A-MIR223HG in the regulation of CLEC12A function, but they could also provide a roadmap to study the other uncharacterized chimeric RNAs that are continuously recognized by RNA-Seq analyses [11].…”

“…An interesting study has analyzed the genetic structure and biological roles of CLEC12A-MIR223HG, a novel chimeric transcript produced through trans-splicing by the fusion of the cell surface receptor CLEC12A (C-Type Lectin Domain Family 12 Member A) and the miRNA-223 host gene (MIR223HG), first identified through transcriptome profiling of chronic myeloid leukemia (CML) patients. Unexpectedly, CLEC12A-MIR223HG was detected not only in CML, but also in a variety of normal tissues and cell lines as pro-monocytic cells resistant to chemotherapy or during monocyte-to-macrophage differentiation [11]. Transcriptional activation of CLEC12A increased CLEC12A-MIR223HG expression.…”

“…In this Special Issue, a total of 18 excellent and interesting papers [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20], consisting of 13 original research studies [3][4][5][6][10][11][12][14][15][16][18][19][20], as well as five reviews, are published [7][8][9]13,17]. They cover many subjects of transcriptional regulation, including studies on cis-regulatory elements, transcription factors (TF), chromatin regulators, and ncRNAs.…”

“…Another emerging field, especially in cancer, is represented by chimeric RNAs, which are transcripts consisting of exons from different parental genes. They can be produced by several mechanisms mostly involving chromosomal rearrangements; besides, they can also be generated by intergenic splicing, cis-splicing from two same-strand adjacent genes, and trans-splicing from two separate RNA transcripts [11]. Although these events were initially considered rare, human transcriptome profiles have revealed that a huge amount of chimeric RNAs develop from intergenic splicing and can be also detected in normal tissues, thus contributing to transcriptomic complexity.…”

Functional and regulatory impact of chimeric RNAs in human normal and cancer cells

“…This could support the hypothesis that trans‐spliced RNA could act as a template that facilitates genomic fusion (Sun & Li, 2022). In another study, CLEC12A‐MIR223HG chimeric RNA was detected in normal cell and cell lines which was previously detected in CML patients, and it highlighted that this chimeric RNA in a normal cell is generated by trans‐splicing (Dhungel et al, 2021). A highly recurrent chimeric RNA, TMEM79‐SMG5 with discernible 5′ and 3′ splice sites at the RNA junction was detected in 90% of prostate cancer samples which could potentially generated by noncanonical splicing (Kannan et al, 2011).…”