Novel mechanism of conjoined gene formation in the human genome

Abstract

Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.

Immunohistochemistry, Fluorescence in Situ Hybridization, and Reverse Transcription–Polymerase Chain Reaction for the Detection of Anaplastic Lymphoma Kinase Gene Rearrangements in Patients With Non–Small Cell Lung Cancer: Potential Advantages and Methodologic Pitfalls

“…As the biological and clinical significance of such events are still unknown, the detection of EML4/ALK fusion transcripts without confirmation by FISH or IHC cannot be considered positive. 34 In summary, our data strongly support the necessity of combining all current diagnostic approaches for optimal ALK testing in NSCLC. Immunohistochemistry seems to be the most reliable screening method for large-scale clinical practice, when performed with a sensitive antibody clone and enhanced amplification system.…”

Transcription-Mediated Chimeric RNAs in Prostate Cancer: Time to Revisit Old Hypothesis?

“…In fact, transcription-induced chimeric RNAs, generated in normal healthy cells, without corresponding genomic rearrangements have been well recognized in the field of genetic research (Akiva, 2005;Fang et al, 2012;Gingeras, 2009;Kim DS, et al, 2007;Kim DS, et al, 2012;Kim P, et al, 2010;Kim RN, et al, 2012;Li et al, 2008;Parra, 2005;Prakash et al, 2010;Thomson et al, 2000;Zhang et al, 2012). However, the existence of transcription-induced chimeric RNAs has not been well appreciated in the cancer research field, where fusion genes play an important role in disease development, progression, and treatment (Edwards, 2010;Mitelman et al, 2007).…”

“…Although the mechanism of formation and the functional roles of chimeric transcripts remain elusive (Kannan et al, 2011;Kim RN, et al, 2012;Parra, 2005), two main mechanisms involved in the generation of transcription-induced chimeric transcripts have been established: 1) Through conjoined genes (two or more closely located genes on the same strand of a chromosome (Kannan et al, 2011;Kim DS, et al, 2012;Kim RN, et al, 2012;Parra, 2005;Prakash et al, 2010), where chimeric transcripts can be generated either by run-off transcription of the upstream gene followed by cis-splicing (Kannan et al, 2011;Prakash et al, 2010;Zhang et al, 2012) or skipping/truncation of the final exon in the upstream gene (Kim RN, et al, 2012); 2) Trans-splicing of RNAs, which generates inter-and intra-chromosomal chimeric transcripts (Fang et al, 2012;Gingeras, 2009;Kannan et al, 2011;Li et al, 2008). The USP9Y and TTTY15 genes are located next to each other in the same direction, meeting the criteria for a conjoined gene.…”

“…Therefore, USP9Y-TTTY15 is a transcription-induced chimeric RNA (an RNA created in normal cells by combining exons from two or more distinctly known parental genes) (Akiva, 2005;Fang et al, 2012;Gingeras, 2009;Kannan et al, 2011;Kim DS et al, 2007Kim P et al, 2010;Kim RN et al, 2012;Li et al, 2008;Parra, 2005;Prakash et al, 2010;Thomson et al, 2000;Zhang et al, 2012). Linked to this finding, we also investigated the expression of another transcription-induced chimeric RNA previously studied in prostate cancer from Western countries, SLC45A3-ELK4, of which both partner genes lie on the same chromosome within a short genomic distance (1q32) (Maher et al, 2009;Rickman et al, 2009;Zhang et al, 2012).…”

Upregulation of INS-IGF2 read-through expression and identification of a novel INS-IGF2 splice variant in insulinomas

“…3), in line with Wernersson et al (29) who found INS-IGF2 expression to be barely detectable in normal pancreatic tissue. kim et al (35) states that read-through transcripts are expressed at extremely low levels in human tissues with read-through transcripts showing a tumor-biased expression. Increased expression-level of read-through transcripts and increased number of read-through transcripts expressed seems therefore to be a cancer-specific event (35).…”