Dysregulation of H3K36 tri-methylation
In clear cell renal cell carcinoma (ccRCC), read-through transcription and DoG formation are extensive due to defective transcription termination and consequent aberrant splicing [1]. Notably, H3K36 methyl transferase gene SETD2 is frequently mutated. SETD2 knockout in ccRCC cells induced read-through transcription[1]. Read-through transcription has also been observed in a variety of cancers, underlining this transcription defect being a general cause of cellular transformation[2, 3].
Absence of Histone H2A.Z
Histone H2A.Z is an alternative histone variant associated with DNA repair. DoGs are detected in non-proliferative senescent cells where H2A.Z is absent (Fig.1)[4]. The DoGs are thought to play a key role in controlling gene expression by acting as antisense transcripts.
Figure 1. Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes. During senescence, a family of functional antisense RNAs, referred as START RNAs for Senescence-Triggered
Antisense Read-through RNAs, are produced by transcriptional read-through downstream of the convergent genes. These RNAs are activated by mechanisms relying on the control of POL II elongation rate and H2A.Z local occupancy[4].
RNA modifications
RNA modifications, such as m6A, affect transcription termination[5, 6]. In plants, a mutant of the m6A writer-associated factor FIP37 induces read-through transcription and formation of chimeric mRNAs in a subset of genes[7]. m6A–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity, which requires the m6A writer-associated factor FIP37 and m6A reader CPSF30L[7]. Targeted m-ASP pathway in FIP37- and CPSF30L-deficient plants causes transcriptional read-through and mRNA chimera formation (Fig.2). Additionally, the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript and possibly control transposable elements at specific locus. Taken together, selective recognition of 3’-UTR m6A acts as a safeguard mechanism to restrict inappropriate gene expression and ensure transcriptome integrity[7].
Figure 2. Model for m6A-assisted polyadenylation (m-ASP) pathway in DoG formation [7]. (1) m6A writer-associated factor FIP37 is required for m6A deposition at the 3’-UTR of GENE1. (2) The m6A is recognized by the YTHDC-type domain of CPSF30L reader that promotes cleavage and polyadenylation at the 3’-UTR of GENE1. (3) mRNA chimera formation is thereby restricted.
m6A modification and R-loop
Nascent RNA m6A modification promotes R-loop formation in the terminator regions of genes to facilitate transcription termination (Fig.3)[8]. Depletion of the m6A methyltransferase METTL3 dramatically reduces R-loop accumulation in m6A genes around TES, resulting in termination defect and read-through transcription[8]. Restoration of R-loops at affected TESs and suppression of consequent read-through activities require METTL3 methyltransferase activity[8].
Figure 3. m6A modification promotes R-loop formation in the terminator regions for efficient transcription termination[8].
Recently, it has been found that R-loops serve as chromatin anchors for the recruitment of DDX21 and METTL3, which together facilitate the co-transcriptional installation of m6A on nascent transcripts. The presence of m6A on the nascent RNA plays a critical role in the recruitment and loading of XRN2, a major nuclear 5' to 3' exoribonuclease. In torpedo model of transcription termination, XRN2 enters at poly(A) cleavage site, degrades the RNA emerging from the ongoing transcription, and chases down RNAPII to dislodge it from the DNA, effectively terminating transcription. m6A reader proteins such as YTHDC1 can bind and recruit XRN2 to the transcription termination sites to promote termination. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination and transcriptional read-through (Fig. 4)[9].
Figure 4. DDX21-METTL3-m6A axis installs m6A on nascent RNAs, resolves R-loops at the TES, and recruits XRN2 to terminate transcription. The lack of their activities can lead to defect in transcription termination, DoG formation, and consequent DNA damage[9].
Related Service
Downstream-of-Gene Transcript (DoG RNA) Array Service
Related Reviews
What Are DoG RNAs?
DoG RNAs Modulate Gene Rranscription in Diseases
DoG-derived Chimera RNAs and Circular RNAs in Cancers and Diseases
Epigenetic and Epitranscriptomic Regulation of DoG RNAs
References
1. Grosso AR et al: Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. Elife 2015, 4.[PMID: 26575290]
2. Maher CA et al: Transcriptome sequencing to detect gene fusions in cancer. Nature 2009, 458(7234):97-101.[PMID: 19136943]
3. Kannan K et al: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proc Natl Acad Sci U S A 2011, 108(22):9172-9177.[PMID: 21571633]
4. Muniz L et al: Control of Gene Expression in Senescence through Transcriptional Read-Through of Convergent Protein-Coding Genes. Cell Rep 2017, 21(9):2433-2446.[PMID: 29186682]
5. Frye M, Harada BT, Behm M, He C: RNA modifications modulate gene expression during development. Science 2018, 361(6409):1346-1349.[PMID: 30262497]
6. Anreiter I et al: New Twists in Detecting mRNA Modification Dynamics. Trends Biotechnol 2021, 39(1):72-89.[PMID: 32620324]
7. Pontier D et al: The m(6)A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci Alliance 2019, 2(3).[PMID: 31142640]
8. Yang X et al: m(6)A promotes R-loop formation to facilitate transcription termination. Cell Res 2019, 29(12):1035-1038.[PMID: 31606733]
9. Hao JD et al: DDX21 mediates co-transcriptional RNA m(6)A modification to promote transcription termination and genome stability. Mol Cell 2024, 84(9):1711-1726 e1711.[PMID: 38569554]