Maestro of the Epitranscriptome Symphony:Molecular Insights into Co-transcriptional m6A Deposition for Transcription Termination and Genome Stability
In the vast orchestra of gene expression and genome stability, where the symphony of the epitranscriptome unfolds, a conductor is essential to maintain the harmony of different instruments, i.e., transcription and replication. A new study published online in Molecular Cell on Apr 2nd, 2024, revealed the identity of this maestro.
Led by Prof. REN Jie and Prof. YANG Yungui from Beijing Institute of Genomics of Chinese Academy of Sciences (China National Center for Bioinformation), research teams have now unveiled a cellular maestro responsible for the co-transcriptional deposition of N6-methyladenosine (m6A) and its on-site functions. This intricate performance involves concerted actions between the unique nucleic acid structure R-loops, the multi-tasking helicase DDX21, and the m6A writer METTL3. As the baton rises, let us delve into the captivating performance led by DDX21, unraveling the symphony of co-transcriptional RNA modifications that shape the complexities of cellular life.
In the grand symphony of the epitranscriptome, the melodic notes of m6A modification play indispensable roles in a variety of developmental processes, exerting their influences throughout the entire life cycle of mRNA. Dynamic as it is, the composition of m6A modification begins even as mRNA emerges from transcription. Yet, how can these m6A notes be written onto nascent mRNA at their destined positions, and how can they resonate in harmony with all other instruments in the orchestration of gene expression and genome stability? These questions have long puzzled researchers.
Building upon their previous discovery of the presence of m6A modifications on R-loops, which can be formed by the hybridization of nascent RNA transcripts onto the template DNA strand during transcription (Cell Research 2019), these research teams embarked on addressing these questions. Their hypothesis centered on the notion that this dynamic co-transcriptional structure of R-loops may play a role in guiding the co-transcriptional installation of m6A. However, a perplexing challenge arose: the R-loop also presents an obstacle for METTL3 to access the nascent transcript within it.
To solve this conundrum, researchers resorted to mass spectrometry (MS) and identified the DEAD-box helicase DDX21 as a novel interacting partner of the m6A methyltransferase complex (MTC). Combining chromatin-associated photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation coupled with high-throughput sequencing (caPAR-CLIP-seq) and single-strand DNA ligation-based library construction from DNA:RNA hybrid immunoprecipitation followed by sequencing (ssDRIP-seq) data analysis, they discovered that R-loops, DDX21, and METTL3 strongly colocalize. Mechanistically, R-loops serve as anchor points for the recruitment of DDX21 and METTL3 to chromatin. The helicase activity of DDX21 then presents nascent transcripts in R-loops for the methyltransferase activity of METTL3. Depletion of R-loops or DDX21 leads to a notable decrease in global m6A levels, particularly at gene ends. Thus, DDX21, in collaboration with R-loops and METTL3, takes up the baton, guiding the synchronized interplay of co-transcriptional RNA modifications.
Furthermore, researchers have revealed that DDX21, in conjunction with METTL3 and the resulting m6A modification, together with its reader YTHDC1, plays a crucial role in facilitating XRN2-mediated transcription termination, thereby ensuring genome stability. Disruption of these concerted actions at any step may lead to incomplete transcription termination, or readthrough, potentially resulting in DNA damage. Such genome instability at readthrough regions can be mitigated by blocking replication or by inhibiting transcription precisely with a CRISPR-targeting strategy. Again, like a maestro, DDX21 takes the center stage of the vast orchestra of transcription termination and genome stability, making the notes of m6A modification resonate with purpose.
This study uncovered new functions of DDX21 in promoting co-transcriptional m6A deposition, forging the missing link for co-transcriptional methylation and its regulatory roles. By orchestrating a nexus of coordinated recruitment and enzymatic activities, it bridges the knowledge gap at the intersection of establishing the epitranscriptome, coordinating transcriptional termination, and striking a delicate balance with genome stability. Further exploration of the mediating domains and essential enzymatic activities of the DDX21-METTL3-m6A axis holds promise for identifying new targets to modulate the m6A epitranscriptome. These insights may contribute to the development of innovative strategies to address diseases associated with dysregulated m6A metabolism, including aging, cancer, and neurological disorders.
This work was supported by the National Key Research and Development Program of China, the National Natural Science Foundation of China, and the Strategic Priority Research Program of the Chinese Academy of Sciences.
DDX21 mediates co-transcriptional RNA m6A modification to promote transcription termination and genome stability. (Image by REN Jie's group)
Contact：
Prof. REN Jie
Email: renjie@big.ac.cn
