DDX21 mediates co-transcriptional RNA m6A modification to promote transcription termination and genome stability

N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.

The YTHDF proteins display distinct cellular functions on m6A-modified RNA

YTHDF proteins are main cytoplasmic 'reader' proteins of RNA N6-methyladenosine (m6A) methylation in mammals. They are largely responsible for m6A-mediated regulation in the cell cytosol by controlling both mRNA translation and degradation. Recent functional and mechanistic investigations of the YTHDF proteins revealed that these proteins have different functions to enable versatile regulation of the epitranscriptome. Their divergent functions largely originate from their different amino acid sequences in the low-complexity N termini. Consequently, they have different phase separation propensities and possess distinct post-translational modifications (PTMs). Different PTMs, subcellular localizations, and competition among partner proteins have emerged as three major mechanisms that control the functions of these YTHDF proteins. We also summarize recent progress on critical roles of these YTHDF proteins in anticancer immunity and the potential for targeting these proteins for developing new anticancer therapies.

Exploring RNA methylation as a promising biomarker for assessing sublethal effects of fipronil on honeybees (Apis mellifera L.)

Honeybees play a crucial role as pollinators for crops and are regarded as sensitive bioindicators of environmental health. The widespread use of pesticides poses a severe threat to honeybee survival. However, there is limited information available on the specific risks associated with fipronil exposure in honeybees, particularly concerning the impact on RNA methylation throughout their lifespan. This study aimed to evaluate the effects of sublethal concentrations of fipronil on RNA m⁶A and m⁵C methylations, along with the associated genes in honeybee larvae and newly emerged adults. LC-MS/MS analysis revealed a notable hypomethylation of m⁵C in larvae, while hypermethylation of m⁶A was observed in the adult brain. Significant changes in the expression of genes such as AmWTAP, AmYTHDF, AmALKBH4, AmALKBH6, AmALKBH8, AmNSUN5, AmNOP2, AmTET1, and AmYBX1 were observed in the adult brain, whereas alterations in the expression of AmNSUN2, AmMETTL14, AmALKBH1, AmALKBH4, AmALKBH6 AmALYREF, AmTET1, and AmYBX1 were observed in the larvae. Notably, the expression of AmALKBH1 was not detected in any fipronil-treated larvae, suggesting its potential as an early risk indicator for honeybee larvae in future assessments. This pioneering study provides insights into the effects of fipronil on RNA methylations in honeybees and explores the possibility of employing RNA methylation as a tool for assessing pesticide risks in this important pollinator species. These findings offer new perspectives on honeybee protection and the development of toxicity evaluation systems for pesticides.

Fine particulate matter induces METTL3-mediated m6A modification of BIRC5 mRNA in bladder cancer

Long-term exposure to fine particulate matter (PM_2.5) is reportedly related to a variety of cancers including bladder cancer. However, little is known about the biological mechanism underlying this association. In the present study, PM_2.5 exposure was significantly associated with increased levels of m⁶A modification in bladder cancer patients and bladder cells. METTL3 expression was aberrantly upregulated after PM_2.5 exposure, and METTL3 was involved in PM_2.5-induced m⁶A methylation. Higher METTL3 expression was observed in bladder cancer tissues and METTL3 knockdown dramatically inhibited bladder cancer cell proliferation, colony formation, migration and invasion, inducing apoptosis and disrupting the cell cycle. Mechanistically, PM_2.5 enhanced the expression of METTL3 by inducing the promoter hypomethylation of its promoter and increasing the binding affinity of the transcription factor HIF1A. BIRC5 was identified as the target of METTL3 through m⁶A sequencing (m⁶A-Seq) and KEGG analysis. The methylated BIRC5 transcript was subsequently recognized by IGF2BP3, which increased its mRNA stability. In particular, PM_2.5 exposure promoted the m⁶A modification of BIRC5 and its recognition by IGF2BP3. In addition, BIRC5 was involved in bladder cancer proliferation and metastasis, as well as VEGFA-regulated angiogenesis_. This comprehensive study revealed that PM_2.5 exposure exerts epigenetic regulatory effects on bladder cancer via the HIF1A/METTL3/IGF2BP3/BIRC5/VEGFA network.

Polymorphisms in METTL3 gene and hepatoblastoma risk in Chinese children: A seven-center case-control study

Hepatoblastoma is the most common malignant liver cancer in childhood, yet its etiology remains unclear. As an m⁶A methylation modifier, methyltransferase like 3 (METTL3) has an active methyltransferase domain that functionally participates in various tumor occurrence and development. However, little is known about how METTL3 polymorphisms affect the occurrence of hepatoblastoma. Here, we attempted to investigate the associations between METTL3 gene polymorphisms and hepatoblastoma risk in a seven-center case-control study. We genotyped four METTL3 polymorphisms (rs1061026 T > G, rs1061027 C > A, rs1139130 A > G, rs1263801 G > C) by TaqMan technique in 313 cases and 1446 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the contributions of these four single nucleotide polymorphisms (SNPs) to hepatoblastoma susceptibility. In single genotype analysis, we detected no significant correlation between these four polymorphisms in METTL3 and hepatoblastoma risk. However, in the combined analysis, the presence of 2-4 risk genotypes of METTL3 was associated with an increased risk of hepatoblastoma compared with that of 0-1 risk genotypes (adjusted OR = 1.48, 95% CI = 1.03-2.12, P = 0.035). The stratified analysis further revealed that carriers of 2-4 risk genotypes are more susceptible to hepatoblastoma in the subgroups of subjects aged under 17 months (adjusted OR = 1.88, 95% CI = 1.12-3.16, P = 0.016) and females (adjusted OR = 1.79, 95% CI = 1.06-3.05, P = 0.031). Overall, our results revealed that none of these four SNPs could increase susceptibility to hepatoblastoma individually. Carriers with 2-4 risk genotypes in the combined analysis tend to increase the risk of hepatoblastoma.