Rbmx Regulates YTHDC1 Nuclear Condensates to Promote Nascent Transcription in Acute Myeloid Leukemia

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.627-627
• Main Authors: Wakiro, Isaac, Huang, Yue, Yang, Xuejing, Xie, Xueqin, Luo, Hanzhi, Chang, Kathryn, Pierson, Aspen, Batchelor, Emily, Cheng, Yuanming, Nguyen, Diu T.T., Liu, Zhaoqi, Kharas, Michael G.
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-211338

Genetic mutations and altered expression of transcription factors and chromatin modulators are critical drivers for myeloid leukemogenesis. We and others previously found that the RNA binding protein and mRNA methylation associated factor RBMX/L1 is upregulated in AML and essential for myeloid leukemia development through control of nascent transcription of key chromatin regulators (Prieto, C., Nguyen, T.T.D., et al., Nat Cancer 2021). However, how this regulatory axis is controlled is not known. We postulated that discovery of RBMX interactors and associated programs could elucidate this mechanism. To identify such programs, we first performed RBMX co-immunoprecipitation followed by mass spectrometry. We found that YTHDC1 a nuclear RNA methylation (m6A) reader was enriched. Immunofluorescence coupled with high resolution microscopy revealed 80% of endogenous YTHDC1 to co-localize with RBMX while 20% of RBMX co-localized with YTHDC1. We previously reported that YTHDC1 binds m6A modified transcripts and forms a distinct class of liquid-like nuclear condensates required for myeloid leukemogenesis (Cheng, Y., et al., Cancer Cell, 2021). We found that RBMX depletion increased liquid-like properties of YTHDC1 condensates while ectopic expression reduced their liquid-like properties, number, and size, suggesting that RBMX alters the biophysical properties and molecular function of YTHDC1. To determine whether this RBMX-YTHDC1 interaction results in co-regulation of shared targets, we first compared YTHDC1's mRNA binding targets mapped by iCLIP and RBMX's binding targets mapped by PARCLIP. We found YTHDC1 to bind 67% of RBMX transcript targets (4,613 transcripts; p < 0.001). Moreover, de-novo motif analysis indicated the two proteins bind a similar motif matching to the known m6A DRACH sequence (p < 10-104). Crucially, our re-analysis of published YTHDC1 ChIP-seq and RBMX CUT&Tag datasets along with the CLIP data above revealed 1,345 sites (p < 0.001) to be bound at both the DNA and RNA level with 45% of the binding within the promoter region. Notably, these sites were enriched for histone modifications associated with active transcription such as H3K4me3 and H3K27ac and depleted for H3K9me3 associated with repressed transcription. Transcriptome profiling of YTHDC1 deficient MOLM13 cells enriched for similar gene expression signatures obtained from the top 300 upregulated (NES = 2.96; p < 0.05) and downregulated genes (NES = -3.44; p < 0.05) following RBMX deplet