Project description:DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive. iCLIP-Seq analyses of DDX46-bound RNAs from uninfected and VSV-infected RAW264.7 cells
Project description:DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive.
Project description:YTHDF3 play important role in regulation of trophoblast activity, we examined the downstream genes of YTHDF3 via transcriptome sequencing
Project description:N6-methyladenosine (m6A) is vital for RNA metabolism and function and is one of the most abundant internal RNA modifications. Recently, m6A has been indicated in regulating replication of multiple viruses; however, the role of m6A in typical arbovirus-alphavirus, is mainly elusive. Alphavirus containing several emerging and re-emerging pathogens that poses great threat to human health. Here, we show that the prototype alphavirus, Sindbis virus (SINV), its replication is regulated by m6A readers. Of which, depleting YTHDF3 results in reduced SINV release but increased viral capsid within the cell. Mechanically, YTHDF3 bind and regulate the mRNA stability of SQSTM1, the major selective autophagy receptor, which targeting of capsid into autophagosomes. Furthermore, we found interaction between YTHDF3, SQSTM1 and capsid in pairs. K27 ubiquitination is the dominant modification for SINV capsid. Besides ubiquitin-associated (UBA) domain, the N-terminal domain of SQSTM1 has stronger interaction with capsid, highlighted the role of RL peptide mimic within the capsid. Further experiments revealed that the interaction between YTHDF3 and SQSTM1 protein relies on their YTH-domain and ZZ-type Zinc finger domain respectively. Together, these results highlight the role of m6A modification reader YTHDF3 in regulating selective autophagy during virus infection and provide new insights into alphavirus replication cycle.
Project description:Long noncoding RNA HOTAIR (HOX antisense intergenic RNA) is an important regulator of breast cancer metastasis. Studies showed that HOTAIR reprograms chromatin state through interacting with Polycomb Repressive Complex 2 (PRC2) to promote breast cancer metastasis. However, it is unclear if there exist other HOTAIR-binding factors which participate in promoting breast cancer metastasis. In the current study, we utilized mass spectrometry (ChIRP-MS) to comprehensively identify RNA-binding proteins (RBPs) associated with HOTAIR. We also performed a high-throughput CRISPR screen to investigate HOTAIR-interacting proteins involved in cell metastasis. We found that many m6A-reader proteins were involved in this progress, including YTHDF3, which is a newly identified HOTAIR partner. We further demonstrated that HOTAIR and YTHDF3 co-regulated the expression of several metastasis-associated genes by modifying their chromatin accessibility in breast cancer cells. Altogether, our work detailed the functional interactome of HOTAIR involved in promoting breast cancer cell metastasis, and suggested a mechanism whereby HOTAIR regulates chromatin state in cooperation with the m6A-reader YTHDF3.
Project description:Long noncoding RNA HOTAIR (HOX antisense intergenic RNA) is an important regulator of breast cancer metastasis. Studies showed that HOTAIR reprograms chromatin state through interacting with Polycomb Repressive Complex 2 (PRC2) to promote breast cancer metastasis. However, it is unclear if there exist other HOTAIR-binding factors which participate in promoting breast cancer metastasis. In the current study, we utilized mass spectrometry (ChIRP-MS) to comprehensively identify RNA-binding proteins (RBPs) associated with HOTAIR. We also performed a high-throughput CRISPR screen to investigate HOTAIR-interacting proteins involved in cell metastasis. We found that many m6A-reader proteins were involved in this progress, including YTHDF3, which is a newly identified HOTAIR partner. We further demonstrated that HOTAIR and YTHDF3 co-regulated the expression of several metastasis-associated genes by modifying their chromatin accessibility in breast cancer cells. Altogether, our work detailed the functional interactome of HOTAIR involved in promoting breast cancer cell metastasis, and suggested a mechanism whereby HOTAIR regulates chromatin state in cooperation with the m6A-reader YTHDF3.
Project description:N1-methyladenosine (m1A) is one of messenger RNA modification in eukaryotes, but the potential roles of m1A methylated mRNA in trophoblast upon hypoxia remain elusive.
