February 16th, 2025
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers,
- Liu et al. find that SNORA73 binds mRNA and 7SL RNA and acts as a ternary-glue snoRNA by utilising snoKARR-seq and polysome-seq.
- Wang et al. used polysome-seq and m6A-seq to discover how loss of YTHDF1 in B cells decreases IgG response by reducing IgG transcript life in ASCs.
- Sjövall et al. uncovers that defective ribosome assembly impairs leukemia progression in p53-deficient AML with the help of polysome-seq.
snoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification
Cell, 2024
Liu, B., Wu, T., Miao, B.A., et al.
Small nucleolar RNAs (snoRNAs) are non-coding RNAs whose main function is guiding RNA modifications. They are also known to interact with mRNA, however, full interactome is not yet elucidated. The authors developed a snoKARR-seq approach based on a chemical crosslinking that allows the detection of RNA targets of snoRNAs. In addition, polysome profiling was used to further confirm some of the interactions.
The authors discovered that a large fraction of snoRNA-target mRNA interactions occur independently of RNA modifications. It turned out that there are over 1,000 previously unknown snoRNA-mRNA interactions in human cell lines and mouse brain tissue.
One of the detected interactions, mRNA-SNORA73-7SL, which was shown to function in co-translational protein translocation, was supported by a polysome profiling experiment. One would expect if this interaction occurs, there is an enrichment of SNORA73 and its canonical protein binding partners, such as DKC1, in cytosolic ribosome complexes. Indeed, enrichment of SNORA73, 7SL, and DKC1 was observed in the cytosolic ribosome fraction, confirming the association of SNORA73 snoRNP with cytosolic ribosomes. Besides, SNORA73, 7SL, and CLU mRNA was shown to colocalize in the monosome and low-polysome fractions. This could be explained by the fact that the signal recognition particle (SRP) interacts with signal peptides in the N Terminus at the monosome stage resulting in the translational arrest until it binds to the SRP receptor on the ER membrane. Such an enrichment of SNORA73 in the light polysome fraction indicates that SNORA73 may dissociate from the ribosome early in translation.
Learn more about EIRNA Bio’s polysome profiling service here.
Progressive polyadenylation and m6A modification of Ighg1 mRNA maintain IgG1 antibody homeostasis in antibody-secreting cells
Immunity, 2024
Wang, Y., Zhang, S., Kang, N., Dong, L., et al.
Antigen-specific antibodies are generated by antibody-secreting cells (ASCs). mRNAs are known to be post-transcriptionally modified, however, it is not yet clear how such modifications can influence the antibody homeostasis. In this study, researchers uncovered that N6-methyladenosine (m6A) modifications maintain IgG1 antibody production in ASCs.
First, with the help of m6A-sequencing (m6A-seq), it was demonstrated that IgG heavy-chain transcripts (Ighg) possessed m6A sites along their long 3’UTR. Furthermore, RNA immunoprecipitation sequencing (RIP-seq) identified Ighg1 transcripts as the primary targets of m6A reader YTHDF1. B cell-specific YTHDF1 deficiency mice were utilised to show that depletion of YTHDF1 impairs IgG antibody response due to a significant downregulation of antibody expression. To test whether YTHDF1 has an effect on the mRNA translation in ASC, polysome profiling was performed. It was shown that YTHDF1 protein was enriched in the non-ribosome mRNA-protein particles fraction. Moreover, YTHDF1 deficiency did not affect Ighg1 mRNA association with polysomes.
Further investigation suggested that YTHDF1 primarily functions in the nucleus of ASCs, orchestrating Ighg1 stability and consequently influencing antibody production. By means of single-cell RNAseq, a cell subpopulation of ASC was found with upregulated YTHDF1 in the systemic lupus erythematosus (SLE) patients. YTHDF1 inhibitor reduced autoantibody production in a murine lupus model. This suggests YTHDF1 as a potential target for SLE treatment.
Learn more about EIRNA Bio’s polysome profiling service here.
Defective ribosome assembly impairs leukemia progression in a murine model of acute myeloid leukemia
Cell Rep., 2024
Sjövall, D., Ghosh, S., Fernandez-Fuentes, N., Velasco-Hernandez, T., et al.
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy characterized by clonal expansion of aberrant myeloid precursor cells and bone marrow failure. Unfortunately, for the majority of patients there has been no universal cure found so far. By analysing patients’ datasets and murine models, scientists demonstrated that immature AML cells exhibit higher ribosome biogenesis rates.
As the key model, the study utilises mice that allow inducible overexpression of eIF6. eIF6 overexpression is known to sequester 60S subunits in the cytoplasm, disrupt ribosomal subunit joining, and attenuate protein synthesis. With the help of polysome profiling, it was shown that high eIF6 overexpression caused a rapid collapse of polysomes as expected. By utilising this mice model, it was demonstrated that defective ribosome assembly prolongs survival in mice with MLL-AF9 AML.
With addition of the scRNA-seq approach, researches showed that there is a subset of leukemia cells that can adapt to defective ribosome assembly through global transcriptional reprogramming. This reprogramming involves upregulation of genes belonging to ribosome biogenesis, translation, peptide biosynthetic process, and RNA processing.
In the p53-deficient AML model, induction of a defective ribosome assembly led to a robust increase of apoptosis supporting the antileukemia efficacy. To summarise, this study suggests that high protein synthesis rate is essential for leukemia progression, and highlights the potential that ribosome assembly might be used as a therapeutic target in AML.
Learn more about EIRNA Bio’s polysome profiling service here.