tRNA related RNA fragments (tRFs), also known as tRNA-derived RNAs (tdRNAs), are abundant small RNAs reported to be associated with Argonaute proteins, yet their function is unclear. We show that endogenous 18 nucleotide tRFs derived from the 3' ends of tRNAs (tRF-3) post-transcriptionally repress genes in HEK293T cells in culture. tRF-3 levels increase upon parental tRNA overexpression. This represses target genes with a sequence complementary to the tRF-3 in the 3' UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent, and the targets are recognized by sequence complementarity. Furthermore, tRF-3:target mRNA pairs in the RNA induced silencing complex associate with GW182 proteins, known to repress translation and promote the degradation of target mRNAs. RNA-seq demonstrates that endogenous target genes are specifically decreased upon tRF-3 induction. Therefore, Dicer-independent tRF-3s, generated upon tRNA overexpression, repress genes post-transcriptionally through an Argonaute-GW182 containing RISC via sequence matches with target mRNAs.

Edited by Karin Musier-Forsyth tRNA fragments (tRFs) and tRNA halves have been implicated in various cellular processes, including gene silencing, translation, stress granule assembly, cell differentiation, retrotransposon activity, symbiosis, apoptosis, and more. Overexpressed angiogenin (ANG) cleaves tRNA anticodons and produces tRNA halves similar to those produced in response to stress. However, it is not clear whether endogenous ANG is essential for producing the stress-induced tRNA halves. It is also not clear whether smaller tRFs are generated from the tRNA halves. Here, using global short RNA-Seq approach, we found that ANG overexpression selectively cleaves a subset of tRNAs, including tRNA Glu , tRNA Gly , tRNA Lys , tRNA Val , tRNA His , tRNA Asp , and tRNA SeC to produce tRNA halves and tRF-5s that are 26-30 bases long. Surprisingly, ANG knockout revealed that the majority of stress-induced tRNA halves, except for the 5 half from tRNA HisGTG and the 3 half from tRNA AspGTC , are ANG independent, suggesting there are other RNases that produce tRNA halves. We also found that the 17-25 bases-long tRF-3s and tRF-5s that could enter into Argonaute complexes are not induced by ANG overexpression, suggesting that they are generated independently from tRNA halves. Consistent with this, ANG knockout did not decrease tRF-3 levels or gene-silencing activity. We conclude that ANG cleaves specific tRNAs and is not the only RNase that creates tRNA halves and that the shorter tRFs are not generated from the tRNA halves or from independent tRNA cleavage by ANG.

Cyclin-dependent kinases drive cell division cycle progression in eukaryotic cells. In the model eukaryotic organism Saccharomyces cerevisiae (budding yeast), a single cyclin-dependent kinase, Cdk1, is essential and sufficient to drive the cell cycle. Misregulated CDK activity induces unscheduled proliferation as well as genomic instability, which are hallmarks of the cancer. Here, we report a novel Cdk1-interacting protein, YPL014W, which we name Cip1 (for Cdk1-interacting protein 1). Our results show that Cip1 specifically interacts with G 1 /S-phase Cln2-Cdk1 complex but not with S-phase Clb5-Cdk1 or M-phase Clb2-Cdk1 complexes. Also Cip1 phosphorylation is cell cycle regulated in a S-phase Cdk1-dependent manner. Over-expression of Cip1 blocks cell cycle progression in G 1 and stabilizes the S-phase Cdk1 inhibitor Sic1 in vivo. In addition, disruption of CIP1 (cip1D) leads to faster G 1 /S-phase transition compared to wild-type cells. Moreover, Cip1 inhibits Cln2-CDK activity both in vivo and in vitro. Our finding proves Cip1 as a novel negative regulator of cyclin-dependent kinase in S. cerevisiae.

SummaryRegulated gene expression makes an important contribution to cell cycle control mechanisms. In fission yeast, a group of genes is coordinately expressed during a late stage of the cell cycle (M phase and cytokinesis) that is controlled by common cis-acting promoter motifs named pombe cell cycle boxes (PCBs), which are bound by a trans-acting transcription factor complex, PCB binding factor (PBF). PBF contains at least three transcription factors, a MADS box protein Mbx1p and two forkhead transcription factors, Sep1p and Fkh2p. Here we show that the fission yeast Cdc14p-like phosphatase Clp1p (Flp1p) controls M-G1 specific gene expression through PBF. Clp1p binds in vivo both to Mbx1p, a MADS box-like transcription factor, and to the promoters of genes transcribed at this cell cycle time. Because Clp1p dephosphorylates Mbx1p in vitro, and is required for Mbx1p cell cycle-specific dephosphorylation in vivo, our observations suggest that Clp1p controls cell cycle-specific gene expression through binding to and dephosphorylating Mbx1p.

The acquisition of a high number of mutations, notably, the gain of two mutations L452R and F486V in RBD, and the ability to evade vaccine/natural infection-induced immunity suggests that Omicron is continuing to use “immune-escape potential” as an evolutionary space to maintain a selection advantage within the population. Despite the low hospitalizations and lower death rate, the surges by these variants may offset public health measures and disrupt health care facilities as seen recently in Portugal and the USA. Interestingly these BA.4/BA.5 variants have been found to be more severe than the earlier-emerged Omicron variants. We believe that aggressive COVID-19 surveillance using affordable testing strategies might actually help understand the evolution and transmission pattern of new variants. The sudden dip in reporting of new cases in some of the low- and middle-income countries is an alarming situation and needs to be addressed as this could lead to undetected transmission of future variants of interest/concern of SARS-CoV-2 in large population settings, including advent of a ‘super’ virus. It would be interesting to examine the possible role/influence, if any, of the two different kinds of vaccines, the spike protein-based versus the inactivated whole virus, in the evolution of BA.4/BA.5.