Paclitaxel-induced stress granules increase LINE-1 mRNA stability to promote drug resistance in breast cancer cells

Abnormal expression of long interspersed element-1(LINE-1)has been implicated in drug resistance,while our previous study showed that chemotherapy drug paclitaxel(PTX)increased LINE-1 level with unknown mechanism.Bioinformatics analysis suggested the regulation of LINE-1 mRNA by drug-induced stress granules(SGs).This study aimed to explore whether and how SGs are involved in drug-induced LINE-1 increase and thereby promotes drug resistance of triple negative breast cancer(TNBC)cells.We demonstrated that SGs increased LINE-1 expression by recruiting and stabilizing LINE-1 mRNA under drug stress,thereby adapting TNBC cells to chemotherapy drugs.Moreover,LINE-1 inhibitor efavirenz(EFV)could inhibit drug-induced SG to destabilize LINE-1.Our study provides the first evidence of the regulation of LINE-1 by SGs that could be an important survival mechanism for cancer cells exposed to chemotherapy drugs.The findings provide a useful clue for developing new chemotherapeutic strategies against TNBCs.

rhe Mitochondrion-Targeted PENTATRICOPEPTIDE REPEAT78 Protein Is Required for nad5 Mature mRNA Stability and Development in Maize

Pentatricopepetide repeat （PPR） proteins are a large family of RNA-binding proteins involved in RNA meta- bolism in plant organelles. Although many PPR proteins have been functionally studied, few of them are identified with a function in mitochondrial RNA stability. By using a reverse genetic approach, we characterized the role of the mitochondrion-targeted PPR78 protein in nad5 mature mRNA stability and maize （Zea mays） seed development. Loss of PPR78 function leads to a dramatic reduction in the steady-state level of mitochondrial nad5 mature mRNA, blocks the assembly of complex I in the electron transport chain, and causes an arrest in embryogenesis and endosperm development. Characterization of a second strong allele confirms the function of PPR78 in nad5 mRNA accumulation and maize seed development. The generation of mature nad5 requires the assembly of three distinct precursor RNAs via transsplicing reactions, and the accumulation ofnad5T1 precursor is reduced in the ppr78 mutants. However, it is the instability of mature nad5 rather than nad5T1 causing loss of the full-length nad5 transcript, and degradation of nad5 losing both translation start and stop codons is enriched in the mutant. Our data imply the assembly of mature nad5 mRNA precedes the protection of PPR78.

Emerging roles of lncRNAs in the post-transcriptional regulation in cancer

Accumulating evidence indicates that long non-coding RNAs(lncRNAs)can play a pivotal role in regulation of diverse cellular processes.In particular,lncRNAs can serve as master gene regulators at transcriptional and posttranscriptional levels,leading to tumorigenesis.In this review,we discuss latest developments in lncRNA-meditated gene expression at the post-transcriptional level,including gene splicing,mRNA stability,protein stability and nuclear trafficking.

YB-1 stabilizes HIV-1 genomic RNA and enhances viral production

HIV-1 utilizes cellular factors for effi cient replication.The viral RNA is different from cellular mRNAs in many aspects,and is prone to attacks by cellular RNA quality control systems.To establish effective infection,the virus has evolved multiple mechanisms to protect its RNA.Here,we show that expression of the Y-box binding protein 1(YB-1)enhanced the production of HIV-1.Downregulation of endogenous YB-1 in producer cells decreased viral production.YB-1 increased viral protein expression by stabilizing HIV-1 RNAs.The stem loop 2 in the HIV-1 RNA packaging signal was mapped to be the YB-1-responsive element.Taken together,these results indicate that YB-1 stabilizes HIV-1 genomic RNA and thereby enhances HIV-1 gene expression and viral production.

Characterizing RNA Pseudouridylation by Convolutional Neural Networks

Pseudouridine(Ψ)is the most prevalent post-transcriptional RNA modification and is widespread in small cellular RNAs and m RNAs.However,the functions,mechanisms,and precise distribution ofΨs(especially in m RNAs)still remain largely unclear.The landscape ofΨs across the transcriptome has not yet been fully delineated.Here,we present a highly effective model based on a convolutional neural network(CNN),called Pseudo Uridy Lation Site Estimator(PULSE),to analyze large-scale profiling data ofΨsites and characterize the contextual sequence features of pseudouridylation.PULSE,consisting of two alternatively-stacked convolution and pooling layers followed by a fully-connected neural network,can automatically learn the hidden patterns of pseudouridylation from the local sequence information.Extensive validation tests demonstrated that PULSE can outperform other state-of-the-art prediction methods and achieve high prediction accuracy,thus enabling us to further characterize the transcriptome-wide landscape ofΨsites.We further showed that the prediction results derived from PULSE can provide novel insights into understanding the functional roles of pseudouridylation,such as the regulations of RNA secondary structure,codon usage,translation,and RNA stability,and the connection to single nucleotide variants.The source code and final model for PULSE are available at https://github.com/mlcb-thu/PULSE.

Expression of YB-1 enhances production of murine leukemia virus vectors by stabilizing genomic viral RNA

Murine leukemia virus(MLV)-based retroviral vectors is widely used for gene transfer and basic research,and production of high-titer retroviral vectors is very important.Here we report that expression of the Y-box binding protein 1(YB-1)enhanced the production of infectious MLV vectors.YB-1 specifically increased the stability of viral genomic RNA in virus-producing cells,and thus increasing viral RNA levels in both producer cells and virion particles.The viral element responsive to YB-1 was mapped to the repeat sequence(R region)in MLV genomic RNA.These results identified YB-1 as a MLV mRNA stabilizer,which can be used for improving production of MLV vectors.

A Small Multifunctional Pentatricopeptide Repeat Protein in the Chloroplast of Chlamydomonas reinhardtii

Organellar biogenesis is mainly regulated by nucleus-encoded factors, which act on various steps of gene expression including RNA editing, processing, splicing, stabilization, and translation initiation. Among these regulatory factors, pentatricopeptide repeat （PPR） proteins form the largest family of RNA binding proteins, with hundreds of members in flowering plants. In striking contrast, the genome of the unicellular green alga Chlamydomonas reinhardtii encodes only 14 such proteins. In this study, we analyzed PPR7, the smallest and most highly expressed PPR protein in C. reinhardtii. Green fluorescent protein-based localization and gel-filtration analysis revealed that PPR7 forms a part of a high-molecular-weight ribonu- cleoprotein complex in the chloroplast stroma. RIP-chip analysis of PPRT-bound RNAs demonstrated that the protein associates with a diverse set of chloroplast transcripts in vivo, i.e. rrnS, psbH, rpoC2, rbcL, atpA, cemA-atpH, tscA, and atpl-psaJ. Furthermore, the investigation of PPR7 RNAi strains revealed that deple- tion of PPR7 results in a light-sensitive phenotype, accompanied by altered levels of its target RNAs that are compatible with the defects in their maturation or stabilization. PPR7 is thus an unusual type of small multi- functional PPR protein, which interacts, probably in conjunction with other RNA binding proteins, with numerous target RNAs to promote a variety of post-transcriptional events.