Plotnikova, O. | Search bioRxiv

bioRxiv2019

Comprehensive analysis of human microRNA-mRNA interactome

MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA-mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions, and an abundance of false positive results.\n\nHere we present the landscape of microRNA-mRNA human interactions, which we derived from comprehensive analysis of datasets describing direct microRNA-mRNA interactions experimentally defined in HEK293 and Huh7.5 cell lines, along with other available microRNA and mRNA expression data. We have also established a collection of reliable microRNA binding regions that we systematically extracted in course of analysis of 79 CLIP datasets, which is available at http://score.generesearch.ru/services/mirna/.\n\nWhile only 1-2% of human genes interact with microRNAs, some RNAs display a substantial sponge effect, which is specific to the cell line of study. Some microRNAs are expressed at a very high level, while interacting with only a few mRNAs, thus, indeed, serving as specific gene expression regulators. Other miRNAs might be expressed at relatively low levels, and interact with many mRNAs. Some of the microRNAs might switch between these two classes, depending on cellular context. Results of our study provide an initial resolution into the complex patterns of human microRNA-mRNA interactions.

bioinformatics↗

bioRxiv2019

Structural basis for the transport mechanism of the human glutamine transporter SLC1A5 (ASCT2)

Alanine-serine-cysteine transporter 2 (ASCT2, SLC1A5) is the primary transporter of glutamine in cancer cells and regulates the mTORC1 signaling pathway. The SLC1A5 function involves finely tuned orchestration of two domain movements that include the substrate-binding transport domain and the scaffold domain. Here, we present cryo-EM structures of human SLC1A5 and its complex with the substrate, L-glutamine in an outward-facing conformation. These structures reveal insights into the conformation of the critical ECL2a loop which connects the two domains, thus allowing rigid body movement of the transport domain throughout the transport cycle. Furthermore, the structures provide new insights into substrate recognition, which involves conformational changes in the HP2 loop. A putative cholesterol binding site was observed near the domain interface in the outward-facing state. Comparison with the previously determined inward-facing structure of SCL1A5 provides a basis for a more integrated understanding of substrate recognition and transport mechanism in the SLC1 family. Our structures are likely to aid the development of potent and selective SLC1A5 inhibitors for the treatment of cancer and autoimmune disorders.

biophysics↗