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PLoS One 2021 14;16(4):e0249424. Epub 2021 Apr 14.

Faculty of Biology and Biotechnology, HSE University, Moscow, Russia.

Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their intronic miRNAs. Read More

Cancer Lett 2021 Apr 10. Epub 2021 Apr 10.

Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada. Electronic address:

Therapeutic effectiveness in breast cancer can be limited by the underlying mechanisms of pathogenesis, including epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs) and drug resistance. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are master regulators of gene expression and are functionally important mediators in these mechanisms of pathogenesis. Intricate crosstalks between these non-coding RNAs form complex regulatory networks of post transcriptional gene regulation. Read More

Front Genet 2021 25;12:589160. Epub 2021 Mar 25.

UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France.

Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid species (Poaceae, Chloridoideae) that successively diverged in the last 6-10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids (2 = 6 = 62) and (2 = 6 = 60) that resulted in two sterile F1 hybrids: × (2 = 6 = 62) in England and × (2 = 6 = 62) in France. Read More

Toxicol Appl Pharmacol 2021 Apr 8;420:115523. Epub 2021 Apr 8.

School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China. Electronic address:

Metformin, as the first-line drug for the treatment of type 2 diabetes mellitus, has been shown to possess a capability to activate or inhibit the production of reactive oxygen species (ROS) in different ways. However, the detailed mechanisms of the opposite effect are poorly understood. Here we provide evidence that metformin induces accumulation of ROS by inhibiting the expression of a core antioxidant transcription factor nuclear factor erythroid 2 like 1 (NFE2L1/Nrf1) in human hepatocellular carcinoma HepG2 cells. Read More

Methods Mol Biol 2021 ;2284:271-287

Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy.

The field of transcriptional regulation generally assumes that changes in transcripts levels reflect changes in transcriptional status of the corresponding gene. While this assumption might hold true for a large population of transcripts, a considerable and still unrecognized fraction of the variation might involve other steps of the RNA lifecycle, that is the processing of the premature RNA, and degradation of the mature RNA. Discrimination between these layers requires complementary experimental techniques, such as RNA metabolic labeling or block of transcription experiments. Read More