Decoding protein binding landscape on circular RNAs with base-resolution transformer models.

Circular RNAs (circRNAs), a class of endogenous RNA with a covalent loop structure, can regulate gene expression by serving as sponges for microRNAs and RNA-binding proteins (RBPs). To date, most computational methods for predicting RBP binding sites on circRNAs focus on circRNA fragments instead of circRNAs. These methods detect whether a circRNA fragment contains binding sites, but cannot determine where are the binding sites and how many binding sites are on the circRNA transcript.

Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.

Circular RNAs (circRNAs) interact with RNA-binding proteins (RBPs) to play crucial roles in gene regulation and disease development. Computational approaches have attracted much attention to quickly predict highly potential RBP binding sites on circRNAs using the sequence or structure statistical binding knowledge. Deep learning is one of the popular learning models in this area but usually requires a lot of labeled training data.

[Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice].

The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools.

Inhibition of Notch Signaling Promotes the Adipogenic Differentiation of Mesenchymal Stem Cells Through Autophagy Activation and PTEN-PI3K/AKT/mTOR Pathway.

Background: The Notch signaling pathway is implicated in a broad range of developmental processes, including cell fate decisions. This study was designed to determine the role of Notch signaling in adipogenic differentiation of human bone marrow derived MSCs (BM-MSCs).

Methods: The Notch signaling was inhibited by the γ-secretase inhibitor N-[N-(3,5-difluor- ophenacetyl-L-alanyl)]-S-phenylglycine t-butylester (DAPT).