Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates

miRstring: An RNA language model enables mature miRNA decoding and artificial small RNA design across species

Introduction MicroRNAs (miRNAs) are processed from structured precursors and subsequently loaded into Argonaute proteins to repress target mRNAs. Accurate decoding of mature miRNAs from precursor sequences is fundamental to miRNA annotation and the rational engineering of artificial miRNAs. However, existing computatio...

Expanding the repertoire of microRNA target mimicry in plants.

This work systematically investigates the pairing architectures that enable plant TM-directed miRNA degradation (pTDMD), and identifies endogenous TMs with alternative pairing architectures, including EARLY NODULIN-LIKE PROTEIN5 (ENODL5), which fine-tunes miR159 levels during Arabidopsis floral development in an HWS-de...

Complementary Approaches for Accurate Detection of tRNA-Derived Small RNAs (tsRNAs): Small RNA Northern Blotting and Dumbbell PCR.

Homology-Based Prediction of Putative miRNA Loci and Their Candidate Target Genes in Phaseolus vulgaris

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression through a sequence-specific recognition of their targets, leading to degradation or inhibition of translation. In the case of plant miRNAs, they have been involved in a multitude of biological processes, from developmental processes to environmen...

Small RNA Analysis in Cancer Cells.

The preparation and analysis of standard, miRNA-enriched libraries that contain 5'-monophosphorylated RNAs and 3'-hydroxyl ends are described, as well as a custom protocol for the analysis of sRNAs containing 5'-cap modifications.

Target-Directed miRNA Degradation: Mechanisms and Significance.