I am pleased to present a new tool for analysis of small RNA sequencing data -- ShortStack. This program is designed for comprehensive annotation of small RNA-producing genes, including siRNA clusters, phased small RNAs, hairpin-derived small RNAs, and MIRNAs. Loci are discovered de novo and annotated with the statistics that are relevant for small RNAs .. size, polarity, repetitiveness, phasing, and underlying hairpins. In addition, ShortStack can be run in 'count' mode to quantify and annotate a set of loci provided a priori by the user. If you have smallRNA-seq data (and a reference genome to align it to), give the beta ShortStack version a try (and give me your comments at email@example.com).
Congratulations to Chenggang Liu on publishing this study in Plant Physiology. In this work, the results of a hyl1 suppressor screen are reported: several novel, dominant DCL1 alleles with mutations either in the helicase domain or in the RNaseIIIa domain. These alleles rescue hyl1 phenotypes but do not fix the microRNA processing accuracy defects typical of the hyl1 null mutant. In vitro, these alleles cleave pri-miRNAs with enhanced kinetics. In addition, a requirement for the DCL1 helicase domain for accurate processing of select pri-miRNAs is found.
-- THIS WEBSITE HAS BEEN REPLACED ... please go to http://sites.psu.edu/axtell for the current Axtell Lab Website! --
Michael Axtell, lab PI