Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy.

Alternative splicing is a regulated process that results in expression of specific mRNA and protein isoforms. Alternative splicing factors determine the relative abundance of each isoform. Here we focus on MBNL1, a splicing factor misregulated in the disease myotonic dystrophy. By altering the concentration of MBNL1 in cells across a broad dynamic range, we show that different splicing events require different amounts of MBNL1 for half-maximal response, and respond more or less steeply to MBNL1. Motifs around MBNL1 exon 5 were studied to assess how cis-elements mediate the MBNL1 dose-dependent splicing response. A framework was developed to estimate MBNL concentration using splicing responses alone, validated in the cell-based model, and applied to myotonic dystrophy patient muscle. Using this framework, we evaluated the ability of individual and combinations of splicing events to predict functional MBNL concentration in human biopsies, as well as their performance as biomarkers to assay mild, moderate, and severe cases of DM.

Phylogenetic and taxonomic evaluation of Chalara, Chalaropsis, and Thielaviopsis anamorphs associated with Ceratocystis.

Parsimony analysis of sequences of the internal transcribed spacer region of the nuclear rDNA and partial sequences of the large subunit (LSU) place four anamorphic Chalara species as a monophyletic grouping within the teleomorph genus Ceratocystis. Chalara ovoidea, Ch. thielavioides, Ch. populi, and Ch. elegans (synanamorph: Thielaviopsis basicola) form aleurioconidia typical of the anamorph genus Thielaviopsis, to which the species are transferred. Three of these species (T. ovoidea, T. thielavioides, and T. populi) are morphologically similar to each other but are shown to be distinct by rDNA sequences. The anamorphic genera Chalaropsis and Hughesiella are considered synonyms of Thielaviopsis. Thielaviopsis punctulata, which forms aleurioconidia singly, is shown to be the anamorph of Ce. radicicola. The respective anamorphs for Ce. coerulescens, Ce. fagacearum, and Ce. eucalypti, which lack aleurioconidia, are also transferred to the amended genus Thielaviopsis as T. ungeri, T. quercina, and T. eucalypti. Although Ch. australis and Ch. neocaledoniae do not form aleurioconidia, they are placed in Thielaviopsis based on their endoconidial state and clear affinities to Ceratocystis eucalypti. Three apparently asexual Ambrosiella species belong in the Ce. moniliformis clade based on LSU rDNA sequences, but the cultures available are not suitable for detailed morphological study, and these species are not transferred to Thielaviopsis.