Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures

Abstract

Facioscapulohumeralmuscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defectsmostly due to SMCHD1mutation. Previous reports showed DUX4-induced gene expression changes as well as changes inmicroRNA expression in FSHDmuscle cells. However, a genome wide analysis of small noncoding RNAs thatmight be regulated by DUX4 or bymutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including knownmicroRNAs that are differentially expressed in FSHD2muscle cells compared to control. Although fewer small RNAs were differentially expressed duringmuscle differentiation in FSHD2 cells compared to controls,most of the knownmyogenicmicroRNAs, such asmiR1,miR133a andmiR206were induced in both FSHD2 and controlmuscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1- specific changes in FSHD2muscle cells. Six FSHD2microRNAs were affected by DUX4 overexpression in controlmyoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNAtranscriptome changes in FSHD2might be different from those in FSHD1 and that these differencesmay provide new diagnostic and therapeutic tools specific to FSHD2.