E-GEOD-45883 - Retroelements and DUX4 Create Primate-specific Promoters for Germline Genes

Released on 1 October 2013, last updated on 25 November 2013
Homo sapiens
Samples (4)
Protocols (4)
The human double-homeodomain retrogene DUX4 is normally expressed at high levels in germ cells of the testis. When aberrantly expressed in muscle its protein product causes facioscapulohumeral muscular dystrophy (FSHD), perhaps partly by inducing inappropriate expression of germline genes. DUX4 can bind >60,000 locations in the human genome that contain a strongly enriched sequence motif. Numerous long terminal repeat (LTR) class repetitive elements are enriched among DUX4 binding sites, including many from the mammalian apparent LTR-retrotransposon (MaLR) family as well as some ERVL and ERVK types, with MaLRs comprising ~1/3 of DUX4’s binding sites. We performed RNA-seq on myoblasts over-expressing DUX4 and find that DUX4 binding activates transcription of some but not all bound repeat types. Some of these activated repetitive elements comprise novel promoters for genes, long non-coding RNAs and antisense transcripts. We show that some of these chimeric repeat-initiated transcripts are expressed in testis and FSHD patient myotubes. The acquisition of MaLR-LTR elements during mammalian evolution may therefore have allowed rewiring of the transcriptional network. We also find that the pericentromeric satellite HSATII can be bound by DUX4 and that its transcription is massively induced by DUX4 over-expression. Our findings suggest a role for repetitive element transcripts in muscle disease and in the biology of normal testis. RNA-seq of two myoblast cell lines transduced with lentivirus carrying DUX4, and two control myoblast lines
Experiment type
RNA-seq of coding RNA 
Zizhen yao <yzizhen@fhcrc.org>, Bhavatharini Kasinathan, Janet M Young, Jennifer L Whiddon, Lauren Snider, Linda N Geng, Rabi Tawil, Silvere M van der Maarel, Stephen J Tapscott, Zizhen Yao
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-45883.idf.txt
Sample and data relationshipE-GEOD-45883.sdrf.txt
Additional data (1)E-GEOD-45883.additional.1.zip