title: RNAPol-ChIP analysis of transcription from FSHD-linked tandem repeats and satellite DNA.
abstract: RNA interference (RNAi) is implicated in maintaining tandem DNA arrays as constitutive heterochromatin. We used chromatin immunoprecipitation with antibodies to RNA polymerase II (RNAPol-ChIP) to test for transcription of the following repeat arrays in human cells: subtelomeric D4Z4, pericentromeric satellite 2, and centromeric satellite alpha. D4Z4 has a promoter-like sequence upstream of an ORF in its 3.3-kb repeat unit. A short D4Z4 array at 4q35 is linked to facioscapulohumeral muscular dystrophy (FSHD). By RNAPol-ChIP and RT-PCR, little or no transcription of D4Z4 was detected in FSHD and normal myoblasts; lymphoblasts from an FSHD patient, a control, and a patient with D4Z4 hypomethylation due to mutation of DNMT3B (ICF syndrome); and normal or cancer tissues. However, RNAPol-ChIP assays indicated transcription of D4Z4 in a chromosome 4-containing human-mouse somatic cell hybrid. ChIP and RT-PCR showed satellite DNA transcription in some cancers and lymphoblastoid cell lines, although only at a low level. Given the evidence for the involvement of RNAi in satellite DNA heterochromatinization, it is surprising that, at most, a very small fraction of satellite DNA was associated with RNA Pol II. In addition, our results do not support the previously hypothesized disease-linked differential transcription of D4Z4 sequences in short, FSHD-linked arrays.
authors.affiliation: Genpathway, Inc., San Diego, CA 92121, USA.
authors.forename: Vassilios
authors.initials: V
authors.lastname: Alexiadis
authors.forename: Mary E
authors.initials: ME
authors.lastname: Ballestas
authors.forename: Cecilia
authors.initials: C
authors.lastname: Sanchez
authors.forename: Sara
authors.initials: S
authors.lastname: Winokur
authors.forename: Vettaikorumakankav
authors.initials: V
authors.lastname: Vedanarayanan
authors.forename: Mary
authors.initials: M
authors.lastname: Warren
authors.forename: Melanie
authors.initials: M
authors.lastname: Ehrlich
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D004276:DNA, Satellite; D006801:Humans; D006822:Hybrid Cells; D051379:Mice; D020391:Muscular Dystrophy, Facioscapulohumeral / Q000235:genetics*; D032446:Myoblasts; D012319:RNA Polymerase II; D020080:Tandem Repeat Sequences; D014158:Transcription, Genetic
chemical_list: D004276:DNA, Satellite; D012319:RNA Polymerase II