Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH

Tandemly repetitive DNA sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize (Zea mays), including the 180-bp knob repeat, the telomeric (TTTAGGG)(n) repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat. Although few transcripts derived from these four repeats were found in the expressed sequence tag and RNA-seq databases, RNA-FISH consistently detected the transcripts from three of the four repeats on interphase nuclei, suggesting that the transcripts from the three repeats are largely integrated into chromatin. The transcripts from the knob and telomeric repeats were mapped to the related DNA loci. In contrast, the transcripts from the CentC repeats were mainly localized to the nucleolus, although nucleoplasmic CentC transcripts were also detectable. The nucleolus and nuclear RNAs appeared to be important for the nuclear localization for at least one centromeric protein, Mis12. We demonstrate that RNA-FISH is a powerful tool to assess the level of transcription as well as to physically map the nuclear locations of the transcripts derived from satellite repeats.