Eukaryotic transcriptome analyses have revealed the presence of a huge number of mRNA-type non-coding RNAs (ncRNAs). Expression of them is often developmentally regulated, but little is known about their function. We have recently demonstrated that cascade of RNA polymerase II (RNAPII)-mediated transcription initiation of such mRNA-type long ncRNAs (mlonRNA) results in stepwise disruption of local chromatin structure at the fission yeast Schizosaccharomyces pombe fbp1(+) locus during transcriptional activation upon glucose derepression. Similar transition of RNA transcripts coupled with local chromatin alteration is observed meiotically in the fission yeast recombination hotspot ade6-M26. Here, we hypothesize that RNAPII transcription of mlonRNAs disrupts chromatin array. This idea may provide a new clue to understand why so many species of ncRNAs are expressed in eukaryotic cells.