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Significance Some noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (RNAPII) affect gene expression by altering chromatin structures. Since transcriptional regulation by ncRNA is critically important in developmental process and diseases, clarification of the principles ensuring the locus-specific chromatin regulation is of great interest. Here, we found that inSchizosaccharomyces pombe Ser7 of the C-terminal domain (CTD) of RNAPII is involved in locus-specific siRNA amplification within heterochromatin and facilitates heterochromatin formation. Ser7 and a chromodomain protein Chp1, which binds to H3K9 methylation and RNAs, cooperatively promote chromatin retention of the nascent heterochromatic RNAs (hRNAs) across heterochromatin. Our findings present a principle of epigenetic regulation by ncRNAs in which the RNAPII CTD links hRNA transcription to RNAi for heterochromatin formation.

Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi