PhpNF-Y drives heterochromatic transcription to generate splicing machinery-dependent small RNAs (small RNA-Seq)

ABSTRACT: Heterochromatin regions of the genome are transcriptionally repressive in nature. However, constitutive heterochromatin, such as at centromeres and telomeres, coats regions harboring multiple repetitive DNA elements that are preferentially transcribed during S-phase by RNA polymerase II. RNAi machinery processes the transcripts to generate small RNAs (siRNAs) that are crucial for heterochromatin assembly. Despite significant mechanistic advances in the field, the contribution of transcription factor (TF) based mechanisms to repeat element transcription and siRNA production is unclear. Here, we discover that the conserved TF PhpCNF-Y, which contains a histone fold motif, collaborates with a Zn-finger domain-containing factor, Moc3, to access specific sites within the heterochromatin region, regardless of the presence of the repressive histone methylation mark. The cooperative function of the TFs is essential for gaining access to the heterochromatin region, where they bind to specific CCAAT motif sites within the heterochromatic repeat elements cenH and dh. Perturbation of heterochromatin has minimal effect on the binding of the TFs to these specific sites, and they remain bound even outside of the S-phase. We find that PhpCNF-Y and Moc3 mediate the transcription of the repeat elements originating from a bottom strand of cenH, which the spliceosome targets to generate siRNAs in a Swi6HP1-independent manner. This pathway for generating the initial transcripts is crucial for de novo heterochromatin assembly. Collectively, our study uncovers a fundamental transcription factor-based mechanism that gains access to the heterochromatin to enforce transcriptional silencing of repeat elements. Our findings provide significant insights into de novo heterochromatin assembly.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE269095 | GEO | 2024/12/06

REPOSITORIES: GEO