Small RNA-directed heterochromat in formation in DNA elimination of Tetrahymena
Heterochromatin is a closed and mostly transcriptionally repressed state of chromatin, which is critical for gene silencing, cell differentiation and genome maintenance. The maintenance heterochromatin in cell proliferations is well understood, but its initial formation is still poorly understood. Heterochromatin is established de novo during the programmed DNA elimination in the ciliated protozoan Tetrahymena and this process can be synchronously induced in laboratory in a large scale. Therefore, DNA elimination in Tetrahymena serves as a unique model for initiation, spreading and aggregation processes of heterochromatin that can be studied genetically and biochemically.
Small RNA-mediated genome-wide trans-recognition network in Tetrahymena DNA elimination
Small RNAs are used to silence transposable elements (TEs) by heterochromatin formation in many eukaryotes. In ciliated protozoans, small RNA-mediated comparison of the germline and somatic genomes underlies identification of TE-related sequences, which are then eliminated from the soma. We reported that an additional mechanism of small RNA-mediated identification of TE-related sequences in the ciliate Tetrahymena. We showed that a limited set of internal eliminated sequences (IESs) containing potentially active TEs produces a class of small RNAs that recognize not only the IESs from which they are derived but also other IESs in trans. This trans-recognition triggers the expression of yet another novel class of small RNAs that identify other IESs. Therefore, TE-related sequences in Tetrahymena are robustly targeted for heterochromatin formation and subsequent elimination by a genome-wide trans-recognition network accompanied by a chain reaction of small RNA production.
Regulation of the heterochromatin aggregation process by phosphorylation of HP1-like protein
In addition to the local compaction of a single heterochromatin locus, in some cell types, multiple heterochromatic loci are assembled into aggregated higher-order structures called heterochromatin bodies. The formation and biological roles of heterochromatin bodies are poorly understood. In Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. We reported that the novel heterochromatin body component Jub1p promotes heterochromatin body formation and dephosphorylation of the heterochromatin protein 1 (HP1)-like protein Pdd1p. Through the identification and mutagenesis of the phosphorylated residues of Pdd1p, we demonstrated that Pdd1p dephosphorylation promotes the electrostatic interaction between Pdd1p and RNA in vitro and heterochromatin body formation in vivo. We therefore suggested that heterochromatin bodies are assembled by the Pdd1p-RNA interaction. Jub1p and Pdd1p dephosphorylation are required for heterochromatin body formation and DNA elimination but not for local heterochromatin assembly, indicating that heterochromatin body of itself plays an essential role in DNA elimination.