title: TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.
abstract: Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium, and establishes for the first time a specific role of TFIIS in non-coding transcription in eukaryotes.
authors.affiliation: Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland.
authors.forename: Kamila
authors.initials: K
authors.lastname: Maliszewska-Olejniczak
authors.affiliation: Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland.
authors.forename: Julita
authors.initials: J
authors.lastname: Gruchota
authors.affiliation: Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland.
authors.forename: Robert
authors.initials: R
authors.lastname: Gromadka
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Denby Wilkes
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Arnaiz
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Mathy
authors.affiliation: Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Duharcourt
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Bétermier
authors.affiliation: Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland.
authors.forename: Jacek K
authors.initials: JK
authors.lastname: Nowak
mesh_terms: D019070:Cell Lineage; D016678:Genome; D005854:Germ Cells; D059014:High-Throughput Nucleotide Sequencing; D016805:Paramecium tetraurelia / Q000235:genetics; D012319:RNA Polymerase II / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D012319:RNA Polymerase II