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Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium.

Arambasic M, Sandoval PY, Hoehener C, Singh A, Swart EC, Nowacki M - PLoS ONE (2014)

Bottom Line: We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny.Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs) and chromatin modification patterns during development.Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Cell Biology, University of Bern, Bern, Switzerland.

ABSTRACT
The epigenetic influence of maternal cells on the development of their progeny has long been studied in various eukaryotes. Multicellular organisms usually provide their zygotes not only with nutrients but also with functional elements required for proper development, such as coding and non-coding RNAs. These maternally deposited RNAs exhibit a variety of functions, from regulating gene expression to assuring genome integrity. In ciliates, such as Paramecium these RNAs participate in the programming of large-scale genome reorganization during development, distinguishing germline-limited DNA, which is excised, from somatic-destined DNA. Only a handful of proteins playing roles in this process have been identified so far, including typical RNAi-derived factors such as Dicer-like and Piwi proteins. Here we report and characterize two novel proteins, Pdsg1 and Pdsg2 (Paramecium protein involved in Development of the Somatic Genome 1 and 2), involved in Paramecium genome reorganization. We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny. Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs) and chromatin modification patterns during development. Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.

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Proposed model of Pdsg1 and Pdsg2 roles in elimination of mcIESs during MAC development.(A) Early development, MIC germline genome is transcribed and transcripts are processed by Dcl2/3 into scnRNAs. (B) scnRNAs are transported from the MIC to parental MAC by Ptiwi01/09. Once in the parental MAC, scanning takes place filtering out the MAC genome-matching scnRNAs. We propose that the matching of scnRNAs to complementary sequences may be driven by a multiprotein complex that may include Pdsg1. (C) scnRNAs without matching sequences are transported to the new MAC where they target the excision of complementary sequences. This study suggests that Pdsg2 may be part of the DNA excision machinery. (D) After the excision, IESs are used as templates for iesRNA production to ensure reinforce the signal for an efficient targeting of IES excision.
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pone-0112899-g006: Proposed model of Pdsg1 and Pdsg2 roles in elimination of mcIESs during MAC development.(A) Early development, MIC germline genome is transcribed and transcripts are processed by Dcl2/3 into scnRNAs. (B) scnRNAs are transported from the MIC to parental MAC by Ptiwi01/09. Once in the parental MAC, scanning takes place filtering out the MAC genome-matching scnRNAs. We propose that the matching of scnRNAs to complementary sequences may be driven by a multiprotein complex that may include Pdsg1. (C) scnRNAs without matching sequences are transported to the new MAC where they target the excision of complementary sequences. This study suggests that Pdsg2 may be part of the DNA excision machinery. (D) After the excision, IESs are used as templates for iesRNA production to ensure reinforce the signal for an efficient targeting of IES excision.

Mentions: PDSG1 reaches the highest level of expression at the beginning of sexual development and remains expressed at a high level until the new MAC is formed. The localization of PDSG1 is very similar to that of Nowa1 protein, which was shown to be involved in the excision of maternally-controlled IESs [15]. Nowa1 is an Argonaute and RNA binding domain-containing protein [15], and its putative role is to facilitate the interactions between Piwi-bound small RNAs and their targets in the maternal MAC (RNA scanning process) and in the developing MAC (targeting DNA excision).We show that depletion of PDSG1 also blocks the excision of some maternally-controlled IESs, which may suggest that both Pdsg1 and Nowa1 are components of the same molecular machinery (Fig. 6). Surprisingly, the silencing of PDSG1 does not affect the elimination of Sardine and Thon transposons which is strongly affected by NOWA1 silencing [15]. No other protein in Paramecium is known to affect only the excision of mcIESs but not the transposons. This difference may indicate that the machinery involved in the process of marking transposons for elimination differs from the one employed in the selection of mcIESs even though the two germline-specific DNA elements seem to require sRNA machinery for their recognition and/or excision.


Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium.

Arambasic M, Sandoval PY, Hoehener C, Singh A, Swart EC, Nowacki M - PLoS ONE (2014)

Proposed model of Pdsg1 and Pdsg2 roles in elimination of mcIESs during MAC development.(A) Early development, MIC germline genome is transcribed and transcripts are processed by Dcl2/3 into scnRNAs. (B) scnRNAs are transported from the MIC to parental MAC by Ptiwi01/09. Once in the parental MAC, scanning takes place filtering out the MAC genome-matching scnRNAs. We propose that the matching of scnRNAs to complementary sequences may be driven by a multiprotein complex that may include Pdsg1. (C) scnRNAs without matching sequences are transported to the new MAC where they target the excision of complementary sequences. This study suggests that Pdsg2 may be part of the DNA excision machinery. (D) After the excision, IESs are used as templates for iesRNA production to ensure reinforce the signal for an efficient targeting of IES excision.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232520&req=5

pone-0112899-g006: Proposed model of Pdsg1 and Pdsg2 roles in elimination of mcIESs during MAC development.(A) Early development, MIC germline genome is transcribed and transcripts are processed by Dcl2/3 into scnRNAs. (B) scnRNAs are transported from the MIC to parental MAC by Ptiwi01/09. Once in the parental MAC, scanning takes place filtering out the MAC genome-matching scnRNAs. We propose that the matching of scnRNAs to complementary sequences may be driven by a multiprotein complex that may include Pdsg1. (C) scnRNAs without matching sequences are transported to the new MAC where they target the excision of complementary sequences. This study suggests that Pdsg2 may be part of the DNA excision machinery. (D) After the excision, IESs are used as templates for iesRNA production to ensure reinforce the signal for an efficient targeting of IES excision.
Mentions: PDSG1 reaches the highest level of expression at the beginning of sexual development and remains expressed at a high level until the new MAC is formed. The localization of PDSG1 is very similar to that of Nowa1 protein, which was shown to be involved in the excision of maternally-controlled IESs [15]. Nowa1 is an Argonaute and RNA binding domain-containing protein [15], and its putative role is to facilitate the interactions between Piwi-bound small RNAs and their targets in the maternal MAC (RNA scanning process) and in the developing MAC (targeting DNA excision).We show that depletion of PDSG1 also blocks the excision of some maternally-controlled IESs, which may suggest that both Pdsg1 and Nowa1 are components of the same molecular machinery (Fig. 6). Surprisingly, the silencing of PDSG1 does not affect the elimination of Sardine and Thon transposons which is strongly affected by NOWA1 silencing [15]. No other protein in Paramecium is known to affect only the excision of mcIESs but not the transposons. This difference may indicate that the machinery involved in the process of marking transposons for elimination differs from the one employed in the selection of mcIESs even though the two germline-specific DNA elements seem to require sRNA machinery for their recognition and/or excision.

Bottom Line: We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny.Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs) and chromatin modification patterns during development.Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Cell Biology, University of Bern, Bern, Switzerland.

ABSTRACT
The epigenetic influence of maternal cells on the development of their progeny has long been studied in various eukaryotes. Multicellular organisms usually provide their zygotes not only with nutrients but also with functional elements required for proper development, such as coding and non-coding RNAs. These maternally deposited RNAs exhibit a variety of functions, from regulating gene expression to assuring genome integrity. In ciliates, such as Paramecium these RNAs participate in the programming of large-scale genome reorganization during development, distinguishing germline-limited DNA, which is excised, from somatic-destined DNA. Only a handful of proteins playing roles in this process have been identified so far, including typical RNAi-derived factors such as Dicer-like and Piwi proteins. Here we report and characterize two novel proteins, Pdsg1 and Pdsg2 (Paramecium protein involved in Development of the Somatic Genome 1 and 2), involved in Paramecium genome reorganization. We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny. Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs) and chromatin modification patterns during development. Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.

Show MeSH
Related in: MedlinePlus