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Ciliate Genetics and Epigenetics
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Ciliate Genetics and Epigenetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2019) | Viewed by 13409

Special Issue Editors

Prof. Dr. Martin Simon

E-Mail Website
Guest Editor
Molecular Cell Biology and Microbiology, Faculty for Biology, Wuppertal University, Wuppertal, Germany
Interests: RNA interference (RNAi); chromatin; siRNA and miRNA biogenesis; genetics
Prof. Dr. Marcel Schulz

E-Mail Website
Guest Editor
Institute of Cardiovascular Regeneration, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
Interests: machine learning; computational biology; transcriptional and post-transcriptional regulation
Prof. Dr. Douglas Chalker

E-Mail Website
Guest Editor
Department of Biology, Washington University, St.Louis, MO, USA
Interests: molecular genetics; genomics; development; molecular microbiology

Special Issue Information

Dear Colleagues,

Ciliates have been well-established as model organisms to investigate genetics and epigenetics. These single cell eukaryotes have two types of nuclei: germline micro- and somatic macronuclei. Some of the first epigenetic phenomena were described in these organisms, and research over the last few decades has elucidated mechanisms that underlie these phenomena. Ciliates helped pioneer the current understanding of RNA interference, both for siRNA-mediated silencing and for small RNA-directed chromatin modification and DNA rearrangements, which provide cells a powerful tool to transmit epigenetic information to sexual progeny. Progress in our understanding of molecular mechanisms came from classical genetics studies and from genomics, post-genomics and the recent advances in epigenomics technologies.

This Special Issue provides an overview on the genetics and epigenetics in ciliates and their impacts on adaptation and evolution. We invite submissions for reviews, research articles, or short-communications reporting molecular genetics and epigenomics studies of ciliate research.

We will accept manuscripts starting in September until the deadline.

Prof. Dr. Martin Simon
Dr. Marcel Schulz
Prof. Dr. Douglas Chalker
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genetics
  • Genomics
  • Epigenomics
  • RNA interference
  • Non coding RNA
  • Genome rearrangement
  • Chromatin modification

Published Papers (4 papers)

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Research

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15 pages, 2979 KiB  
Article
Loss of a Fragile Chromosome Region leads to the Screwy Phenotype in Paramecium tetraurelia
by Irina Nekrasova, Vera Nikitashina, Simran Bhullar, Olivier Arnaiz, Deepankar P. Singh, Eric Meyer and Alexey Potekhin
Genes 2019, 10(7), 513; https://doi.org/10.3390/genes10070513 - 06 Jul 2019
Cited by 1 | Viewed by 2595
Abstract
A conspicuous cell-shape phenotype known as “screwy” was reported to result from mutations at two or three uncharacterized loci in the ciliate Paramecium tetraurelia. Here, we describe a new screwy mutation, Spinning Top, which appeared spontaneously in the cross of an unrelated [...] Read more.
A conspicuous cell-shape phenotype known as “screwy” was reported to result from mutations at two or three uncharacterized loci in the ciliate Paramecium tetraurelia. Here, we describe a new screwy mutation, Spinning Top, which appeared spontaneously in the cross of an unrelated mutant with reference strain 51. The macronuclear (MAC) genome of the Spinning Top mutant is shown to lack a ~28.5-kb segment containing 18 genes at the end of one chromosome, which appears to result from a collinear deletion in the micronuclear (MIC) genome. We tested several candidate genes from the deleted locus by dsRNA-induced silencing in wild-type cells, and identified a single gene responsible for the phenotype. This gene, named Spade, encodes a 566-aa glutamine-rich protein with a C2HC zinc finger. Its silencing leads to a fast phenotype switch during vegetative growth, but cells recover a wild-type phenotype only 5–6 divisions after silencing is stopped. We analyzed 5 independently-obtained mutant alleles of the Sc1 locus, and concluded that all of them also lack the Spade gene and a number of neighboring genes in the MAC and MIC genomes. Mapping of the MAC deletion breakpoints revealed two different positions among the 5 alleles, both of which differ from the Spinning Top breakpoint. These results suggest that this MIC chromosome region is intrinsically unstable in strain 51. Full article
(This article belongs to the Special Issue Ciliate Genetics and Epigenetics)
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21 pages, 3041 KiB  
Article
A Novel Role for Polycystin-2 (Pkd2) in P. tetraurelia as a Probable Mg2+ Channel Necessary for Mg2+-Induced Behavior
by Megan S. Valentine, Junji Yano and Judith Van Houten
Genes 2019, 10(6), 455; https://doi.org/10.3390/genes10060455 - 14 Jun 2019
Cited by 4 | Viewed by 3163
Abstract
A human ciliopathy gene codes for Polycystin-2 (Pkd2), a non-selective cation channel. Here, the Pkd2 channel was explored in the ciliate Paramecium tetraurelia using combinations of RNA interference, over-expression, and epitope-tagging, in a search for function and novel interacting partners. Upon depletion of [...] Read more.
A human ciliopathy gene codes for Polycystin-2 (Pkd2), a non-selective cation channel. Here, the Pkd2 channel was explored in the ciliate Paramecium tetraurelia using combinations of RNA interference, over-expression, and epitope-tagging, in a search for function and novel interacting partners. Upon depletion of Pkd2, cells exhibited a phenotype similar to eccentric (XntA1), a Paramecium mutant lacking the inward Ca2+-dependent Mg2+ conductance. Further investigation showed both Pkd2 and XntA localize to the cilia and cell membrane, but do not require one another for trafficking. The XntA-myc protein co-immunoprecipitates Pkd2-FLAG, but not vice versa, suggesting two populations of Pkd2-FLAG, one of which interacts with XntA. Electrophysiology data showed that depletion and over-expression of Pkd2 led to smaller and larger depolarizations in Mg2+ solutions, respectively. Over-expression of Pkd2-FLAG in the XntA1 mutant caused slower swimming, supporting an increase in Mg2+ permeability, in agreement with the electrophysiology data. We propose that Pkd2 in P. tetraurelia collaborates with XntA for Mg2+-induced behavior. Our data suggest Pkd2 is sufficient and necessary for Mg2+ conductance and membrane permeability to Mg2+, and that Pkd2 is potentially a Mg2+-permeable channel. Full article
(This article belongs to the Special Issue Ciliate Genetics and Epigenetics)
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Review

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9 pages, 3189 KiB  
Review
Biogenesis of Developmental Master Regulatory 27nt-RNAs in Stylonychia—Can Coding RNA Turn into Non-Coding?
by Jan Postberg, Patrick Philipp Weil and Anton Pembaur
Genes 2019, 10(11), 940; https://doi.org/10.3390/genes10110940 - 18 Nov 2019
Cited by 2 | Viewed by 2485
Abstract
In the ciliate Stylonychia, somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the [...] Read more.
In the ciliate Stylonychia, somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the list of developmentally expressed genes. Simultaneously, 27nt-ncRNAs that match sequences retained in new macronuclei are synthesized and bound by PIWI1. Recently, we proposed a mechanistic model for ‘RNA-induced DNA replication interference’ (RIRI): during polytene chromosome formation PIWI1/27nt-RNA-complexes target macronucleus-destined sequences (MDS) by base-pairing and temporarily cause locally stalled replication. At polytene chromosomal segments with ongoing replication, H3.4K27me3-nucleosomes become selectively deposited, thus dictating the prospective heterochromatin structure of these areas. Consequently, these micronucleus-specific sequences become degraded, whereas 27nt-RNA-covered sites remain protected. However, the biogenesis of the 27nt-RNAs remains unclear. It was proposed earlier that in stichotrichous ciliates 27nt-RNA precursors could derive from telomere-primed bidirectional transcription of nanochromosomes and subsequent Dicer-like (DCL) activity. As a minimalistic explanation, we propose here that the 27nt-RNA precursor could rather be mRNA or pre-mRNA and that the transition of coding RNA from parental macronuclei to non-coding RNAs, which act in premature developing macronuclei, could involve RNA-dependent RNA polymerase (RDRP) activity creating dsRNA intermediates prior to a DCL-dependent pathway. Interestingly, by such mechanism the partition of a parental somatic genome and possibly also the specific nanochromosome copy numbers could be vertically transmitted to the differentiating nuclei of the offspring. Full article
(This article belongs to the Special Issue Ciliate Genetics and Epigenetics)
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22 pages, 1086 KiB  
Review
Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review
by Alejandro Saettone, Syed Nabeel-Shah, Jyoti Garg, Jean-Philippe Lambert, Ronald E. Pearlman and Jeffrey Fillingham
Genes 2019, 10(5), 333; https://doi.org/10.3390/genes10050333 - 01 May 2019
Cited by 10 | Viewed by 4658
Abstract
Identification and characterization of protein complexes and interactomes has been essential to the understanding of fundamental nuclear processes including transcription, replication, recombination, and maintenance of genome stability. Despite significant progress in elucidation of nuclear proteomes and interactomes of organisms such as yeast and [...] Read more.
Identification and characterization of protein complexes and interactomes has been essential to the understanding of fundamental nuclear processes including transcription, replication, recombination, and maintenance of genome stability. Despite significant progress in elucidation of nuclear proteomes and interactomes of organisms such as yeast and mammalian systems, progress in other models has lagged. Protists, including the alveolate ciliate protozoa with Tetrahymena thermophila as one of the most studied members of this group, have a unique nuclear biology, and nuclear dimorphism, with structurally and functionally distinct nuclei in a common cytoplasm. These features have been important in providing important insights about numerous fundamental nuclear processes. Here, we review the proteomic approaches that were historically used as well as those currently employed to take advantage of the unique biology of the ciliates, focusing on Tetrahymena, to address important questions and better understand nuclear processes including chromatin biology of eukaryotes. Full article
(This article belongs to the Special Issue Ciliate Genetics and Epigenetics)
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