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{"title"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements", "type"=>"journal", "authors"=>[{"first_name"=>"Kamila", "last_name"=>"Maliszewska-Olejniczak", "scopus_author_id"=>"56768238800"}, {"first_name"=>"Julita", "last_name"=>"Gruchota", "scopus_author_id"=>"56768032900"}, {"first_name"=>"Robert", "last_name"=>"Gromadka", "scopus_author_id"=>"6603472660"}, {"first_name"=>"Cyril", "last_name"=>"Denby Wilkes", "scopus_author_id"=>"55440882900"}, {"first_name"=>"Olivier", "last_name"=>"Arnaiz", "scopus_author_id"=>"15058857300"}, {"first_name"=>"Nathalie", "last_name"=>"Mathy", "scopus_author_id"=>"56767959500"}, {"first_name"=>"Sandra", "last_name"=>"Duharcourt", "scopus_author_id"=>"6603204570"}, {"first_name"=>"Mireille", "last_name"=>"Bétermier", "scopus_author_id"=>"6701610390"}, {"first_name"=>"Jacek K.", "last_name"=>"Nowak", "scopus_author_id"=>"36625954300"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"0000871400", "pmid"=>"26177014", "doi"=>"10.1371/journal.pgen.1005383", "issn"=>"15537404", "pui"=>"605567896", "sgr"=>"84938818552", "scopus"=>"2-s2.0-84938818552"}, "id"=>"82494b3a-a215-318c-826c-e3917ad9fabe", "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.", "link"=>"http://www.mendeley.com/research/tfiisdependent-noncoding-transcription-regulates-developmental-genome-rearrangements", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>13, "Neuroscience"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}}, "reader_count_by_country"=>{"Poland"=>1}, "group_count"=>3}

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• http://doi.org/10.1007/s00018-020-03555-2
• http://doi.org/10.1186/s12864-017-3887-z
• http://doi.org/10.12688/f1000research.12121.1
• http://doi.org/10.1016/j.cub.2019.06.052
• http://doi.org/10.1016/j.tig.2017.01.005
• http://doi.org/10.1093/nar/gky772
• http://doi.org/10.1101/gr.245332.118
• http://doi.org/10.1016/j.cell.2017.02.020
• http://doi.org/10.1093/nar/gkw1318

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• {"id"=>"623553098439630849", "text"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements http://t.co/lnab0Dd3YV", "created_at"=>"2015-07-21T18:00:18Z", "user"=>"DNAtopologyBot", "user_name"=>"DNA topology papers", "user_profile_image"=>"http://pbs.twimg.com/profile_images/567463202280058880/aeNIY2TT_normal.png"}
• {"id"=>"623553222347767808", "text"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements http://t.co/gAMbdHfHw4", "created_at"=>"2015-07-21T18:00:47Z", "user"=>"TransxnNoiseBot", "user_name"=>"Transcrp'n noise bot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/569464210942226432/thlJM4zO_normal.png"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/2177037"], "description"=>"<p>(A) Domain organization and neighbor-joining tree of <i>P</i>. <i>tetraurelia</i> TFIIS proteins. The evolutionary history was inferred in MEGA4 [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.ref076\" target=\"_blank\">76</a>] based on the alignment of entire protein sequences (342 positions in the final dataset) and the following parameters: deletion of gaps in pairwise sequence comparisons, uniform rates among sites, bootstrap 1000 (bootstrap values displayed next to the branches), Poisson correction. The scale is in the units of the number of amino acid substitutions per site. Accession numbers in ParameciumDB: TFIIS1a—GSPATP00003556001, TFIIS1c—GSPATP00008714001, TFIIS2a—PTETP1100023001, TFIIS2b—GSPATP00003298001, TFIIS3—GSPATP00019582001, TFIIS4—GSPATP00025792001. The Dst1 protein from <i>S</i>. <i>cerevisiae</i> was used as an outgroup. (B) Mean expression signals obtained in microarray experiment “<i>Paramecium tetraurelia</i> autogamy series 1” from [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.ref028\" target=\"_blank\">28</a>]. Values obtained for <i>TFIIS2a</i> were recalculated using the signals obtained only for microarray probes covering the corrected gene annotation. V: vegetative; -3.5: meiosis; 0: 50% of cells with fragmented MAC; 5 to 20: 5 to 20 hours after “0” time point. Y-axis shows mean signals.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484256, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g001", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_multigenic_TFIIS_family_in_Paramecium_tetraurelia_and_its_expression_profiles_/1484256", "title"=>"The multigenic TFIIS family in <i>Paramecium tetraurelia</i> and its expression profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177039"], "description"=>"<p>For each transgene, representative images illustrate different developmental stages observed in a population of cells derived from a single injected caryonide. Panels a, f, l and s show vegetative cells (note that one vegetative cell is also present in the middle of panel b and on the left of panel h). All other panels show successive stages of autogamy: panels g, m and t–meiotic crescent stage; panels b and n–first meiotic division; panels h and u–cells with 8 haploid nuclei resulting from meiosis II; panels c, i, o and v–fragmentation of old MAC; panels d, j, p, and w–early MAC development; panels e, k, r and x–late MAC development. Note that panel b contains not only one meiotic cell (on the left) but also one vegetative cell (in the middle) and two cells with their fragmented old MAC (at the top and on the right). In all panels, white arrows point at MICs (some were omitted when MICs were not clearly distinguishable by DAPI staining), white arrowheads indicate new MACs. Yellow arrowheads in panels i and o point to division products of the zygotic nucleus. (A) A GFP-TFIIS1a fusion localizes to old, then new MACs. (B) A GFP-TFIIS2a fusion localizes to old MAC during meiosis, then to new MACs and is present in meiotic MICs. (C) As in B for a GFP-TFIIS3 fusion. GFP-TFIIS3 cannot be seen in division products of the zygotic nucleus. (D) A GFP-TFIIS4 fusion is essentially restricted to the new MACs specifically during early MAC development. Very weak GFP signal is visible in the old MAC during meiosis.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484258, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_of_GFP_fusion_proteins_forTFIIS1a_TFIIS2a_TFIIS3_and_TFIIS4_/1484258", "title"=>"Localization of GFP fusion proteins forTFIIS1a, TFIIS2a, TFIIS3 and TFIIS4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177042"], "description"=>"<p>New developing macronuclei (new MAC) are indicated by white arrowheads, while white arrows point at MICs that are clearly visible only in panel d. Panel a and d show vegetative cells, b and e: early MAC development, c and f: late MAC development. (A) Cells silenced for <i>PiggyMac</i>. The efficiency of <i>PiggyMac</i> silencing was confirmed by the observation of 100% lethality in the sexual progeny. (B) Control experiment, in which the nonessential <i>ICL7</i> gene was silenced. The silencing of <i>ICL7</i> gene does not interfere with autogamy (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.t001\" target=\"_blank\">Table 1</a>) and does not influence the localization of TFIIS4 relative to cells grown in standard <i>K</i>. <i>pneumoniae</i> medium.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484260, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g003", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_of_the_GFP_TFIIS4_fusion_protein_upon_PiggyMac_RNAi_/1484260", "title"=>"Localization of the GFP-TFIIS4 fusion protein upon <i>PiggyMac</i> RNAi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177044"], "description"=>"<p>(A) PCR analysis of the excision of IESs located in the surface antigen gene <i>A</i>^<i>51</i> using primers located around each IES. In each panel, the larger fragment corresponds to the non-excised form (IES+), the smaller fragment to the excised form (IES-). Known maternally controlled IESs are labeled with an asterisk. The autogamy time-course experiment was performed using a strain harboring a somatic (macronuclear) deletion of part of surface antigen gene <i>A</i>^<i>51</i>, which overlaps 3 tested IESs – 51A1835, 51A4404, 51A2591 and partially 51A4578. In this experiment, we obtained 93% lethality in post-autogamous progeny of <i>TFIIS4</i>-silenced cells. (B) As in A for IESs located in other regions. The PCR products corresponding to each IES- form are amplified mostly from the fragments of the old MAC. Oligonucleotide sequences are listed in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.s013\" target=\"_blank\">S2 Table</a>. (C) IES retention scores calculated from the genome-wide sequencing of DNA extracted from purified nuclei of cells silenced for <i>TFIIS4</i> during an independent RNAi experiment (87% lethality in post-autogamous progeny). (D) Superimposed histogram of TFIIS4 retention scores for all IESs (dark blue) and for IESs that are significantly retained in TFIIS4-depleted cells (light blue). Around 25,000 IESs are not significantly affected by the inactivation of <i>TFIIS4</i> and a large fraction of IESs exhibits a retention score equal to 0. For TFIIS4-dependent IESs, retention scores are almost uniformly distributed between 0.1 and 0.7. (E) The graph shows a positive correlation between IES size and retention score in <i>TFIIS4</i> RNAi. The box plot displays the IES size distribution for all IESs and for each of <i>TFIIS4</i> retention score (RS) quartiles. The median retention score (horizontal line inside the box) and the first (top of box) and third (bottom of box) quartiles are shown. Range of RS for particular quartiles are as follows: Q1: [0–0.01[; Q2: [0.01–0.12[; Q3: [0.12–0.39[; Q4: [0.39–1.00]. The medians are significantly different between all the groups (p < 2e-40). (F) Venn diagram of significantly retained IESs after <i>TFIIS4</i>, <i>DCL5</i> or <i>DCL2/3</i> silencing. Almost all IESs that are dependent upon Dcl2/3 or Dcl5 for their excision are also dependent upon TFIIS4.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484263, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g004", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_IES_excision_in_TFIIS4_silenced_cells_/1484263", "title"=>"Analysis of IES excision in <i>TFIIS4</i>-silenced cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177045"], "description"=>"<p>(A) Southern blot analysis of <i>Pst</i>I-restricted genomic DNA from the autogamy time-course experiment in which 51mt8 <i>∆A∆ND7</i> cells were silenced for <i>ICL7</i> and <i>TFIIS4</i>. Autogamy stages are marked as follows (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.s006\" target=\"_blank\">S6 Fig</a>): V–vegetative cells, -2.5 –cells during meiosis, 0 to 56 –autogamy stages in hours (with T0 corresponding to the stage when around 50% of cells harbor a fragmented old MAC). The blot was hybridized with probes corresponding to different sequences from the locus carrying the <i>G</i> surface antigen gene: Sardine, reveals the <i>Sardine</i> transposon located downstream of the <i>G</i>-gene (arrowhead) and other related transposon sequences in the genome; tel51G hybridizes to the non-fragmented germline chromosome (upper band) and its fragmented MAC version obtained by telomere addition downstream of the <i>G</i> gene (lower band); Gmac hybridizes with fragments containing (upper band) or not (lower band) IES 51G4404. The same blot was hybridized with a mitochondrial DNA probe (Mit probe) as a loading control. (B) Phenotypic test of the ability to discharge trichocysts in the sexual progeny of cells carrying a macronuclear deletion of the <i>ND7</i> gene, following <i>ICL7</i> or <i>TFIIS4</i> gene silencing. <i>TFIIS4</i> silencing restores a wild-type trich+ phenotype, most probably due to lack of inheritance of the macronuclear deletion.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484264, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g005", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inhibition_of_imprecise_genome_rearrangements_in_TFIIS4_silenced_cells_/1484264", "title"=>"Inhibition of imprecise genome rearrangements in <i>TFIIS4</i>-silenced cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177047"], "description"=>"<p>(A) RT-PCR and Southern blot detection of IES-containing transcripts (IES+) in a control culture (cells silenced for <i>ICL7</i> gene expression) and in <i>TFIIS4</i>-silenced cells. Autogamy stages are marked as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.s006\" target=\"_blank\">S6 Fig</a>: V–vegetative cells, -2.5 –cells during meiosis, 0 to 56 –autogamy stages in hours. Time-window when IES excision take place based on PCR shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.g004\" target=\"_blank\">Fig 4</a> is indicated. PCR primers were located within each tested IESs: 51G4404, 51A6649 and 51A4404. The TMP1b panel shows the RT-PCR signal obtained for the constitutively expressed gene encoding trichocyst matrix protein TMP1b. (B) Histograms showing the normalization of IES+ signals shown in (A) with TMP1b mRNA. (C) Detection of IES-containing transcripts (IES+) with PCR primers located within IES 51G4404 in a control experiment, in which the <i>ND7</i> gene was silenced, and in <i>PiggyMac</i>-silenced cells. See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.s008\" target=\"_blank\">S8 Fig</a>, panel B for details about autogamy stages.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484266, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g006", "stats"=>{"downloads"=>1, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_IES_containing_IES_transcripts_/1484266", "title"=>"Detection of IES-containing (IES+) transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177051"], "description"=>"<p>(A) Total RNA samples corresponding to the T0, T5, T10 and T15 time-points from the above experiment were run on a denaturing 15% polyacrylamide-urea gel. After electrophoresis the gel was stained with SYBR Gold (Invitrogen). M: DNA Low Molecular Weight Marker (USB). Arrowhead points to the ~25 nt signal that was shown to correspond to the fraction of scnRNAs [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.ref015\" target=\"_blank\">15</a>]. In the control, at the T15 time-point, additional bands corresponding to 26–30 nt iesRNAs are present (indicated by a bracket). In <i>TFIIS4</i>-silenced samples iesRNAs can clearly not be seen. (B) Small RNA libraries corresponding to the T0 and T10 time-points from the above experiment were sequenced and mapped to the reference genomes (<i>P</i>. <i>tetraurelia</i> MAC reference genome and MAC+IES reference genome). The top panel corresponds to a control culture (cells silenced for <i>ICL7</i> gene expression), while results for <i>TFIIS4</i>-silencing are shown below. Histograms show normalized number of sRNA reads that match to: the target silencing regions (<i>ICL7</i> or <i>TFIIS4</i> gene, respectively) – in purple; the rest of MAC genome – in blue; all annotated IESs – in yellow; all other not mapped sRNA – in gray.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484270, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g007", "stats"=>{"downloads"=>3, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_sRNA_populations_in_TFIIS4_silenced_cells_/1484270", "title"=>"Analysis of sRNA populations in <i>TFIIS4</i>-silenced cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177052"], "description"=>"<p>(A) Possible role of TFIIS4 in the new developing MAC. Description in the text. (B) Summary of the impact of <i>TFIIS4</i>, <i>EZL1</i>, <i>DCL2/3</i> or <i>DCL5</i> silencing of on IES excision. The area of each circle is proportional to the fraction of IESs that significantly depend on each factor.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484271, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g008", "stats"=>{"downloads"=>7, "page_views"=>136, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proposed_role_of_TFIIS4_in_RNA_dependent_DNA_elimination_/1484271", "title"=>"Proposed role of TFIIS4 in RNA-dependent DNA elimination.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177053"], "description"=>"<p>Survival test of post-autogamous cells submitted to RNAi against all <i>TFIIS</i> genes and control non-essential genes—<i>ICL7</i> and <i>ND7</i>. The last column “none” corresponds to the control grown in standard non-feeding <i>K</i>. <i>pneumoniae</i> medium. For each condition, the number of replicate experiments is indicated in the last line. In one replicate experiment, wild-type survivors were systematically tested for MAC regeneration (as previously described [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.ref052\" target=\"_blank\">52</a>]) and all turned out to be true postautogamous cells.</p><p>RNAi-screening for essential <i>TFIIS</i> genes.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484272, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.t001", "stats"=>{"downloads"=>5, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNAi_screening_for_essential_TFIIS_genes_/1484272", "title"=>"RNAi-screening for essential <i>TFIIS</i> genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177054"], "description"=>"<p>IESs retained in different samples (in column) are described according to their size and their presence in the TFIIS4-dependent IES set. Almost all IESs retained in other RNAi experiments are also retained in <i>TFIIS4</i> silencing, with high retention score. Apart from Dcl5-dependent IESs, IESs retained following <i>TFIIS4</i> RNAi are larger (on average) than the overall set.</p><p>Global analysis of genome rearrangements in <i>TFIIS4</i> silencing—comparison with <i>EZL1</i>, <i>DCL2/3</i> and <i>DCL5</i>.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484273, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.t002", "stats"=>{"downloads"=>3, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_analysis_of_genome_rearrangements_in_TFIIS4_silencing_comparison_with_EZL1_DCL2_3_and_DCL5_/1484273", "title"=>"Global analysis of genome rearrangements in <i>TFIIS4</i> silencing—comparison with <i>EZL1</i>, <i>DCL2/3</i> and <i>DCL5</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-15 04:07:52"}
• {"files"=>["https://ndownloader.figshare.com/files/2177066", "https://ndownloader.figshare.com/files/2177067", "https://ndownloader.figshare.com/files/2177068", "https://ndownloader.figshare.com/files/2177069", "https://ndownloader.figshare.com/files/2177070", "https://ndownloader.figshare.com/files/2177071", "https://ndownloader.figshare.com/files/2177072", "https://ndownloader.figshare.com/files/2177073", "https://ndownloader.figshare.com/files/2177074", "https://ndownloader.figshare.com/files/2177075", "https://ndownloader.figshare.com/files/2177076", "https://ndownloader.figshare.com/files/2177077", "https://ndownloader.figshare.com/files/2177078", "https://ndownloader.figshare.com/files/2177080"], "description"=>"<div><p>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 <i>Paramecium tetraurelia</i>, 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 <i>P</i>. <i>tetraurelia</i> genome. Using RNA interference, we showed that <i>TFIIS4</i>, 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 <i>TFIIS4</i> 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 <i>Paramecium</i>, and establishes for the first time a specific role of TFIIS in non-coding transcription in eukaryotes.</p></div>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484275, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005383.s001", "https://dx.doi.org/10.1371/journal.pgen.1005383.s002", "https://dx.doi.org/10.1371/journal.pgen.1005383.s003", "https://dx.doi.org/10.1371/journal.pgen.1005383.s004", "https://dx.doi.org/10.1371/journal.pgen.1005383.s005", "https://dx.doi.org/10.1371/journal.pgen.1005383.s006", "https://dx.doi.org/10.1371/journal.pgen.1005383.s007", "https://dx.doi.org/10.1371/journal.pgen.1005383.s008", "https://dx.doi.org/10.1371/journal.pgen.1005383.s009", "https://dx.doi.org/10.1371/journal.pgen.1005383.s010", "https://dx.doi.org/10.1371/journal.pgen.1005383.s011", "https://dx.doi.org/10.1371/journal.pgen.1005383.s012", "https://dx.doi.org/10.1371/journal.pgen.1005383.s013", "https://dx.doi.org/10.1371/journal.pgen.1005383.s014"], "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TFIIS_Dependent_Non_coding_Transcription_Regulates_Developmental_Genome_Rearrangements_/1484275", "title"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-07-15 04:07:52"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}

F1000Prime