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Papadaki et al., 2009 Supplementary Supplemental Data Index x Supplemental Figures 1-6 x Supplemental Tables 1a, 1b, 2 Papadaki et al., 2009 Supplementary Supplemental Figure 1. Thymocyte restricted inactivation of the Elavl1 locus. + fl (A) Diagrammatic representation of the wild-type (Elavl1P P), floxed (Elavl1P P) and Cre- - recombined (Elavl1P P) Elavl1/HuR loci on mouse chromosome 8; Noted are the loxP sequences (triangles) flanking the selection marker (neo) used in gene targeting and the ATG containing exon 2 (white box); (H) denotes restriction sites for loci mapping. (B) Detection of native (+), targeted (fl) and Cre-recombinant (-) loci in thymocyte DNA extracts from control and test mice following HindIII digestion and Southern blotting. (C) Western blot of total thymic protein extracts probed with ĮHuR Ab + fl/fl indicating the loss of HuR protein in LckCreP PElavl1P P thymi. Į-actin is shown for quantitation. (D) Flow cytometric detection of intracellular mHuR protein in + fl/+ LckCreP PElavl1P P thymocytes (open histogram), and its respective loss in + fl/fl LckCreP PElavl1P P thymocytes (shaded histogram). The dotted histogram depicts the + isotype-matched background staining. (E) Flow cytometric detection of HuRP P or - + + + fl/+ HuRP P cells in gated splenic CD4P Por CD8P P T-cells from 8 week old LckCreP PElavl1P + fl/fl - Pand LckCreP PElavl1P P mice respectively. (F) Enumeration of HuRP P cells in + fl/fl LckCreP PElavl1P P thymocyte subsets and splenic T-cells; Data are percentages (+SEM) derived from the flow cytometric detection of HuR- cells in CD4/CD8/DP and DN gated populations (n=12-15) at 8-10 weeks of age. Papadaki et al., 2009 Supplementary - Supplemental Figure 2. The increased expansion of HuRP PDN relates to - increases in immature thymocytes and the exclusive presence of HuRP PT- lymphocytes in mutant mice. (A) Detection of DN-descendant immature hi lo + lo + fl/+ CD24P PCD5P PSP cells in CD8P PTCRȕP Pgated LckCreP PElavl1P P(open + fl/fl histogram) and LckCreP PElavl1P Pthymi (filled histogram) and their respective + lo counts (+SD) as CD8P PTCRȕP P immature cells; (*)p,0.05. (B)Contour plots - + showing the representation of HuRP P and HuRP P cells expressing surface TCRȕ + fl/+ + fl/fl in gated LckCreP PElavl1P Pand LckCrePPElavl1P PDP and SP thymocytes as well as splenic T cells. Papadaki et al., 2009 Supplementary Supplemental Figure 3. Effects of HuR deletion on the presence of TCR- + + + + restricted thymocytes (A) Detection of HuR in F5P P LckCreP PElavl1fl/P PandPPF5P P + fl/fl LckCreP PElavl1P Pthymocytes expressing the F5-TCR (Vȕ11). (B) Detection of F5 + + transgenic cells as Vȕ11-gated CD4/8 thymocytes or splenic CD8P P T cells in F5P P + fl/fl LckCreP PElavl1P Ptransgenic mice, relative to the corresponding control subsets. + + + fl/fl (C) F5P P T-cell counts in thymi and spleens of F5P P LckCreP PElavl1P Pmice relative controls. Data (+SD) derived from n=7 mice/group at 8 weeks of age; (*)underlined numbers are p values of statistical difference. (D) Detection of HuR in female + + fl/fl tgHYP P LckCreP PElavl1P Ptransgenic thymocytes or splenocytes, expressing the HY- + + fl/+ TCR (T3.70) relative to the corresponding tgHYP P LckCreP PElavl1P Pcontrols. (E) + + Detection of HY-TCRP P transgenic cells as T3.70-gated DN, DP and CD8P PSP + + + fl/fl thymocytes as well as CD8P P splenocytes in female tgHYP P LckCreP PElavl1P Pmice + + relative to the corresponding controls.(F) HY-TCRP P T-cell counts in female tgHYP P + fl/fl LckCreP PElavl1P Pthymi and spleens relative to control values. Data (+SD) from n=7 mice/group at 10 weeks of age; (*) underlined numbers correspond to p values. Papadaki et al., 2009 Supplementary Supplemental Figure 4. Changes in the presence of chemokine - responsive HuRP Pthymocyte subsets are not due to defects in the expression of chemokine receptors. (A) qRT-PCR detection of S1PR1R (EDG- 1), Klf2, CXCR4 and CCR7 mRNAs in thymocyte extracts derived from + fl/fl LckCreP PElavl1P Pmice. Black bar graphs denote expression values (+SD) in + fl/fl LckCreP PElavl1P Pcultures as fold change relative to those from + fl/+ LckCreP PElavl1P Pcontrols (White Bar-Ref). (B) Intracellular flow cytometry histograms showing the expression of S1PR1R (EDG-1), Klf2, CXCR4 or CCR7 + + + fl/+ proteins in gated CD4P P and CD8P P SP thymocytes of LckCreP PElavl1P P(open + fl/fl histogram) and LckCreP PElavl1P P(filled histogram) thymocytes. Dashed histograms refer to isotype match stainings. (C) Representative histograms + fl/+ showing that intracellular HuR levels in SP subsets from LckCreP PElavl1P Pthymi are not altered between resting (open histograms) and chemokine treated (filled histograms) cells. Papadaki et al., 2009 Supplementary 8 - Supplemental Figure 5. Differences in HuRP P thymocyte deletion following antigenic or corticosteroid stimulation and detection of death-related + fl/+ mRNAs. (A) Flow cytometric detection of thymocyte loss in LckCreP PElavl1P + fl/fl Pand LckCreP PElavl1P Pmice following the in vivo injection of ĮCD3 or saline. (B) + + fl/+ + Detection of F5-TCR expressing thymocytes in F5P P LckCreP PElavl1P Pand F5P P + fl/fl LckCreP PElavl1P Pmice injected with variable doses of the NP68 peptide. (C) Response of HuR-deficient thymocytes to dexamethasone induced apoptosis. Thymocytes were cultured in vitro and apoptosis was induced with 100nM dexamethasone. Cells were collected at 0, 4, 16, 24 hours post stimulation. + fl/fl LckCreP PElavl1P Pthymocytes (filled histogram) appear to be as susceptible as control thymocytes (solid line) to dexamethasone induced apoptosis as shown by Annexin V/Propidium iodide staining and flow cytometric analysis. The line + + graphs show both the percentages of dead and apoptotic CD4P PCD8P P cells. Results shown are representative of two independent experiments with n=3 mice/group. (D) qRT-PCR detection of pro-apoptotic mRNAs in + fl/fl LckCreP PElavl1P Pthymocytes. Data (+SD) are fold changes relative to control values (White bar-Ref) and (*) p<0.05. Papadaki et al., 2009 Supplementary Supplemental Figure 6. Expression of known HuR-targets in activated HuR-deficient thymocytes. Microarray analysis of thymocyte mRNAs previously reported to interact with HuR. Shown are normalized relative + +/+ fl/fl expression values from control LckCreP P Elavl1P P (Ɣ) and Elavl1P P (ż) as well + fl/fl as test LckCreP P Elavl1P P (Ɣ) thymocyte cultures stimulated with PMA/ionomycin for 0,4 and 12 hrs. Papadaki et al., 2009-Supplementary @ Supplementary Table 1a. List of Downregulated Genes in HuR-deficient thymocytes before and after mitogenic stimulationP O Hrs En Gene Name GeneIDP Description Score 1* FC** Score 2* FC** Bbc3 170770 Bcl-2 Binding Component 3 -3,601 1,575 -5,283 1,808 Cacna1e 12290 Voltage-Dependent R-Type Calcium Channel Alpha-1e Subunit -2,734 1,883 -6,186 2,148 Camk2n1 66259 Calcium/Calmodulin-Dependent Protein Kinase II Inhibitor -4,542 1,419 -7,791 1,891 Col15a1 12819 Procollagen, Type XV -4,023 1,915 -2,627 2,916 Cyp2j6 74519 Cytochrome P450 2j5 -5,336 1,386 -5,023 1,499 D130020L05Rik 68734 Riken Cdna D130020l05 Gene -3,408 1,409 -2,784 1,206 D15Wsu75e 28075 D15wsu75e Protein -3,235 1,405 -4,176 1,439 Doc2g 60425 Double C2, Gamma -3,183 7,126 -5,934 4,116 Flt4 14257 Vascular Endothelial Growth Factor Receptor 3 Precursor -4,063 1,450 -4,644 1,604 Gpr161 240888 G Protein-Coupled Receptor 161 -5,153 1,755 -2,957 1,796 Gzmm 50701 Complement Factor D Precursor -2,626 1,391 -3,977 1,227 Lpin1 14245 Lipin 1 (Fatty Liver Dystrophy Protein) -3,779 1,346 -3,655 1,374 Lta 16992 Lymphotoxin-Alpha Precursor (Lt-Alpha) -3,646 2,087 -3,095 1,776 Med25 75613 Mediator Of RNA Polymerase II Transcription, Subunit 25 Homolog -2,934 1,147 -2,884 1,152 Oxa1L 69089 Oxidase Assembly 1-Like -3,799 1,420 -4,003 1,379 Phlpp 98432 Ph Domain And Leucine Rich Repeat Protein Prosphatase -3,042 1,368 -2,689 1,628 Ppfibp2 19024 Protein Tyrosine Phosphatase, F Interacting Protein, Binding Protein 2 -5,098 1,625 -3,010 1,346 Q8BZ64-2 654470 Tect1_Mouse Isoform 2 Of Q8bz64 -2,626 1,290 -3,129 1,365 Rtel1 269400 Regulator Of Telomere Elongation Helicase 1 -4,273 1,343 -3,080 1,299 Shf 435684 Src Homology 2 Domain Containing F -4,957 1,427 -10,059 1,449 Slc13a1 55961 Solute Carrier Family 13, Member 1 -3,401 1,913 -3,309 2,114 Ssrp1 20833 Structure-Specific Recognition Protein 1 -2,842 1,287 -3,167 1,182 Stx5a 56389 Syntaxin 5a -3,021 1,350 -4,915 1,359 Tfpi 21788 Tissue Factor Pathway Inhibitor Precursor -9,815 2,178 -10,552 1,757 Tnfrsf25 85030 Tumor Necrosis Factor Receptor Superfamily, Member 25 -3,054 2,133 -3,592 1,886 Unc13a 382018 Unc-13 Homolog A (C. Elegans) -3,057 1,769 -2,710 1,354 4 Hrs Gene Name Gene ID Description Score 1 FC Score 2 FC 1500011H22Rik 68948 Riken Cdna 1500011h22 Gene -7,065 1,403 -2,650 1,292 1700003H04Rik 384775 RIKEN Cdna 1700003H04 GENE -3,359 2,470 -3,232 2,607 4930404H21Rik 73808 RIKEN Cdna 4930404H21 GENE -3,515 1,541 -3,854 1,569 4930579E17Rik 75847 Riken Cdna 4930579e17 Gene -8,278 1,965 -5,110 2,011 4933431D05Rik 381714 RIKEN Cdna 4933431D05 GENE -3,344 1,787 -5,589 2,328 5730557B15Rik 67434 RIKEN Cdna 5730557B15 GENE -3,613 2,324 -3,151 1,992 9430057O19Rik 231093 RIKEN Cdna 9430057O19 GENE -3,344 1,787 -6,657 2,173 Papadaki et al., 2009-Supplementary A830093I24Rik 207921 RIKEN Cdna A830093I24 GENE -3,313 1,319 -11,589 1,839 Abca4 11304 Atp-Binding Cassette, Sub-Family A, Member 4 -5,152 1,651 -2,981 1,289 Atf7ip2 75329 Activating Transcription Factor 7 Interacting Protein 2 -9,664 1,292 -3,818 1,175
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    5 6 6 5 . 4 2 1 1 1 2 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 A A A A A A A A A A A A A A A A A A A A C C C C C C C C C C C C C C C C C C C C R R R R R R R R R R R R R R R R R R R R B , B B B B B B B B B B B B B B B B B B B , 9 , , , , 4 , , 3 0 , , , , , , , , 6 2 , , 5 , 0 8 6 4 , 7 5 7 0 2 8 9 1 3 3 3 1 1 7 5 0 4 1 4 0 7 1 0 2 0 6 7 8 0 2 5 7 8 0 3 8 5 4 9 0 1 0 8 8 3 5 6 7 4 7 9 5 2 1 1 8 2 2 1 7 9 6 2 1 7 1 1 0 4 5 3 5 8 9 1 0 0 4 2 5 0 8 1 4 1 6 9 0 0 6 3 6 9 1 0 9 0 3 8 1 3 5 6 3 6 0 4 2 6 1 0 1 2 1 9 9 7 9 5 7 1 5 8 9 8 8 2 1 9 9 1 1 1 9 6 9 8 9 7 8 4 5 8 8 6 4 8 1 1 2 8 6 2 7 9 8 3 5 4 3 2 1 7 9 5 3 1 3 2 1 2 9 5 1 1 1 1 1 1 5 9 5 3 2 6 3 4 1 3 1 1 4 1 4 1 7 1 3 4 3 2 7 6 4 2 7 2 1 2 1 5 1 6 3 5 6 1 3 6 4 7 1 6 5 1 1 4 1 6 1 7 6 4 7 e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m
  • Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories

    Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories

    Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002)
  • Original Article Dynamics of Lamins B and A/C and Nucleoporin Nup160 During Meiotic Maturation in Mouse Oocytes

    Original Article Dynamics of Lamins B and A/C and Nucleoporin Nup160 During Meiotic Maturation in Mouse Oocytes

    Original Article Dynamics of Lamins B and A/C and Nucleoporin Nup160 during Meiotic Maturation in Mouse Oocytes (oocytes / meiosis / meiotic spindle / nuclear lamina / Nup107-160 / nuclear pore complex) V. NIKOLOVA, S. DELIMITREVA, I. CHAKAROVA, R. ZHIVKOVA, V. HADZHINESHEVA, M. MARKOVA Department of Biology, Medical Faculty, Medical University of Sofia, Bulgaria Abstract. This study was aimed at elucidating the plex reorganization of the cytoskeleton and nuclear en- fate of three important nuclear envelope components velope (Delimitreva et al., 2012). Although the early – lamins B and A/C and nucleoporin Nup160, during meiotic stages have been relatively well studied, the meiotic maturation of mouse oocytes. These proteins events of final steps of oocyte meiosis (from meiotic re- were localized by epifluorescence and confocal mi- sumption in late prophase I until metaphase II) are still croscopy using specific antibodies in oocytes at dif- poorly understood. The oocyte nucleus in late prophase ferent stages from prophase I (germinal vesicle) to I, traditionally called GV (germinal vesicle), becomes metaphase II. In immature germinal vesicle oocytes, competent to resume meiosis upon accumulation of all three proteins were detected at the nuclear pe- pericentriolar heterochromatin called karyosphere, sur- riphery. In metaphase I and metaphase II, lamin B rounded nucleolus or rimmed nucleolus (Can et al., co-localized with the meiotic spindle, lamin A/C was 2003; De la Fuente et al., 2004; Tan et al., 2009). Then, found in a diffuse halo surrounding the spindle and the nucleus disaggregates in the so-called germinal ve- to a lesser degree throughout the cytoplasm, and sicle breakdown (GVBD) stage.