title: LIA4 encodes a chromoshadow domain protein required for genomewide DNA rearrangements in Tetrahymena thermophila.
abstract: Extensive DNA elimination occurs as part of macronuclear differentiation during Tetrahymena sexual reproduction. The identification of sequences to excise is guided by a specialized RNA interference (RNAi) machinery that targets the methylation of histone H3 lysine 9 (K9) and K27 on chromatin associated with these internal eliminated sequences (IESs). This modified chromatin is reorganized into heterochromatic subnuclear foci, which is a hallmark of their subsequent elimination. Here, we demonstrate that Lia4, a chromoshadow domain-containing protein, is an essential component in this DNA elimination pathway. LIA4 knockout (ΔLIA4) lines fail to excise IESs from their developing somatic genome and arrest at a late stage of conjugation. Lia4 acts after RNAi-guided heterochromatin formation, as both H3K9 and H3K27 methylation are established. Nevertheless, without LIA4, these cells fail to form the heterochromatic foci associated with DNA rearrangement, and Lia4 accumulates in the foci, indicating that Lia4 plays a key role in their structure. These data indicate a critical role for Lia4 in organizing the nucleus during Tetrahymena macronuclear differentiation.
authors.affiliation: Department of Biology, Washington University, St. Louis, Missouri, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Horrell
authors.affiliation: Department of Biology, Washington University, St. Louis, Missouri, USA dchalker@biology2.wustl.edu.
authors.forename: Douglas L
authors.identifier: http://orcid.org/0000-0002-0285-3344
authors.initials: DL
authors.lastname: Chalker
mesh_terms: D002843:Chromatin / Q000235:genetics; D016770:Ciliophora Infections / Q000235:genetics* / Q000469:parasitology; D055786:Gene Knockout Techniques; D015321:Gene Rearrangement / Q000235:genetics*; D018503:Genome, Protozoan; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D034622:RNA Interference; D012098:Reproduction / Q000235:genetics; D016808:Tetrahymena thermophila / Q000235:genetics*
chemical_list: D002843:Chromatin; D015800:Protozoan Proteins
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: Cell. 2009 Apr 17;137(2):356-68
references.pmid: 19379699
references.citation: PLoS Genet. 2009 Dec;5(12):e1000769
references.pmid: 20011120
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
references.pmid: 15980461
references.citation: Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3734-9
references.pmid: 11891286
references.citation: Cell. 2011 Mar 4;144(5):732-44
references.pmid: 21353298
references.citation: BMC Genomics. 2008 Nov 26;9:562
references.pmid: 19036158
references.citation: Eukaryot Cell. 2006 Aug;5(8):1347-59
references.pmid: 16896218
references.citation: PLoS Genet. 2013;9(12):e1004032
references.pmid: 24348275
references.citation: J Cell Sci. 2007 Jun 15;120(Pt 12):1978-89
references.pmid: 17519286
references.citation: J Biol Chem. 1998 Mar 6;273(10):5858-68
references.pmid: 9488723
references.citation: Eukaryot Cell. 2010 Sep;9(9):1343-53
references.pmid: 20656911
references.citation: EMBO J. 2000 Apr 3;19(7):1587-97
references.pmid: 10747027
references.citation: Genes Dev. 2007 Jun 15;21(12):1530-45
references.pmid: 17575054
references.citation: Eukaryot Cell. 2014 Feb;13(2):190-201
references.pmid: 24297443
references.citation: EMBO J. 2004 Feb 11;23(3):489-99
references.pmid: 14765118
references.citation: Adv Exp Med Biol. 2011;722:156-73
references.pmid: 21915788
references.citation: Cell. 2010 Mar 5;140(5):692-703
references.pmid: 20211138
references.citation: EMBO J. 2002 Nov 1;21(21):5797-806
references.pmid: 12411497
references.citation: Science. 2001 Apr 6;292(5514):110-3
references.pmid: 11283354
references.citation: Eukaryot Cell. 2004 Feb;3(1):157-69
references.pmid: 14871946
references.citation: Genetics. 1997 May;146(1):135-47
references.pmid: 9136007
references.citation: J Cell Biol. 2006 Mar 13;172(6):823-34
references.pmid: 16520385
references.citation: Eukaryot Cell. 2007 Aug;6(8):1320-9
references.pmid: 17586719
references.citation: Mol Biol Cell. 2010 May 15;21(10):1753-62
references.pmid: 20357003
references.citation: Exp Cell Res. 1982 Jul;140(1):227-36
references.pmid: 7106201
references.citation: Genetics. 1981 Aug;98(4):747-62
references.pmid: 7333457
references.citation: Genes Dev. 2001 May 15;15(10):1287-98
references.pmid: 11358871
references.citation: Genes Dev. 2012 Aug 1;26(15):1729-42
references.pmid: 22855833
references.citation: Science. 2002 May 3;296(5569):922-7
references.pmid: 11934988
references.citation: Cell. 1996 Oct 4;87(1):75-84
references.pmid: 8858150
references.citation: Cell. 1987 Mar 13;48(5):779-88
references.pmid: 3815524
references.citation: Annu Rev Genet. 2011;45:227-46
references.pmid: 21910632
references.citation: Nature. 2001 Mar 1;410(6824):120-4
references.pmid: 11242054
references.citation: Mol Cell Biol. 2005 Oct;25(20):9151-64
references.pmid: 16199890
references.citation: Mol Cell Biol. 2007 Apr;27(7):2648-60
references.pmid: 17242195
references.citation: J Biol Chem. 2011 Mar 18;286(11):9308-20
references.pmid: 21224386
references.citation: Nature. 2011 Mar 24;471(7339):480-5
references.pmid: 21179089
references.citation: Cell. 2001 Nov 2;107(3):323-37
references.pmid: 11701123
references.citation: Cell. 2002 Sep 20;110(6):701-11
references.pmid: 12297044
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1679-84
references.pmid: 14755052
references.citation: Mol Biol Cell. 2012 Jun;23(11):2213-25
references.pmid: 22513090
references.citation: Mol Cell. 1999 Nov;4(5):865-72
references.pmid: 10619033
references.citation: Nat Rev Genet. 2007 Jan;8(1):35-46
references.pmid: 17173056
references.citation: Biochim Biophys Acta. 2008 Nov;1783(11):2130-6
references.pmid: 18706458
references.citation: Genes Dev. 2008 Aug 15;22(16):2228-41
references.pmid: 18708581
references.citation: Nucleic Acids Res. 2002 Jun 1;30(11):2524-37
references.pmid: 12034842
references.citation: Mol Cell Biol. 1999 Aug;19(8):5631-41
references.pmid: 10409752
references.citation: Methods Cell Biol. 2000;62:533-47
references.pmid: 10503216
references.citation: PLoS One. 2013 Sep 17;8(9):e75337
references.pmid: 24069402
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: G3 (Bethesda). 2011 Nov;1(6):515-22
references.pmid: 22384362
references.citation: Cell. 2002 Sep 20;110(6):689-99
references.pmid: 12297043
references.citation: Methods Cell Biol. 2000;62:219-28
references.pmid: 10503193
references.citation: Genetics. 2005 Aug;170(4):1611-21
references.pmid: 15956677
references.citation: Sci China Life Sci. 2011 Jan;54(1):65-7
references.pmid: 21253873
references.citation: J Microbiol Methods. 2010 Sep;82(3):342-6
references.pmid: 20624430
references.citation: Genes Dev. 2005 Jan 1;19(1):77-89
references.pmid: 15598983
references.citation: Eukaryot Cell. 2010 Jul;9(7):1087-99
references.pmid: 20495055
references.citation: Eukaryot Cell. 2011 Dec;10(12):1648-59
references.pmid: 22021239
references.citation: J Cell Sci. 1997 Apr;110 ( Pt 7):889-97
references.pmid: 9133676
references.citation: Methods Cell Biol. 2000;62:501-12
references.pmid: 10503214
references.citation: Nucleic Acids Res. 2000 Feb 15;28(4):895-900
references.pmid: 10648780
references.citation: Nucleic Acids Res. 2006;34(20):5778-89
references.pmid: 17053100