Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.
Identifieur interne : 000F68 ( Main/Corpus ); précédent : 000F67; suivant : 000F69Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.
Auteurs : Paul-Andre Genest ; Loren Baugh ; Alex Taipale ; Wanqi Zhao ; Sabrina Jan ; Henri G A M. Van Luenen ; Jonas Korlach ; Tyson Clark ; Khai Luong ; Matthew Boitano ; Steve Turner ; Peter J. Myler ; Piet BorstSource :
- Nucleic acids research [ 1362-4962 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , analogs & derivatives : Uracil.
- chemical , analysis : Glucosides, Uracil.
- chemical , metabolism : DNA-Binding Proteins, Glucosides, Protozoan Proteins, Uracil.
- genetics : Leishmania, Plasmids.
- Sequence Analysis, DNA.
Abstract
Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication.
DOI: 10.1093/nar/gkv095
PubMed: 25662217
PubMed Central: PMC4344527
Links to Exploration step
pubmed:25662217Le document en format XML
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Van Luenen</name><affiliation><nlm:affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Korlach, Jonas" sort="Korlach, Jonas" uniqKey="Korlach J" first="Jonas" last="Korlach">Jonas Korlach</name><affiliation><nlm:affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Clark, Tyson" sort="Clark, Tyson" uniqKey="Clark T" first="Tyson" last="Clark">Tyson Clark</name><affiliation><nlm:affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Luong, Khai" sort="Luong, Khai" uniqKey="Luong K" first="Khai" last="Luong">Khai Luong</name><affiliation><nlm:affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Boitano, Matthew" sort="Boitano, Matthew" uniqKey="Boitano M" first="Matthew" last="Boitano">Matthew Boitano</name><affiliation><nlm:affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Turner, Steve" sort="Turner, Steve" uniqKey="Turner S" first="Steve" last="Turner">Steve Turner</name><affiliation><nlm:affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Myler, Peter J" sort="Myler, Peter J" uniqKey="Myler P" first="Peter J" last="Myler">Peter J. Myler</name><affiliation><nlm:affiliation>Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA Department of Global Health, University of Washington, Seattle, WA 98195, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Borst, Piet" sort="Borst, Piet" uniqKey="Borst P" first="Piet" last="Borst">Piet Borst</name><affiliation><nlm:affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands p.borst@nki.nl.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA-Binding Proteins (metabolism)</term><term>Glucosides (analysis)</term><term>Glucosides (metabolism)</term><term>Leishmania (genetics)</term><term>Plasmids (genetics)</term><term>Protozoan Proteins (metabolism)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Uracil (analogs & derivatives)</term><term>Uracil (analysis)</term><term>Uracil (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Uracil</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Glucosides</term><term>Uracil</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA-Binding Proteins</term><term>Glucosides</term><term>Protozoan Proteins</term><term>Uracil</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Leishmania</term><term>Plasmids</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25662217</PMID><DateCompleted><Year>2015</Year><Month>07</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>43</Volume><Issue>4</Issue><PubDate><Year>2015</Year><Month>Feb</Month><Day>27</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res</ISOAbbreviation></Journal><ArticleTitle>Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.</ArticleTitle><Pagination><MedlinePgn>2102-15</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkv095</ELocationID><Abstract><AbstractText>Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication. </AbstractText><CopyrightInformation>© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Genest</LastName><ForeName>Paul-Andre</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baugh</LastName><ForeName>Loren</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taipale</LastName><ForeName>Alex</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Wanqi</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jan</LastName><ForeName>Sabrina</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Luenen</LastName><ForeName>Henri G A M</ForeName><Initials>HG</Initials><AffiliationInfo><Affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Korlach</LastName><ForeName>Jonas</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clark</LastName><ForeName>Tyson</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luong</LastName><ForeName>Khai</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Boitano</LastName><ForeName>Matthew</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Turner</LastName><ForeName>Steve</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Myler</LastName><ForeName>Peter J</ForeName><Initials>PJ</Initials><AffiliationInfo><Affiliation>Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA Department of Global Health, University of Washington, Seattle, WA 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Borst</LastName><ForeName>Piet</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands p.borst@nki.nl.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 AI103858</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>02</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004268">DNA-Binding Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005960">Glucosides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C402790">J-specific DNA-binding protein, protozoa</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015800">Protozoan Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>53910-96-6</RegistryNumber><NameOfSubstance UI="C084880">5-((glucopyranosyloxy)methyl)uracil</NameOfSubstance></Chemical><Chemical><RegistryNumber>56HH86ZVCT</RegistryNumber><NameOfSubstance UI="D014498">Uracil</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004268" MajorTopicYN="N">DNA-Binding Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005960" MajorTopicYN="N">Glucosides</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007891" 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PubStatus="entrez"><Year>2015</Year><Month>2</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>2</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>7</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25662217</ArticleId><ArticleId IdType="pii">gkv095</ArticleId><ArticleId IdType="doi">10.1093/nar/gkv095</ArticleId><ArticleId IdType="pmc">PMC4344527</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Mol Biochem Parasitol. 2000 Jul;109(2):133-45</Citation><ArticleIdList><ArticleId IdType="pubmed">10960172</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2012 Jun 8;287(24):19886-95</Citation><ArticleIdList><ArticleId IdType="pubmed">22514282</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2012 Aug 31;150(5):909-21</Citation><ArticleIdList><ArticleId IdType="pubmed">22939620</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(2):860-9</Citation><ArticleIdList><ArticleId IdType="pubmed">24163102</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2012 Nov;13(11):770-80</Citation><ArticleIdList><ArticleId IdType="pubmed">23032257</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 2011 Apr;31(8):1690-700</Citation><ArticleIdList><ArticleId IdType="pubmed">21321080</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2013 Sep;41(16):7635-55</Citation><ArticleIdList><ArticleId IdType="pubmed">23814188</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2002 Sep 15;30(18):3919-26</Citation><ArticleIdList><ArticleId IdType="pubmed">12235375</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Nanotechnol. 2009 Apr;4(4):265-70</Citation><ArticleIdList><ArticleId IdType="pubmed">19350039</ArticleId></ArticleIdList></Reference><Reference><Citation>Angew Chem Int Ed Engl. 2007;46(16):2839-43</Citation><ArticleIdList><ArticleId IdType="pubmed">17295375</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2014 Sep;42(15):9717-29</Citation><ArticleIdList><ArticleId IdType="pubmed">25104019</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Microbiol. 2002 Oct;46(1):37-47</Citation><ArticleIdList><ArticleId IdType="pubmed">12366829</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biochem Parasitol. 2007 Nov;156(1):24-31</Citation><ArticleIdList><ArticleId IdType="pubmed">17706299</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Microbiol. 2008;62:235-51</Citation><ArticleIdList><ArticleId IdType="pubmed">18729733</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2014 Mar 13;507(7491):175-7</Citation><ArticleIdList><ArticleId IdType="pubmed">24598546</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biochem Parasitol. 2009 Apr;164(2):157-61</Citation><ArticleIdList><ArticleId IdType="pubmed">19114062</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1984 Jan;36(1):163-70</Citation><ArticleIdList><ArticleId IdType="pubmed">6692467</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2002 Jan 11;277(2):958-66</Citation><ArticleIdList><ArticleId IdType="pubmed">11700315</ArticleId></ArticleIdList></Reference><Reference><Citation>J Am Chem Soc. 2012 Aug 15;134(32):13357-65</Citation><ArticleIdList><ArticleId IdType="pubmed">22775585</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2014 Jul 18;289(29):20273-82</Citation><ArticleIdList><ArticleId IdType="pubmed">24891501</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007;35(7):2107-15</Citation><ArticleIdList><ArticleId IdType="pubmed">17389644</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2002 Aug 2;277(31):28150-6</Citation><ArticleIdList><ArticleId IdType="pubmed">12029082</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 1983 Jun 16-22;303(5918):592-7</Citation><ArticleIdList><ArticleId IdType="pubmed">6304531</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 1998 Oct;18(10):5643-51</Citation><ArticleIdList><ArticleId IdType="pubmed">9742081</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2366-71</Citation><ArticleIdList><ArticleId IdType="pubmed">9482891</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005;33(5):1699-709</Citation><ArticleIdList><ArticleId IdType="pubmed">15781496</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2009 Apr;37(5):1452-62</Citation><ArticleIdList><ArticleId IdType="pubmed">19136460</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2009 Jan 2;323(5910):133-8</Citation><ArticleIdList><ArticleId IdType="pubmed">19023044</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Jun;14(6):1188-90</Citation><ArticleIdList><ArticleId IdType="pubmed">15173120</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1993 Dec 17;75(6):1129-36</Citation><ArticleIdList><ArticleId IdType="pubmed">8261512</ArticleId></ArticleIdList></Reference><Reference><Citation>EMBO J. 1992 Oct;11(10):3601-8</Citation><ArticleIdList><ArticleId IdType="pubmed">1396560</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1984 Jul 11;12(13):5235-47</Citation><ArticleIdList><ArticleId IdType="pubmed">6087278</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biochem Parasitol. 2014 Aug;196(1):9-11</Citation><ArticleIdList><ArticleId IdType="pubmed">25064607</ArticleId></ArticleIdList></Reference><Reference><Citation>J Am Soc Mass Spectrom. 2014 Oct;25(10):1763-70</Citation><ArticleIdList><ArticleId IdType="pubmed">25078157</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2010 Jun;7(6):461-5</Citation><ArticleIdList><ArticleId IdType="pubmed">20453866</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007;35(22):7429-55</Citation><ArticleIdList><ArticleId IdType="pubmed">17913750</ArticleId></ArticleIdList></Reference><Reference><Citation>EMBO J. 1999 Nov 15;18(22):6573-81</Citation><ArticleIdList><ArticleId IdType="pubmed">10562569</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2000 Aug 15;28(16):3017-21</Citation><ArticleIdList><ArticleId IdType="pubmed">10931915</ArticleId></ArticleIdList></Reference><Reference><Citation>Acta Trop. 1979 Sep;36(3):289-92</Citation><ArticleIdList><ArticleId IdType="pubmed">43092</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell. 2005 Feb 4;17(3):441-51</Citation><ArticleIdList><ArticleId IdType="pubmed">15694344</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2012 Jan;9(1):75-7</Citation><ArticleIdList><ArticleId IdType="pubmed">22101853</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Integr. 2011 Dec 20;2:10</Citation><ArticleIdList><ArticleId IdType="pubmed">22185597</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biochem Parasitol. 2005 Sep;143(1):111-5</Citation><ArticleIdList><ArticleId IdType="pubmed">15935489</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1996 Jul 1;24(13):2476-82</Citation><ArticleIdList><ArticleId IdType="pubmed">8692684</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2009 May 15;324(5929):930-5</Citation><ArticleIdList><ArticleId IdType="pubmed">19372391</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007;35(7):2116-24</Citation><ArticleIdList><ArticleId IdType="pubmed">17329373</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2011 Jul;39(13):5715-28</Citation><ArticleIdList><ArticleId IdType="pubmed">21415010</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2010 Jul;38(12):3923-35</Citation><ArticleIdList><ArticleId IdType="pubmed">20215442</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 1997 Dec 1;11(23):3232-41</Citation><ArticleIdList><ArticleId IdType="pubmed">9389654</ArticleId></ArticleIdList></Reference><Reference><Citation>Opt Lett. 2008 May 1;33(9):1026-8</Citation><ArticleIdList><ArticleId 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