Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands
Identifieur interne : 000E83 ( Istex/Corpus ); précédent : 000E82; suivant : 000E84Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands
Auteurs : Yoshihisa Watanabe ; Toyoaki Tenzen ; Yasuhiko Nagasaka ; Hidetoshi Inoko ; Toshimichi IkemuraSource :
- Gene [ 0378-1119 ] ; 2000.
English descriptors
- Teeft :
- Band boundaries, Band boundary, Bernardi, Brdu, Chromosome, Chromosome bands, Class junction, Constant amount, Fukagawa, Genbank accession, Genome, Genome sequence level, Human chromosome, Human genome, Human genomic, Ikemura, Locus, Phka1, Plasmid, Plasmid pkf3, Primer, Primer sets, Repetitive, Repetitive sequences, Replication, Replication timing, Room temperature, Tenzen, Uorescence scanning system, Watanabe, Xist, Xist locus, Xist region.
Abstract
Abstract: The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of Alu and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.
Url:
DOI: 10.1016/S0378-1119(00)00208-0
Links to Exploration step
ISTEX:34578070F16B459BF4FD621A3C9214D90061AE7ALe document en format XML
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uniqKey="Nagasaka Y" first="Yasuhiko" last="Nagasaka">Yasuhiko Nagasaka</name><affiliation><mods:affiliation>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</mods:affiliation></affiliation></author><author><name sortKey="Inoko, Hidetoshi" sort="Inoko, Hidetoshi" uniqKey="Inoko H" first="Hidetoshi" last="Inoko">Hidetoshi Inoko</name><affiliation><mods:affiliation>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</mods:affiliation></affiliation></author><author><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><affiliation><mods:affiliation>E-mail: tikemura@lab.nig.ac.jp</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, 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Shizuoka-ken 411-8540, Japan</mods:affiliation></affiliation></author><author><name sortKey="Tenzen, Toyoaki" sort="Tenzen, Toyoaki" uniqKey="Tenzen T" first="Toyoaki" last="Tenzen">Toyoaki Tenzen</name><affiliation><mods:affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</mods:affiliation></affiliation></author><author><name sortKey="Nagasaka, Yasuhiko" sort="Nagasaka, Yasuhiko" uniqKey="Nagasaka Y" first="Yasuhiko" last="Nagasaka">Yasuhiko Nagasaka</name><affiliation><mods:affiliation>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</mods:affiliation></affiliation></author><author><name sortKey="Inoko, Hidetoshi" sort="Inoko, Hidetoshi" uniqKey="Inoko H" first="Hidetoshi" last="Inoko">Hidetoshi Inoko</name><affiliation><mods:affiliation>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</mods:affiliation></affiliation></author><author><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><affiliation><mods:affiliation>E-mail: tikemura@lab.nig.ac.jp</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Gene</title><title level="j" type="abbrev">GENE</title><idno type="ISSN">0378-1119</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2000">2000</date><biblScope unit="volume">252</biblScope><biblScope unit="issue">1–2</biblScope><biblScope unit="page" from="163">163</biblScope><biblScope unit="page" to="172">172</biblScope></imprint><idno 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region</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of Alu and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>xist</json:string><json:string>replication timing</json:string><json:string>genome</json:string><json:string>chromosome</json:string><json:string>replication</json:string><json:string>ikemura</json:string><json:string>primer</json:string><json:string>class junction</json:string><json:string>bernardi</json:string><json:string>watanabe</json:string><json:string>xist locus</json:string><json:string>plasmid</json:string><json:string>phka1</json:string><json:string>tenzen</json:string><json:string>brdu</json:string><json:string>locus</json:string><json:string>human genome</json:string><json:string>fukagawa</json:string><json:string>chromosome bands</json:string><json:string>band boundaries</json:string><json:string>primer sets</json:string><json:string>xist region</json:string><json:string>repetitive sequences</json:string><json:string>genbank accession</json:string><json:string>genome sequence level</json:string><json:string>band boundary</json:string><json:string>repetitive</json:string><json:string>human chromosome</json:string><json:string>human genomic</json:string><json:string>room temperature</json:string><json:string>constant amount</json:string><json:string>plasmid pkf3</json:string><json:string>uorescence scanning system</json:string></teeft></keywords><author><json:item><name>Yoshihisa Watanabe</name><affiliations><json:string>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</json:string></affiliations></json:item><json:item><name>Toyoaki Tenzen</name><affiliations><json:string>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</json:string></affiliations></json:item><json:item><name>Yasuhiko Nagasaka</name><affiliations><json:string>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</json:string></affiliations></json:item><json:item><name>Hidetoshi Inoko</name><affiliations><json:string>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</json:string></affiliations></json:item><json:item><name>Toshimichi Ikemura</name><affiliations><json:string>E-mail: tikemura@lab.nig.ac.jp</json:string><json:string>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Band boundary</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>GC%</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Human genome</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Isochores</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>R and G bands</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>XIST</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>bp, base pair(s)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>GDB, Genome Data Base</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>kb, kilobase or 1000 bp</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Mb, megabase</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MER, medium reiteration frequency sequence</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MHC, major histocompatibility complex</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>nt, nucleotide(s)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Pur/Pyr, polypurine/polypyrimidine</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>STS, sequence-tagged sites</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>XIC, X-inactivation center</value></json:item></subject><arkIstex>ark:/67375/6H6-04LQW4C8-3</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of Alu and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.</abstract><qualityIndicators><score>9.053</score><pdfWordCount>4737</pdfWordCount><pdfCharCount>28588</pdfCharCount><pdfVersion>1.2</pdfVersion><pdfPageCount>10</pdfPageCount><pdfPageSize>596 x 793 pts</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>193</abstractWordCount><abstractCharCount>1283</abstractCharCount><keywordCount>16</keywordCount></qualityIndicators><title>Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</title><pmid><json:string>10903448</json:string></pmid><pii><json:string>S0378-1119(00)00208-0</json:string></pii><genre><json:string>research-article</json:string></genre><host><title>Gene</title><language><json:string>unknown</json:string></language><publicationDate>2000</publicationDate><issn><json:string>0378-1119</json:string></issn><pii><json:string>S0378-1119(00)X0159-X</json:string></pii><volume>252</volume><issue>1–2</issue><pages><first>163</first><last>172</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>2000</json:string></date><geogName></geogName><orgName><json:string>Japan Received</json:string><json:string>Human Genomic Center</json:string><json:string>Tokai University</json:string><json:string>Department of Population Genetics, National Institute of Genetics, Yata</json:string><json:string>Health Science Research Resources Bank</json:string><json:string>Coulter Corp., Miami</json:string><json:string>Research on Priority Areas</json:string><json:string>Ministry of Education, Science, and Culture of Japan</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>T. Tenzen</json:string><json:string>T. Ikemura</json:string><json:string>K. Suzuki</json:string><json:string>Y. Miyauchi</json:string><json:string>Ms K. Kita</json:string></persName><placeName><json:string>Germany</json:string><json:string>Science City</json:string><json:string>UK</json:string><json:string>Buckinghamshire</json:string><json:string>Mannheim</json:string><json:string>Shizuoka</json:string><json:string>San Jose</json:string><json:string>Japan</json:string><json:string>Tokyo</json:string><json:string>CA</json:string></placeName><ref_url><json:string>http://ftp.genome.washington.edu</json:string></ref_url><ref_bibl><json:string>Jurka et al., 1996</json:string><json:string>Fukagawa et al., 1996</json:string><json:string>Hansen et al. (1993)</json:string><json:string>Saccone et al., 1999</json:string><json:string>Gardiner et al., 1990</json:string><json:string>Ohno et al., 2000</json:string><json:string>Ikemura et al., 1990</json:string><json:string>Holmquist, 1989</json:string><json:string>Saccone et al., 1993</json:string><json:string>Fukagawa et al., 1995</json:string><json:string>Torchia et al., 1994</json:string><json:string>Nagaraja et al., 1997</json:string><json:string>Ikemura and Aota, 1988</json:string><json:string>Craig and Bickmore, 1993</json:string><json:string>Pilia et al., 1993</json:string><json:string>Lafreniere et al., 1993</json:string><json:string>Tenzen et al. (1997)</json:string><json:string>Hansen et al. (1995)</json:string><json:string>Boggs and Chinault, 1994</json:string><json:string>Little et al., 1993</json:string><json:string>Hansen et al., 1995</json:string><json:string>Rao, 1994</json:string><json:string>Bernardi, 1989</json:string><json:string>Y. Watanabe et al.</json:string><json:string>Tenzen et al., 1997</json:string><json:string>Torchia and Migeon, 1995</json:string><json:string>Sugaya et al., 1994</json:string><json:string>Bernardi et al., 1985</json:string><json:string>Ikemura and Wada, 1991</json:string><json:string>Aota and Ikemura, 1986</json:string><json:string>Bernardi, 1989, 1993</json:string><json:string>Baran et al., 1991</json:string><json:string>Bernardi, 1993</json:string><json:string>Hansen et al., 1993</json:string><json:string>Bernardi et al. (1985)</json:string><json:string>Lafreniere et al. (1993)</json:string><json:string>Strehl et al. (1997)</json:string><json:string>Ikemura, 1985</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-04LQW4C8-3</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - genetics & heredity</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - developmental biology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Genetics</json:string><json:string>1 - Health Sciences</json:string><json:string>2 - Medicine</json:string><json:string>3 - General Medicine</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string><json:string>4 - genetique des eucaryotes. evolution biologique et moleculaire</json:string></inist></categories><publicationDate>2000</publicationDate><copyrightDate>2000</copyrightDate><doi><json:string>10.1016/S0378-1119(00)00208-0</json:string></doi><id>34578070F16B459BF4FD621A3C9214D90061AE7A</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-04LQW4C8-3/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-04LQW4C8-3/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-04LQW4C8-3/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a">Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©2000 Elsevier Science B.V.</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>2000</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note><note>Received by A. Fujiyama</note><note type="content">Fig. 1: Measurement of replication timing. (A) Flow-cytometry profile of BrdU-labeled THP-1 cells. The BrdU-labeled cells were flow-sorted into six cell-cycle fractions (G1, S1, S2, S3, S4, G2/M). (B) Gel electrophoresis for determination of replication timing by PCR Method I. The PCR products from F9 and PGK1 genes were separated by gel electrophoresis and stained with SYBR GREEN I. (C) Replication timing of PGK1 and F9 determined by Method II. The PCR products electrophoresed were quantified with FluorImager. Methods I and II gave the same conclusion.</note><note type="content">Fig. 2: Gel electrophoresis for determination of replication timing. (A, B) Replication timing of PHKA1 and DXS227 that locate at the two sides of a large inverted duplication (see Fig. 4) was determined by two different methods (I and III). The two methods gave the same conclusion. (C) Method I; the 5′- and 3′-flanking regions of XIST. (D) Method III; the 5′-end of XIST, XPCT, and plasmid pKF3. (E) Method III; p4565-H12, DXS227, and plasmid pKF3.</note><note type="content">Fig. 3: Quantification of PCR products by a fluorescence scanning system. PCR products produced by Method II were electrophoresed, stained and quantified with FluorImager. Results are expressed as means of at least three independent PCR reactions.</note><note type="content">Fig. 4: Replication timing of the XIC region. The minimal XIC region is indicated at the top of the figure. Filled boxes indicate the location of genes in the area. A large inverted duplication is indicated by a set of inverted arrows (→←). Map locations of eight PCR markers, except the XIST locus, are from Lafreniere et al. (1993). Primers in and around XIST were designed in this study. The cell-cycle fraction with the highest level of replicated DNA is shown by closed circles. If the difference in replicated DNA levels between two consecutive cell-cycle fractions was less than 10%, the closed circle is placed in the intermediate position. Replication timing for each locus was determined after quantification of at least three independent PCRs using different plasmid DNA concentrations and a fixed amount of the newly replicated DNA.</note><note type="content">Fig. 5: Transition of GC% distribution and replication timing in the MHC class II–III junction and in and around the XIST locus. (A) GC% distribution in the MHC class II–III junction (GenBank accession nos AF044083 and U89335) and the XIST region (GenBank accession nos U80459 and U80460) analyzed with a window of 10kb. (B) Repetitive elements in these sequences were identified with RepeatMasker, and distributions of the repetitive sequences were analyzed with a window of 5kb. The size of the arrow indicates the size of the NOTCH4 or XIST gene, and the arrow's direction corresponds to the direction of transcription. (C) The y axis represents replication timing. Replication timing in the MHC class II–III junction is redrawn from Tenzen et al. (1997). The time when S phase began was taken as 0h; and 2h, 3h and 4h were assigned as S1.5, S2 and S2.5 respectively in a separate experiment.</note><note type="content">Fig. 6: Sequences common between the MHC class II–III junction and the XIST region. The sequence for the MHC class II–III junction corresponds to the downstream region of NOTCH4 (GenBank accession nos AF044083 and U89335), and that of the XIST region corresponds to the 3′ portion of XIST plus its flanking region (from nt 40000 to 135000 in GenBank accession no. U80460). The region containing a dense Alu or LINE cluster or the 3′ portion of XIST is indicated by an arrow. MER-internal, fragmental sequences of MERs.</note><note type="content">Table 1: Primer sets used for PCR amplification</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</title><author xml:id="author-0000"><persName><forename type="first">Yoshihisa</forename><surname>Watanabe</surname></persName><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Toyoaki</forename><surname>Tenzen</surname></persName><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation></author><author xml:id="author-0002"><persName><forename type="first">Yasuhiko</forename><surname>Nagasaka</surname></persName><affiliation>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</affiliation></author><author xml:id="author-0003"><persName><forename type="first">Hidetoshi</forename><surname>Inoko</surname></persName><affiliation>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</affiliation></author><author xml:id="author-0004"><persName><forename type="first">Toshimichi</forename><surname>Ikemura</surname></persName><email>tikemura@lab.nig.ac.jp</email><note type="correspondence"><p>Corresponding author. Tel.: +81-559-81-6788; fax +81-559-81-6794</p></note><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation></author><idno type="istex">34578070F16B459BF4FD621A3C9214D90061AE7A</idno><idno type="ark">ark:/67375/6H6-04LQW4C8-3</idno><idno type="DOI">10.1016/S0378-1119(00)00208-0</idno><idno type="PII">S0378-1119(00)00208-0</idno></analytic><monogr><title level="j">Gene</title><title level="j" type="abbrev">GENE</title><idno type="pISSN">0378-1119</idno><idno type="PII">S0378-1119(00)X0159-X</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2000"></date><biblScope unit="volume">252</biblScope><biblScope unit="issue">1–2</biblScope><biblScope unit="page" from="163">163</biblScope><biblScope unit="page" to="172">172</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2000</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of Alu and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.</p></abstract><textClass><keywords scheme="keyword"><list><head>Keywords</head><item><term>Band boundary</term></item><item><term>GC%</term></item><item><term>Human genome</term></item><item><term>Isochores</term></item><item><term>R and G bands</term></item><item><term>XIST</term></item></list></keywords></textClass><textClass><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>bp, base pair(s)</term></item><item><term>GDB, Genome Data Base</term></item><item><term>kb, kilobase or 1000 bp</term></item><item><term>Mb, megabase</term></item><item><term>MER, medium reiteration frequency sequence</term></item><item><term>MHC, major histocompatibility complex</term></item><item><term>nt, nucleotide(s)</term></item><item><term>Pur/Pyr, polypurine/polypyrimidine</term></item><item><term>STS, sequence-tagged sites</term></item><item><term>XIC, X-inactivation center</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2000-03-28">Modified</change><change when="2000">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-04LQW4C8-3/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: ce:floats; body; tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"><istex:entity SYSTEM="gr1" NDATA="IMAGE" name="gr1"></istex:entity><istex:entity SYSTEM="gr2" NDATA="IMAGE" name="gr2"></istex:entity><istex:entity SYSTEM="gr3" NDATA="IMAGE" name="gr3"></istex:entity><istex:entity SYSTEM="gr4" NDATA="IMAGE" name="gr4"></istex:entity><istex:entity SYSTEM="gr5" NDATA="IMAGE" name="gr5"></istex:entity><istex:entity SYSTEM="gr6" NDATA="IMAGE" name="gr6"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla"><item-info><jid>GENE</jid><aid>12475</aid><ce:pii>S0378-1119(00)00208-0</ce:pii><ce:doi>10.1016/S0378-1119(00)00208-0</ce:doi><ce:copyright type="full-transfer" year="2000">Elsevier Science B.V.</ce:copyright></item-info><head><ce:title>Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</ce:title><ce:author-group><ce:author><ce:given-name>Yoshihisa</ce:given-name><ce:surname>Watanabe</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Toyoaki</ce:given-name><ce:surname>Tenzen</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Yasuhiko</ce:given-name><ce:surname>Nagasaka</ce:surname><ce:cross-ref refid="AFF2"><ce:sup>b</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Hidetoshi</ce:given-name><ce:surname>Inoko</ce:surname><ce:cross-ref refid="AFF3"><ce:sup>c</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Toshimichi</ce:given-name><ce:surname>Ikemura</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref><ce:cross-ref refid="CORR1">*</ce:cross-ref><ce:e-address>tikemura@lab.nig.ac.jp</ce:e-address></ce:author><ce:affiliation id="AFF1"><ce:label>a</ce:label><ce:textfn>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</ce:textfn></ce:affiliation><ce:affiliation id="AFF2"><ce:label>b</ce:label><ce:textfn>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</ce:textfn></ce:affiliation><ce:affiliation id="AFF3"><ce:label>c</ce:label><ce:textfn>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</ce:textfn></ce:affiliation><ce:correspondence id="CORR1"><ce:label>*</ce:label><ce:text>Corresponding author. Tel.: +81-559-81-6788; fax +81-559-81-6794</ce:text></ce:correspondence></ce:author-group><ce:date-received day="28" month="12" year="1999"></ce:date-received><ce:date-revised day="28" month="3" year="2000"></ce:date-revised><ce:date-accepted day="11" month="5" year="2000"></ce:date-accepted><ce:miscellaneous>Received by A. Fujiyama</ce:miscellaneous><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1<ce:hsp sp="0.25"></ce:hsp>Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of <ce:italic>Alu</ce:italic> and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>Band boundary</ce:text></ce:keyword><ce:keyword><ce:text>GC%</ce:text></ce:keyword><ce:keyword><ce:text>Human genome</ce:text></ce:keyword><ce:keyword><ce:text>Isochores</ce:text></ce:keyword><ce:keyword><ce:text>R and G bands</ce:text></ce:keyword><ce:keyword><ce:text>XIST</ce:text></ce:keyword></ce:keywords><ce:keywords class="abr"><ce:section-title>Abbreviations</ce:section-title><ce:keyword><ce:text>bp, base pair(s)</ce:text></ce:keyword><ce:keyword><ce:text>GDB, Genome Data Base</ce:text></ce:keyword><ce:keyword><ce:text>kb, kilobase or 1000 bp</ce:text></ce:keyword><ce:keyword><ce:text>Mb, megabase</ce:text></ce:keyword><ce:keyword><ce:text>MER, medium reiteration frequency sequence</ce:text></ce:keyword><ce:keyword><ce:text>MHC, major histocompatibility complex</ce:text></ce:keyword><ce:keyword><ce:text>nt, nucleotide(s)</ce:text></ce:keyword><ce:keyword><ce:text>Pur/Pyr, polypurine/polypyrimidine</ce:text></ce:keyword><ce:keyword><ce:text>STS, sequence-tagged sites</ce:text></ce:keyword><ce:keyword><ce:text>XIC, X-inactivation center</ce:text></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands</title></titleInfo><name type="personal"><namePart type="given">Yoshihisa</namePart><namePart type="family">Watanabe</namePart><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Toyoaki</namePart><namePart type="family">Tenzen</namePart><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Yasuhiko</namePart><namePart type="family">Nagasaka</namePart><affiliation>Beckman Coulter, Toranomon, Minato-ku, Tokyo 105-0001, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hidetoshi</namePart><namePart type="family">Inoko</namePart><affiliation>School of Medicine, Tokai University, Bohseidai, Isehara Kanagawa-ken 259-11, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Toshimichi</namePart><namePart type="family">Ikemura</namePart><affiliation>E-mail: tikemura@lab.nig.ac.jp</affiliation><affiliation>Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan</affiliation><description>Corresponding author. Tel.: +81-559-81-6788; fax +81-559-81-6794</description><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">2000</dateIssued><dateModified encoding="w3cdtf">2000-03-28</dateModified><copyrightDate encoding="w3cdtf">2000</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: The human genome is composed of long-range G+C% mosaic structures, which are thought to be related to chromosome bands. Replication timing during S phase is associated with chromosomal band zones; thus, band boundaries are thought to correspond to regions where replication timing switches. The proximal limit of the human X-inactivation center (XIC) has been localized cytologically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based quantification of the newly replicated DNA from cell-cycle fractionated THP-1 cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing changes from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST locus. We propose that the 1Mb late-replicated zone (from the large inverted duplication to XIST) corresponds to a G-band Xq13.2. Several common characteristics were observed in the XIST region and the MHC class II–III junction which was previously defined as a band boundary. These characteristics included differential high-density clustering of Alu and LINE repeats, and the presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B.</abstract><note>Received by A. Fujiyama</note><note type="content">Fig. 1: Measurement of replication timing. (A) Flow-cytometry profile of BrdU-labeled THP-1 cells. The BrdU-labeled cells were flow-sorted into six cell-cycle fractions (G1, S1, S2, S3, S4, G2/M). (B) Gel electrophoresis for determination of replication timing by PCR Method I. The PCR products from F9 and PGK1 genes were separated by gel electrophoresis and stained with SYBR GREEN I. (C) Replication timing of PGK1 and F9 determined by Method II. The PCR products electrophoresed were quantified with FluorImager. Methods I and II gave the same conclusion.</note><note type="content">Fig. 2: Gel electrophoresis for determination of replication timing. (A, B) Replication timing of PHKA1 and DXS227 that locate at the two sides of a large inverted duplication (see Fig. 4) was determined by two different methods (I and III). The two methods gave the same conclusion. (C) Method I; the 5′- and 3′-flanking regions of XIST. (D) Method III; the 5′-end of XIST, XPCT, and plasmid pKF3. (E) Method III; p4565-H12, DXS227, and plasmid pKF3.</note><note type="content">Fig. 3: Quantification of PCR products by a fluorescence scanning system. PCR products produced by Method II were electrophoresed, stained and quantified with FluorImager. Results are expressed as means of at least three independent PCR reactions.</note><note type="content">Fig. 4: Replication timing of the XIC region. The minimal XIC region is indicated at the top of the figure. Filled boxes indicate the location of genes in the area. A large inverted duplication is indicated by a set of inverted arrows (→←). Map locations of eight PCR markers, except the XIST locus, are from Lafreniere et al. (1993). Primers in and around XIST were designed in this study. The cell-cycle fraction with the highest level of replicated DNA is shown by closed circles. If the difference in replicated DNA levels between two consecutive cell-cycle fractions was less than 10%, the closed circle is placed in the intermediate position. Replication timing for each locus was determined after quantification of at least three independent PCRs using different plasmid DNA concentrations and a fixed amount of the newly replicated DNA.</note><note type="content">Fig. 5: Transition of GC% distribution and replication timing in the MHC class II–III junction and in and around the XIST locus. (A) GC% distribution in the MHC class II–III junction (GenBank accession nos AF044083 and U89335) and the XIST region (GenBank accession nos U80459 and U80460) analyzed with a window of 10kb. (B) Repetitive elements in these sequences were identified with RepeatMasker, and distributions of the repetitive sequences were analyzed with a window of 5kb. The size of the arrow indicates the size of the NOTCH4 or XIST gene, and the arrow's direction corresponds to the direction of transcription. (C) The y axis represents replication timing. Replication timing in the MHC class II–III junction is redrawn from Tenzen et al. (1997). The time when S phase began was taken as 0h; and 2h, 3h and 4h were assigned as S1.5, S2 and S2.5 respectively in a separate experiment.</note><note type="content">Fig. 6: Sequences common between the MHC class II–III junction and the XIST region. The sequence for the MHC class II–III junction corresponds to the downstream region of NOTCH4 (GenBank accession nos AF044083 and U89335), and that of the XIST region corresponds to the 3′ portion of XIST plus its flanking region (from nt 40000 to 135000 in GenBank accession no. U80460). The region containing a dense Alu or LINE cluster or the 3′ portion of XIST is indicated by an arrow. MER-internal, fragmental sequences of MERs.</note><note type="content">Table 1: Primer sets used for PCR amplification</note><subject><genre>Keywords</genre><topic>Band boundary</topic><topic>GC%</topic><topic>Human genome</topic><topic>Isochores</topic><topic>R and G bands</topic><topic>XIST</topic></subject><subject><genre>Abbreviations</genre><topic>bp, base pair(s)</topic><topic>GDB, Genome Data Base</topic><topic>kb, kilobase or 1000 bp</topic><topic>Mb, megabase</topic><topic>MER, medium reiteration frequency sequence</topic><topic>MHC, major histocompatibility complex</topic><topic>nt, nucleotide(s)</topic><topic>Pur/Pyr, polypurine/polypyrimidine</topic><topic>STS, sequence-tagged sites</topic><topic>XIC, X-inactivation center</topic></subject><relatedItem type="host"><titleInfo><title>Gene</title></titleInfo><titleInfo type="abbreviated"><title>GENE</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">2000</dateIssued></originInfo><identifier type="ISSN">0378-1119</identifier><identifier type="PII">S0378-1119(00)X0159-X</identifier><part><date>2000</date><detail type="volume"><number>252</number><caption>vol.</caption></detail><detail type="issue"><number>1–2</number><caption>no.</caption></detail><extent unit="issue-pages"><start>1</start><end>228</end></extent><extent unit="pages"><start>163</start><end>172</end></extent></part></relatedItem><identifier type="istex">34578070F16B459BF4FD621A3C9214D90061AE7A</identifier><identifier type="ark">ark:/67375/6H6-04LQW4C8-3</identifier><identifier type="DOI">10.1016/S0378-1119(00)00208-0</identifier><identifier type="PII">S0378-1119(00)00208-0</identifier><accessCondition type="use and reproduction" contentType="copyright">©2000 Elsevier Science B.V.</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource><recordOrigin>Elsevier Science B.V., ©2000</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-04LQW4C8-3/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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