Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
Identifieur interne : 000D54 ( Main/Exploration ); précédent : 000D53; suivant : 000D55Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
Auteurs : Ryohei Nakamura [Japon] ; Ayako Uno [Japon] ; Masahiko Kumagai [Japon] ; Shinichi Morishita [Japon] ; Hiroyuki Takeda [Japon]Source :
- Epigenetics & Chromatin [ 1756-8935 ] ; 2017.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (), Animaux, Apprentissage machine, Assemblage et désassemblage de la chromatine, Motifs nucléotidiques, Méthylation de l'ADN, Nucléosomes (génétique), Nucléosomes (métabolisme), Oryzias, Protéines de poisson (génétique), Protéines de poisson (métabolisme), Régions promotrices (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Fish Proteins, Nucleosomes.
- chemical , metabolism : Fish Proteins, Nucleosomes.
- methods : Sequence Analysis, DNA.
- Animals, Chromatin Assembly and Disassembly, DNA Methylation, Machine Learning, Nucleotide Motifs, Oryzias, Promoter Regions, Genetic.
Abstract
Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed.
Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm,
This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning.
The online version of this article (doi:10.1186/s13072-017-0152-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13072-017-0152-2
PubMed: 28931432
PubMed Central: 5607494
Affiliations:
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Ryohei" uniqKey="Nakamura R" first="Ryohei" last="Nakamura">Ryohei Nakamura</name><affiliation wicri:level="3"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2151 536X</institution-id><institution-id institution-id-type="GRID">grid.26999.3d</institution-id><institution>Department of Biological Sciences, Graduate School of Science,</institution><institution>The University of Tokyo,</institution></institution-wrap>7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>7-3-1 Hongo, Bunkyo-ku, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Uno, Ayako" sort="Uno, Ayako" uniqKey="Uno A" first="Ayako" last="Uno">Ayako Uno</name><affiliation wicri:level="3"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2151 536X</institution-id><institution-id institution-id-type="GRID">grid.26999.3d</institution-id><institution>Department of Biological Sciences, Graduate School of Science,</institution><institution>The University of Tokyo,</institution></institution-wrap>7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>7-3-1 Hongo, Bunkyo-ku, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kumagai, Masahiko" sort="Kumagai, Masahiko" uniqKey="Kumagai M" first="Masahiko" last="Kumagai">Masahiko Kumagai</name><affiliation wicri:level="3"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2151 536X</institution-id><institution-id institution-id-type="GRID">grid.26999.3d</institution-id><institution>Department of Biological Sciences, Graduate School of 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Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>5-1-5 Kashiwanoha, Kashiwa</wicri:regionArea><wicri:noRegion>Kashiwa</wicri:noRegion></affiliation></author><author><name sortKey="Takeda, Hiroyuki" sort="Takeda, Hiroyuki" uniqKey="Takeda H" first="Hiroyuki" last="Takeda">Hiroyuki Takeda</name><affiliation wicri:level="3"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2151 536X</institution-id><institution-id institution-id-type="GRID">grid.26999.3d</institution-id><institution>Department of Biological Sciences, Graduate School of Science,</institution><institution>The University of Tokyo,</institution></institution-wrap>7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>7-3-1 Hongo, Bunkyo-ku, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author></analytic><series><title level="j">Epigenetics & Chromatin</title><idno type="eISSN">1756-8935</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chromatin Assembly and Disassembly</term><term>DNA Methylation</term><term>Fish Proteins (genetics)</term><term>Fish Proteins (metabolism)</term><term>Machine Learning</term><term>Nucleosomes (genetics)</term><term>Nucleosomes (metabolism)</term><term>Nucleotide Motifs</term><term>Oryzias</term><term>Promoter Regions, Genetic</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Animaux</term><term>Apprentissage machine</term><term>Assemblage et désassemblage de la chromatine</term><term>Motifs nucléotidiques</term><term>Méthylation de l'ADN</term><term>Nucléosomes (génétique)</term><term>Nucléosomes (métabolisme)</term><term>Oryzias</term><term>Protéines de poisson (génétique)</term><term>Protéines de poisson (métabolisme)</term><term>Régions promotrices (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fish Proteins</term><term>Nucleosomes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fish Proteins</term><term>Nucleosomes</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Nucléosomes</term><term>Protéines de poisson</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Nucléosomes</term><term>Protéines de poisson</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Chromatin Assembly and Disassembly</term><term>DNA Methylation</term><term>Machine Learning</term><term>Nucleotide Motifs</term><term>Oryzias</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Apprentissage machine</term><term>Assemblage et désassemblage de la chromatine</term><term>Motifs nucléotidiques</term><term>Méthylation de l'ADN</term><term>Oryzias</term><term>Régions promotrices (génétique)</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed.</p></sec><sec><title>Results</title><p id="Par2">Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, <italic>k</italic>-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish.</p></sec><sec><title>Conclusion</title><p id="Par3">This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13072-017-0152-2) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Richmond, Tj" uniqKey="Richmond T">TJ Richmond</name></author><author><name sortKey="Davey, Ca" uniqKey="Davey C">CA Davey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jiang, C" uniqKey="Jiang C">C Jiang</name></author><author><name sortKey="Pugh, Bf" uniqKey="Pugh B">BF 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Zhou</name></author><author><name sortKey="Zhang, Rr" uniqKey="Zhang R">RR Zhang</name></author><author><name sortKey="Zhang, Kl" uniqKey="Zhang K">KL Zhang</name></author><author><name sortKey="Zhou, Jq" uniqKey="Zhou J">JQ Zhou</name></author><author><name sortKey="Xu, Gl" uniqKey="Xu G">GL Xu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sabo, Pj" uniqKey="Sabo P">PJ Sabo</name></author><author><name sortKey="Kuehn, Ms" uniqKey="Kuehn M">MS Kuehn</name></author><author><name sortKey="Thurman, R" uniqKey="Thurman R">R Thurman</name></author><author><name sortKey="Johnson, Be" uniqKey="Johnson B">BE Johnson</name></author><author><name sortKey="Johnson, Em" uniqKey="Johnson E">EM Johnson</name></author><author><name sortKey="Cao, H" uniqKey="Cao H">H Cao</name></author><author><name sortKey="Yu, M" uniqKey="Yu M">M Yu</name></author><author><name sortKey="Rosenzweig, E" uniqKey="Rosenzweig E">E Rosenzweig</name></author><author><name sortKey="Goldy, J" uniqKey="Goldy J">J Goldy</name></author><author><name sortKey="Haydock, A" uniqKey="Haydock A">A Haydock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gupta, S" uniqKey="Gupta S">S Gupta</name></author><author><name sortKey="Stamatoyannopoulos, Ja" uniqKey="Stamatoyannopoulos J">JA Stamatoyannopoulos</name></author><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name></author><author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement></list><tree><country name="Japon"><region name="Région de Kantō"><name sortKey="Nakamura, Ryohei" sort="Nakamura, Ryohei" uniqKey="Nakamura R" first="Ryohei" last="Nakamura">Ryohei Nakamura</name></region><name sortKey="Kumagai, Masahiko" sort="Kumagai, Masahiko" uniqKey="Kumagai M" first="Masahiko" last="Kumagai">Masahiko Kumagai</name><name sortKey="Morishita, Shinichi" sort="Morishita, Shinichi" uniqKey="Morishita S" first="Shinichi" last="Morishita">Shinichi Morishita</name><name sortKey="Takeda, Hiroyuki" sort="Takeda, Hiroyuki" uniqKey="Takeda H" first="Hiroyuki" last="Takeda">Hiroyuki Takeda</name><name sortKey="Uno, Ayako" sort="Uno, Ayako" uniqKey="Uno A" first="Ayako" last="Uno">Ayako Uno</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|étape= Exploration
|type= RBID
|clé= PMC:5607494
|texte= Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
}}
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:28931432" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
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