The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i>
Nuclear Factor Y (NF-Y) is an evolutionarily conserved trimer formed by a Histone-Fold Domain (HFD) heterodimeric module shared by core histones, and the sequence-specific NF-YA subunit. In plants, the genes encoding each of the three subunits have expanded in number, giving rise to hundreds of pote...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/8/10/406 |
| _version_ | 1818959810791473152 |
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| author | Nerina Gnesutta Matteo Chiara Andrea Bernardini Matteo Balestra David S. Horner Roberto Mantovani |
| author_facet | Nerina Gnesutta Matteo Chiara Andrea Bernardini Matteo Balestra David S. Horner Roberto Mantovani |
| author_sort | Nerina Gnesutta |
| collection | DOAJ |
| description | Nuclear Factor Y (NF-Y) is an evolutionarily conserved trimer formed by a Histone-Fold Domain (HFD) heterodimeric module shared by core histones, and the sequence-specific NF-YA subunit. In plants, the genes encoding each of the three subunits have expanded in number, giving rise to hundreds of potential trimers. While in mammals NF-Y binds a well-characterized motif, with a defined matrix centered on the <i>CCAAT</i> box, the specificity of the plant trimers has yet to be determined. Here we report that <i>Arabidopsis thaliana</i> NF-Y trimeric complexes, containing two different NF-YA subunits, bind DNA <i>in vitro</i> with similar affinities. We assayed precisely sequence-specificity by saturation mutagenesis, and analyzed genomic DNA sites bound <i>in vivo</i> by selected HFDs. The plant NF-Y <i>CCAAT</i> matrix is different in nucleotides flanking <i>CCAAT</i> with respect to the mammalian matrix, <i>in vitro</i> and <i>in vivo</i>. Our data point to flexible DNA-binding rules by plant NF-Ys, serving the scope of adapting to a diverse audience of genomic motifs. |
| first_indexed | 2024-12-20T11:47:34Z |
| format | Article |
| id | doaj.art-8d4976a34e6b4fd399d610aae8e2df22 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-12-20T11:47:34Z |
| publishDate | 2019-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-8d4976a34e6b4fd399d610aae8e2df222022-12-21T19:41:50ZengMDPI AGPlants2223-77472019-10-0181040610.3390/plants8100406plants8100406The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i>Nerina Gnesutta0Matteo Chiara1Andrea Bernardini2Matteo Balestra3David S. Horner4Roberto Mantovani5Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyDipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyDipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyDipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyDipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyDipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ItalyNuclear Factor Y (NF-Y) is an evolutionarily conserved trimer formed by a Histone-Fold Domain (HFD) heterodimeric module shared by core histones, and the sequence-specific NF-YA subunit. In plants, the genes encoding each of the three subunits have expanded in number, giving rise to hundreds of potential trimers. While in mammals NF-Y binds a well-characterized motif, with a defined matrix centered on the <i>CCAAT</i> box, the specificity of the plant trimers has yet to be determined. Here we report that <i>Arabidopsis thaliana</i> NF-Y trimeric complexes, containing two different NF-YA subunits, bind DNA <i>in vitro</i> with similar affinities. We assayed precisely sequence-specificity by saturation mutagenesis, and analyzed genomic DNA sites bound <i>in vivo</i> by selected HFDs. The plant NF-Y <i>CCAAT</i> matrix is different in nucleotides flanking <i>CCAAT</i> with respect to the mammalian matrix, <i>in vitro</i> and <i>in vivo</i>. Our data point to flexible DNA-binding rules by plant NF-Ys, serving the scope of adapting to a diverse audience of genomic motifs.https://www.mdpi.com/2223-7747/8/10/406transcription factorplant nf-ytfbsdna matrixlec1 |
| spellingShingle | Nerina Gnesutta Matteo Chiara Andrea Bernardini Matteo Balestra David S. Horner Roberto Mantovani The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> Plants transcription factor plant nf-y tfbs dna matrix lec1 |
| title | The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> |
| title_full | The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> |
| title_fullStr | The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> |
| title_full_unstemmed | The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> |
| title_short | The Plant NF-Y DNA Matrix <i>In Vitro</i> and <i>In Vivo</i> |
| title_sort | plant nf y dna matrix i in vitro i and i in vivo i |
| topic | transcription factor plant nf-y tfbs dna matrix lec1 |
| url | https://www.mdpi.com/2223-7747/8/10/406 |
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