Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin
The control of gene expression by <i>cis</i>-regulatory DNA sequences is a conserved genomic feature. The maize <i>booster1</i> gene (<i>b1</i>) is a naturally occurring locus that serves as a mechanistic model for the control of gene expression from a distal <...
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MDPI AG
2025-06-01
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| author | Jason S. Lynn Kathryn M. Koirtyohann Yacob B. Gebreab Jaliyah Edwards Karen M. McGinnis |
| author_facet | Jason S. Lynn Kathryn M. Koirtyohann Yacob B. Gebreab Jaliyah Edwards Karen M. McGinnis |
| author_sort | Jason S. Lynn |
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| description | The control of gene expression by <i>cis</i>-regulatory DNA sequences is a conserved genomic feature. The maize <i>booster1</i> gene (<i>b1</i>) is a naturally occurring locus that serves as a mechanistic model for the control of gene expression from a distal <i>cis</i> element and a form of allelic interactions called paramutation. Two epi-alleles of <i>b1</i> produce distinct pigmentation phenotypes correlated with transcriptional enhancement and the silencing of <i>b1</i>. These transcriptional dynamics depend on a hepta-tandem repeat sequence located 100 kb upstream of the <i>b1</i> locus. In the heterozygous condition, the <i>B</i>′ epi-allele paramutates <i>B-I</i>, heritably converting the <i>B-I</i> epi-allele to the epigenetic state and expression level of <i>B</i>′, producing lightly pigmented plants. To identify <i>b1TR</i>-associated proteins, we used a targeted chromatin immunoprecipitation approach with a stably integrated transgenic <i>b1TR</i> locus. Applying a conservative filtering strategy, we detected several expected factors, including RNA Polymerase II, as well as the novel putative DNA-binding proteins ZAG4 and DDT4. ZAG4 and DDT4 activated GAL expression using <i>b1TR</i> as bait in yeast one-hybrid, supporting their potential interaction with this sequence. The identification of proteins uniquely associated with the <i>UAS::b1TR</i> chromatin provides insight into potential <i>b1</i> regulatory factors and offers a foundation for future studies to investigate their roles in gene regulation. |
| format | Article |
| id | doaj-art-726aa956b438471182c1953c23c051c2 |
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| issn | 2223-7747 |
| language | English |
| publishDate | 2025-06-01 |
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| series | Plants |
| spelling | doaj-art-726aa956b438471182c1953c23c051c22025-08-20T03:16:36ZengMDPI AGPlants2223-77472025-06-011412186310.3390/plants14121863Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene ChromatinJason S. Lynn0Kathryn M. Koirtyohann1Yacob B. Gebreab2Jaliyah Edwards3Karen M. McGinnis4Department of Biological Science, Florida State University, Tallahassee, FL 32304, USADepartment of Biological Science, Florida State University, Tallahassee, FL 32304, USADepartment of Biological Science, Florida State University, Tallahassee, FL 32304, USADepartment of Biological Science, Florida State University, Tallahassee, FL 32304, USADepartment of Biological Science, Florida State University, Tallahassee, FL 32304, USAThe control of gene expression by <i>cis</i>-regulatory DNA sequences is a conserved genomic feature. The maize <i>booster1</i> gene (<i>b1</i>) is a naturally occurring locus that serves as a mechanistic model for the control of gene expression from a distal <i>cis</i> element and a form of allelic interactions called paramutation. Two epi-alleles of <i>b1</i> produce distinct pigmentation phenotypes correlated with transcriptional enhancement and the silencing of <i>b1</i>. These transcriptional dynamics depend on a hepta-tandem repeat sequence located 100 kb upstream of the <i>b1</i> locus. In the heterozygous condition, the <i>B</i>′ epi-allele paramutates <i>B-I</i>, heritably converting the <i>B-I</i> epi-allele to the epigenetic state and expression level of <i>B</i>′, producing lightly pigmented plants. To identify <i>b1TR</i>-associated proteins, we used a targeted chromatin immunoprecipitation approach with a stably integrated transgenic <i>b1TR</i> locus. Applying a conservative filtering strategy, we detected several expected factors, including RNA Polymerase II, as well as the novel putative DNA-binding proteins ZAG4 and DDT4. ZAG4 and DDT4 activated GAL expression using <i>b1TR</i> as bait in yeast one-hybrid, supporting their potential interaction with this sequence. The identification of proteins uniquely associated with the <i>UAS::b1TR</i> chromatin provides insight into potential <i>b1</i> regulatory factors and offers a foundation for future studies to investigate their roles in gene regulation.https://www.mdpi.com/2223-7747/14/12/1863ChIP-mass specmaizeproteomicsparamutationtranscriptional gene silencingPol II |
| spellingShingle | Jason S. Lynn Kathryn M. Koirtyohann Yacob B. Gebreab Jaliyah Edwards Karen M. McGinnis Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin Plants ChIP-mass spec maize proteomics paramutation transcriptional gene silencing Pol II |
| title | Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin |
| title_full | Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin |
| title_fullStr | Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin |
| title_full_unstemmed | Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin |
| title_short | Identification of Proteins Associated with Stably Integrated Maize <i>b1</i> Tandem Repeat Transgene Chromatin |
| title_sort | identification of proteins associated with stably integrated maize i b1 i tandem repeat transgene chromatin |
| topic | ChIP-mass spec maize proteomics paramutation transcriptional gene silencing Pol II |
| url | https://www.mdpi.com/2223-7747/14/12/1863 |
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