Differences in DNA binding specificity of floral homeotic protein complexes predict organ-specific target genes

Cezary Smaczniak, Jose M. Muiño, Dijun Chen, Gerco C. Angenent, Kerstin Kaufmann*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)

Abstract

Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. However, how these factors achieve their regulatory specificities is still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- and heterodimers to measure their DNA binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 and AGAMOUS. Binding specificity is further modulated by different binding site spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows differentiation between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA binding specificity of floral MADS domain proteins. Differential DNA binding of MADS domain protein complexes plays a role in the specificity of target gene regulation.

Original languageEnglish
Pages (from-to)1822-1835
JournalThe Plant Cell
Volume29
Issue number8
DOIs
Publication statusPublished - 2017

Fingerprint

homeodomain proteins
Homeodomain Proteins
MADS Domain Proteins
DNA
Genes
genes
proteins
SELEX Aptamer Technique
Genome
perianth
DNA-binding domains
genome
site-directed mutagenesis
High-Throughput Nucleotide Sequencing
Homo
Organ Specificity
binding sites
Mutagenesis
transcription factors
promoter regions

Cite this

Smaczniak, Cezary ; Muiño, Jose M. ; Chen, Dijun ; Angenent, Gerco C. ; Kaufmann, Kerstin. / Differences in DNA binding specificity of floral homeotic protein complexes predict organ-specific target genes. In: The Plant Cell. 2017 ; Vol. 29, No. 8. pp. 1822-1835.
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abstract = "Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. However, how these factors achieve their regulatory specificities is still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- and heterodimers to measure their DNA binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 and AGAMOUS. Binding specificity is further modulated by different binding site spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows differentiation between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA binding specificity of floral MADS domain proteins. Differential DNA binding of MADS domain protein complexes plays a role in the specificity of target gene regulation.",
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Differences in DNA binding specificity of floral homeotic protein complexes predict organ-specific target genes. / Smaczniak, Cezary; Muiño, Jose M.; Chen, Dijun; Angenent, Gerco C.; Kaufmann, Kerstin.

In: The Plant Cell, Vol. 29, No. 8, 2017, p. 1822-1835.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Kaufmann, Kerstin

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AB - Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. However, how these factors achieve their regulatory specificities is still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- and heterodimers to measure their DNA binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 and AGAMOUS. Binding specificity is further modulated by different binding site spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows differentiation between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA binding specificity of floral MADS domain proteins. Differential DNA binding of MADS domain protein complexes plays a role in the specificity of target gene regulation.

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