Structural determinants of DNA recognition by plant MADS-domain transcription factors

J.M. Muino Acuna, C. Smaczniak, G.C. Angenent, K. Kaufmann, A.D.J. van Dijk

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)

Abstract

Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.
Original languageEnglish
Pages (from-to)2138-2146
JournalNucleic acids research
Volume42
Issue number4
DOIs
Publication statusPublished - 2014

Fingerprint

Plant DNA
MADS Domain Proteins
Transcription Factors
DNA
Binding Sites
Plant Proteins

Keywords

  • in-vitro
  • binding properties
  • flower development
  • antirrhinum-majus
  • homeotic proteins
  • crystal-structure
  • ternary complex
  • floral organs
  • box proteins
  • chip-chip

Cite this

Muino Acuna, J.M. ; Smaczniak, C. ; Angenent, G.C. ; Kaufmann, K. ; van Dijk, A.D.J. / Structural determinants of DNA recognition by plant MADS-domain transcription factors. In: Nucleic acids research. 2014 ; Vol. 42, No. 4. pp. 2138-2146.
@article{0771b3de493a41aeaff136d62bd74d33,
title = "Structural determinants of DNA recognition by plant MADS-domain transcription factors",
abstract = "Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.",
keywords = "in-vitro, binding properties, flower development, antirrhinum-majus, homeotic proteins, crystal-structure, ternary complex, floral organs, box proteins, chip-chip",
author = "{Muino Acuna}, J.M. and C. Smaczniak and G.C. Angenent and K. Kaufmann and {van Dijk}, A.D.J.",
year = "2014",
doi = "10.1093/nar/gkt1172",
language = "English",
volume = "42",
pages = "2138--2146",
journal = "Nucleic acids research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "4",

}

Structural determinants of DNA recognition by plant MADS-domain transcription factors. / Muino Acuna, J.M.; Smaczniak, C.; Angenent, G.C.; Kaufmann, K.; van Dijk, A.D.J.

In: Nucleic acids research, Vol. 42, No. 4, 2014, p. 2138-2146.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Structural determinants of DNA recognition by plant MADS-domain transcription factors

AU - Muino Acuna, J.M.

AU - Smaczniak, C.

AU - Angenent, G.C.

AU - Kaufmann, K.

AU - van Dijk, A.D.J.

PY - 2014

Y1 - 2014

N2 - Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.

AB - Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.

KW - in-vitro

KW - binding properties

KW - flower development

KW - antirrhinum-majus

KW - homeotic proteins

KW - crystal-structure

KW - ternary complex

KW - floral organs

KW - box proteins

KW - chip-chip

U2 - 10.1093/nar/gkt1172

DO - 10.1093/nar/gkt1172

M3 - Article

VL - 42

SP - 2138

EP - 2146

JO - Nucleic acids research

JF - Nucleic acids research

SN - 0305-1048

IS - 4

ER -