title: Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development.
abstract: BACKGROUND
  Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood.
  
  
  RESULTS
  We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes.
  
  
  CONCLUSIONS
  Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
authors.forename: Alice
authors.initials: A
authors.lastname: Pajoro
authors.forename: Pedro
authors.initials: P
authors.lastname: Madrigal
authors.forename: Jose M
authors.initials: JM
authors.lastname: Muiño
authors.forename: José Tomás
authors.initials: JT
authors.lastname: Matus
authors.forename: Jian
authors.initials: J
authors.lastname: Jin
authors.forename: Martin A
authors.initials: MA
authors.lastname: Mecchia
authors.forename: Juan M
authors.initials: JM
authors.lastname: Debernardi
authors.forename: Javier F
authors.initials: JF
authors.lastname: Palatnik
authors.forename: Salma
authors.initials: S
authors.lastname: Balazadeh
authors.forename: Muhammad
authors.initials: M
authors.lastname: Arif
authors.forename: Diarmuid S
authors.initials: DS
authors.lastname: Ó'Maoiléidigh
authors.forename: Frank
authors.initials: F
authors.lastname: Wellmer
authors.forename: Pawel
authors.initials: P
authors.lastname: Krajewski
authors.forename: José-Luis
authors.initials: JL
authors.lastname: Riechmann
authors.forename: Gerco C
authors.initials: GC
authors.lastname: Angenent
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kaufmann
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D035264:Flowers / Q000254:growth & development* / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism*; D026161:MADS Domain Proteins / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: C091535:AP1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D002843:Chromatin; D018398:Homeodomain Proteins; D026161:MADS Domain Proteins; C121158:SEP3 protein, Arabidopsis; D014157:Transcription Factors