The <i>cis</i>‐regulatory code of Hox function in <i>Drosophila</i>

Sorge, Sebastian; Ha, Nati; Polychronidou, Maria; Friedrich, Jana; Bezdan, Daniela; Kaspar, Petra; Schaefer, Martin H.; Ossowski, Stephan; Henz, Stefan R.; Mundorf, Juliane; Rätzer, Jenny; Papagiannouli, Fani; Lohmann, Ingrid

doi:10.15252/embj.201593321

Cited by 16 publications

(35 citation statements)

References 27 publications

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“…However, additional examples of organizationally constrained enhancers do exist [179–184]. Spatial constraints on select paired TF-TF coassociations and binding-site combinations are found in genome-wide ChIP data [148, 185, 186]. Interactions between TFs can lead to cooperative DNA binding, although this binding does not approach the extreme multifactorial cooperativity required for enhanceosome assembly.…”

Section: Transcription Factor Interactions At Genomic Regulatory Regionsmentioning

confidence: 99%

Absence of a simple code: how transcription factors read the genome

Slattery

Zhou

Yang

et al. 2014

Trends in Biochemical Sciences

476

447

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Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs, based on three-dimensional structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.

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Section: Transcription Factor Interactions At Genomic Regulatory Regionsmentioning

confidence: 99%

Absence of a simple code: how transcription factors read the genome

Slattery

Zhou

Yang

et al. 2014

Trends in Biochemical Sciences

476

447

View full text Add to dashboard Cite

show abstract

“…In this context, two features -cellular heterogeneity and the developmental time window covered -are particularly important, and it should be noted that the binding events detected represent a sum of events occurring in different cell types and/or at different time points. Although generally applicable, these limitations hold especially true for Hox proteins, which are known to pattern fields of cells that encompass diverse cell types in a very dynamic manner by regulating distinct sets of target genes at different time points (Fan et al, 2012;Pavlopoulos and Akam, 2011;Sorge et al, 2012), possibly associated with dynamic genome binding (Fan et al, 2012;Niu et al, 2011). With these limitations in mind, and taking into account the often low false discovery rate (FDR) applied, the numbers (see Table 1) seem comparable to those found for other transcription factors, suggesting that Hox DNA binding might also be widespread.…”

Section: Current Models For Transcription Factor Function: Hox Proteimentioning

confidence: 99%

“…In the case of Drosophila Ubx and Dfd (Sorge et al, 2012) it was found that, despite sharing identical DNA binding sequences, the proteins bind to non-overlapping genomic regions, indicating that in vivo binding is regulated beyond the intrinsic DNA binding potential of Hox proteins. Thus, at least in this single example, it seems that, although widespread, Hox proteins might not share the overlapping genomic binding property that other transcription factors exhibit (MacArthur et al, 2009).…”

Section: Current Models For Transcription Factor Function: Hox Proteimentioning

confidence: 99%

Cellular and molecular insights into Hox protein action

et al. 2015

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Hox genes encode homeodomain transcription factors that control morphogenesis and have established functions in development and evolution. Hox proteins have remained enigmatic with regard to the molecular mechanisms that endow them with specific and diverse functions, and to the cellular functions that they control. Here, we review recent examples of Hox-controlled cellular functions that highlight their versatile and highly context-dependent activity. This provides the setting to discuss how Hox proteins control morphogenesis and organogenesis. We then summarise the molecular modalities underlying Hox protein function, in particular in light of current models of transcription factor function. Finally, we discuss how functional divergence between Hox proteins might be achieved to give rise to the many facets of their action.

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“…The chinmo 5'UTR and 3'UTR sequences were obtained from the EST clone pFLC1--RE59755 (Berkeley Drosophila Genome Project, GOLD collection). The mcherry reporter gene was obtained from the pBPGUw--mCherry plasmid (a gift P. Kaspar (Lohmann's lab)) (Sorge et al, 2012). The primers used were:…”

Section: Generation Of the Mcherry Chinmoutrs Line The 5' And 3' Untmentioning

confidence: 99%