Reviewer's report
Title:Mapping of HNF4alpha target genes in intestinal epithelial cells unravels a
gene regulatory network involving Cdx-2.
Version: 1Date:9 March 2009
Reviewer: Dallas M Swallow
Reviewer's report:
This paper reports a careful study designed to identify promoters upregulated by
HNF4 alpha. The authors made use of differentiated Caco-2 cells, followed by
chromatin immunoprecipitation with specific antibodies for HNF4A, or acetylated
histone, DNA amplification and Chip hybridisation analysis. Identification
depended on inclusion of promoters within a set, supplied by the company
NimbleGen, taken from some 25,000 genes. The data obtained for HNF4A were
matched with gene expression and histone acetylation data. 1541 potential
targets were identified, which when characterised by gene ontology were shown
to include many involved in lipid and amino-acid transport and metabolism..
Additional experimental data was provided for 3 genes (CGN, Cdx-2 and TREH)
and Cdx-2 and Treh binding was confirmed as well for mouse intestine.
By using a combination of bioinformatic, high throughput and detailed
experimental approaches the authors have produced a very detailed and useful
picture of the role of this transcription factor in intestinal gene expression and
differentiation.
This paper is well and clearly written and provides a very useful contribution to
the field
There are a few minor points:
Essential
1 First paragraph of the Introduction; the statement that only two types of cells
occur in the adult colon should be rephrased because as written this may not be
completely true. eg two major cell types predominate in the colon
2 Second paragraph of the Introduction --’which is only expressed in the intestine
of the adult mouse’ should be reworded ‘which in the adult mouse is only
expressed in the intestine.’
3 It might be easier to follow the methodological detail of this paper if it were
ordered to more strictly correspond to the Results section and/or there were
more subheadings. For example the term lysate would be easier if the previous
section was headed ‘preparation of lysate’ –or perhaps rather, cross linked
chromatin fragments?
4 On page 15 a reference is needed for cingulin’s tight junction role.
5 The sentence on page 16 stating that certain promoters were not analysed
correctly with the NimbleGen array needs clarification.
6 The figure legends need clear titles, distinct from the explanations
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
no
Reviewer's report
Title:Mapping of HNF4alpha target genes in intestinal epithelial cells unravels a
gene regulatory network involving Cdx-2.
Version: 1Date:9 March 2009
Reviewer: Dallas M Swallow
Reviewer's report:
This paper reports a careful study designed to identify promoters upregulated by
HNF4 alpha. The authors made use of differentiated Caco-2 cells, followed by
chromatin immunoprecipitation with specific antibodies for HNF4A, or acetylated
histone, DNA amplification and Chip hybridisation analysis. Identification
depended on inclusion of promoters within a set, supplied by the company
NimbleGen, taken from some 25,000 genes. The data obtained for HNF4A were
matched with gene expression and histone acetylation data. 1541 potential
targets were identified, which when characterised by gene ontology were shown
to include many involved in lipid and amino-acid transport and metabolism..
Additional experimental data was provided for 3 genes (CGN, Cdx-2 and TREH)
and Cdx-2 and Treh binding was confirmed as well for mouse intestine.
By using a combination of bioinformatic, high throughput and detailed
experimental approaches the authors have produced a very detailed and useful
picture of the role of this transcription factor in intestinal gene expression and
differentiation.
This paper is well and clearly written and provides a very useful contribution to
the field
There are a few minor points:
Essential
1 First paragraph of the Introduction; the statement that only two types of cells
occur in the adult colon should be rephrased because as written this may not be
completely true. eg two major cell types predominate in the colon
2 Second paragraph of the Introduction --’which is only expressed in the intestine
of the adult mouse’ should be reworded ‘which in the adult mouse is only
expressed in the intestine.’
3 It might be easier to follow the methodological detail of this paper if it were
ordered to more strictly correspond to the Results section and/or there were
more subheadings. For example the term lysate would be easier if the previous
section was headed ‘preparation of lysate’ –or perhaps rather, cross linked
chromatin fragments?
4 On page 15 a reference is needed for cingulin’s tight junction role.
5 The sentence on page 16 stating that certain promoters were not analysed
correctly with the NimbleGen array needs clarification.
6 The figure legends need clear titles, distinct from the explanations
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
no
Please review this paper.
user
Reviewer's report
Title:Mapping of HNF4alpha target genes in intestinal epithelial cells unravels a
gene regulatory network involving Cdx-2.
Version: 1Date:9 March 2009
Reviewer: Dallas M Swallow
Reviewer's report:
This paper reports a careful study designed to identify promoters upregulated by
HNF4 alpha. The authors made use of differentiated Caco-2 cells, followed by
chromatin immunoprecipitation with specific antibodies for HNF4A, or acetylated
histone, DNA amplification and Chip hybridisation analysis. Identification
depended on inclusion of promoters within a set, supplied by the company
NimbleGen, taken from some 25,000 genes. The data obtained for HNF4A were
matched with gene expression and histone acetylation data. 1541 potential
targets were identified, which when characterised by gene ontology were shown
to include many involved in lipid and amino-acid transport and metabolism..
Additional experimental data was provided for 3 genes (CGN, Cdx-2 and TREH)
and Cdx-2 and Treh binding was confirmed as well for mouse intestine.
By using a combination of bioinformatic, high throughput and detailed
experimental approaches the authors have produced a very detailed and useful
picture of the role of this transcription factor in intestinal gene expression and
differentiation.
This paper is well and clearly written and provides a very useful contribution to
the field
There are a few minor points:
Essential
1 First paragraph of the Introduction; the statement that only two types of cells
occur in the adult colon should be rephrased because as written this may not be
completely true. eg two major cell types predominate in the colon
2 Second paragraph of the Introduction --’which is only expressed in the intestine
of the adult mouse’ should be reworded ‘which in the adult mouse is only
expressed in the intestine.’
3 It might be easier to follow the methodological detail of this paper if it were
ordered to more strictly correspond to the Results section and/or there were
more subheadings. For example the term lysate would be easier if the previous
section was headed ‘preparation of lysate’ –or perhaps rather, cross linked
chromatin fragments?
4 On page 15 a reference is needed for cingulin’s tight junction role.
5 The sentence on page 16 stating that certain promoters were not analysed
correctly with the NimbleGen array needs clarification.
6 The figure legends need clear titles, distinct from the explanations
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
no
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