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Constraint of gene expression by the chromatin remodelling protein CHD4 facilitates lineage specification.

O'Shaughnessy-Kirwan A, Signolet J, Costello I, Gharbi S, Hendrich B - Development (2015)

Bottom Line: Embryos lacking CHD4 can form a morphologically normal early blastocyst, but are unable to successfully complete the first lineage decision and form functional trophectoderm (TE).We propose that CHD4 allows cells to undertake lineage commitment in vivo by modulating the frequency with which lineage-specification genes are expressed.This provides novel insight into both how lineage decisions are made in mammalian cells, and how a chromatin remodelling protein functions to facilitate lineage commitment.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.

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CHD4 limits gene expression prior to lineage commitment. (A) Heat map produced from hierarchical clustering of 16-cell expression data. Individual cells are listed from top to bottom, with a white box on the right indicating a wild-type (WT) cell and a black box indicating a Chd4−/− (KO) cell. Genes are listed across the bottom. The clustering algorithm produces two main groups of cells, labelled I and II, and three main groups of genes, labelled 1, 2 and 3. (B) Violin plots of expression data of Group 1, Group 2 and Group 3 genes (as shown in A) in wild-type (WT; blue) or mutant (KO; red) cells isolated from 8-cell (top) or 16-cell (bottom) embryos. The spot shows the mean and the vertical line shows the standard deviation. All P-values were calculated using a two-tailed Mann−Whitney test. (C) Model of how CHD4 is proposed to facilitate lineage commitment. Each large oval represents a cell, and the promoters for different lineage-specification genes are pictured. The genes pictured are either associated with a TE or ICM fate. A grey arrow indicates that the promoter is in a silent conformation, whereas the presence of RNA polymerase machinery (blue circles) and nascent RNA indicates an active conformation. In the wild-type situation (top), CHD4 acts to maintain nucleosome density across the promoters, such that binding by RNA polymerase is an infrequent event. In the absence of CHD4 (bottom), nucleosomes are positioned less densely, and transcription initiation is a much more frequent event. This results in the cell attempting to activate gene expression programmes for multiple lineages, and ultimately unsuccessful TE lineage commitment.
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DEV125450F5: CHD4 limits gene expression prior to lineage commitment. (A) Heat map produced from hierarchical clustering of 16-cell expression data. Individual cells are listed from top to bottom, with a white box on the right indicating a wild-type (WT) cell and a black box indicating a Chd4−/− (KO) cell. Genes are listed across the bottom. The clustering algorithm produces two main groups of cells, labelled I and II, and three main groups of genes, labelled 1, 2 and 3. (B) Violin plots of expression data of Group 1, Group 2 and Group 3 genes (as shown in A) in wild-type (WT; blue) or mutant (KO; red) cells isolated from 8-cell (top) or 16-cell (bottom) embryos. The spot shows the mean and the vertical line shows the standard deviation. All P-values were calculated using a two-tailed Mann−Whitney test. (C) Model of how CHD4 is proposed to facilitate lineage commitment. Each large oval represents a cell, and the promoters for different lineage-specification genes are pictured. The genes pictured are either associated with a TE or ICM fate. A grey arrow indicates that the promoter is in a silent conformation, whereas the presence of RNA polymerase machinery (blue circles) and nascent RNA indicates an active conformation. In the wild-type situation (top), CHD4 acts to maintain nucleosome density across the promoters, such that binding by RNA polymerase is an infrequent event. In the absence of CHD4 (bottom), nucleosomes are positioned less densely, and transcription initiation is a much more frequent event. This results in the cell attempting to activate gene expression programmes for multiple lineages, and ultimately unsuccessful TE lineage commitment.

Mentions: We next looked at 16-cell embryo data to see what influence CHD4 has upon gene expression prior to TE specification. Hierarchical clustering of the 16-cell expression data splits the genes assayed into three broad groups (Fig. 5A). Genes in Group 1, including housekeeping genes, Pou5f1, Gata6 and Tead4, are expressed in nearly all cells, whereas Group 2 genes include later lineage markers, such as Sox17, Dppa1 and Esrrb, and are expressed only rarely in 16-cell embryos. Group 3 genes include lineage markers, such as Cdx2, Gata4, Sox2 and Klf4, but show a less consistent expression pattern than do Group 1 or 2 genes, in that they are expressed in some cells but not others (Fig. 5A).Fig. 5.


Constraint of gene expression by the chromatin remodelling protein CHD4 facilitates lineage specification.

O'Shaughnessy-Kirwan A, Signolet J, Costello I, Gharbi S, Hendrich B - Development (2015)

CHD4 limits gene expression prior to lineage commitment. (A) Heat map produced from hierarchical clustering of 16-cell expression data. Individual cells are listed from top to bottom, with a white box on the right indicating a wild-type (WT) cell and a black box indicating a Chd4−/− (KO) cell. Genes are listed across the bottom. The clustering algorithm produces two main groups of cells, labelled I and II, and three main groups of genes, labelled 1, 2 and 3. (B) Violin plots of expression data of Group 1, Group 2 and Group 3 genes (as shown in A) in wild-type (WT; blue) or mutant (KO; red) cells isolated from 8-cell (top) or 16-cell (bottom) embryos. The spot shows the mean and the vertical line shows the standard deviation. All P-values were calculated using a two-tailed Mann−Whitney test. (C) Model of how CHD4 is proposed to facilitate lineage commitment. Each large oval represents a cell, and the promoters for different lineage-specification genes are pictured. The genes pictured are either associated with a TE or ICM fate. A grey arrow indicates that the promoter is in a silent conformation, whereas the presence of RNA polymerase machinery (blue circles) and nascent RNA indicates an active conformation. In the wild-type situation (top), CHD4 acts to maintain nucleosome density across the promoters, such that binding by RNA polymerase is an infrequent event. In the absence of CHD4 (bottom), nucleosomes are positioned less densely, and transcription initiation is a much more frequent event. This results in the cell attempting to activate gene expression programmes for multiple lineages, and ultimately unsuccessful TE lineage commitment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4529036&req=5

DEV125450F5: CHD4 limits gene expression prior to lineage commitment. (A) Heat map produced from hierarchical clustering of 16-cell expression data. Individual cells are listed from top to bottom, with a white box on the right indicating a wild-type (WT) cell and a black box indicating a Chd4−/− (KO) cell. Genes are listed across the bottom. The clustering algorithm produces two main groups of cells, labelled I and II, and three main groups of genes, labelled 1, 2 and 3. (B) Violin plots of expression data of Group 1, Group 2 and Group 3 genes (as shown in A) in wild-type (WT; blue) or mutant (KO; red) cells isolated from 8-cell (top) or 16-cell (bottom) embryos. The spot shows the mean and the vertical line shows the standard deviation. All P-values were calculated using a two-tailed Mann−Whitney test. (C) Model of how CHD4 is proposed to facilitate lineage commitment. Each large oval represents a cell, and the promoters for different lineage-specification genes are pictured. The genes pictured are either associated with a TE or ICM fate. A grey arrow indicates that the promoter is in a silent conformation, whereas the presence of RNA polymerase machinery (blue circles) and nascent RNA indicates an active conformation. In the wild-type situation (top), CHD4 acts to maintain nucleosome density across the promoters, such that binding by RNA polymerase is an infrequent event. In the absence of CHD4 (bottom), nucleosomes are positioned less densely, and transcription initiation is a much more frequent event. This results in the cell attempting to activate gene expression programmes for multiple lineages, and ultimately unsuccessful TE lineage commitment.
Mentions: We next looked at 16-cell embryo data to see what influence CHD4 has upon gene expression prior to TE specification. Hierarchical clustering of the 16-cell expression data splits the genes assayed into three broad groups (Fig. 5A). Genes in Group 1, including housekeeping genes, Pou5f1, Gata6 and Tead4, are expressed in nearly all cells, whereas Group 2 genes include later lineage markers, such as Sox17, Dppa1 and Esrrb, and are expressed only rarely in 16-cell embryos. Group 3 genes include lineage markers, such as Cdx2, Gata4, Sox2 and Klf4, but show a less consistent expression pattern than do Group 1 or 2 genes, in that they are expressed in some cells but not others (Fig. 5A).Fig. 5.

Bottom Line: Embryos lacking CHD4 can form a morphologically normal early blastocyst, but are unable to successfully complete the first lineage decision and form functional trophectoderm (TE).We propose that CHD4 allows cells to undertake lineage commitment in vivo by modulating the frequency with which lineage-specification genes are expressed.This provides novel insight into both how lineage decisions are made in mammalian cells, and how a chromatin remodelling protein functions to facilitate lineage commitment.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.

Show MeSH
Related in: MedlinePlus