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Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro

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ABSTRACT

Background: The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development.

Methods: In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC.

Results: We observed significant local and global developmental changes despite high levels of correlation between the myotubes and myoblast genomes. Notably, the genes that exhibited the greatest variation in transcript levels between the different developmental stages were predominately within the euchromatic compartment. There was significant re-structuring and changes in the expression of replication-dependent histone variants within the HIST1 locus. Finally, treating terminally differentiated myotubes with AraC resulted in additional changes to the transcriptome and 3D genome organization of sets of genes that were all involved in pyroptosis.

Conclusions: Collectively, our results provide evidence for muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism.

Electronic supplementary material: The online version of this article (doi:10.1186/s13395-017-0122-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Switches between the A and B compartments were observed in pairwise comparisons between the cell populations. a The PC1 values defined using the Hi-C correlation matrices of the three conditions for chr 7 are plotted on the UCSC genome browser. Examples of local changes in the PC1 values between the three conditions are marked with red arrows. b Myogenesis is accompanied by significant changes in chromosome topology evident from the fact that 25% of the genome changed compartment status in at least one of the conditions. Comparisons are done only for bins which have detectable PC1 values in the three conditions (6284 bins in total). c Genes which changed from residing in A compartment to B compartment reduced their average expression levels, whereas genes which changed from residing in B compartment to A compartment increased their average expression levels for myotube-myoblast and AraC-treated myotube-myoblast comparisons. (p values by Wilcoxon test, outliers not plotted). Genes which have expression change of 0 are excluded from the analyses
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Fig2: Switches between the A and B compartments were observed in pairwise comparisons between the cell populations. a The PC1 values defined using the Hi-C correlation matrices of the three conditions for chr 7 are plotted on the UCSC genome browser. Examples of local changes in the PC1 values between the three conditions are marked with red arrows. b Myogenesis is accompanied by significant changes in chromosome topology evident from the fact that 25% of the genome changed compartment status in at least one of the conditions. Comparisons are done only for bins which have detectable PC1 values in the three conditions (6284 bins in total). c Genes which changed from residing in A compartment to B compartment reduced their average expression levels, whereas genes which changed from residing in B compartment to A compartment increased their average expression levels for myotube-myoblast and AraC-treated myotube-myoblast comparisons. (p values by Wilcoxon test, outliers not plotted). Genes which have expression change of 0 are excluded from the analyses

Mentions: We evaluated the degree of plasticity of the A and B compartments during myotube development and found that 8% of the genome changed compartment residence (Fig. 2a, b; Additional file 9). Switching from an A to B compartment during differentiation was significantly correlated (p < 0.001) with a decrease in gene expression levels (Fig. 2c), consistent with previously published observations in mammalian cells during cell differentiation [38, 42] or de-differentiation [65, 66]. However, while relocating from the B to A compartment was generally associated with an increase in expression, this was only significant in comparisons between the AraC-treated myotubes and myoblasts (Fig. 2c). Notably, changes between A and B compartments did not correlate with changes in expression levels, on the global scale, for comparisons between the AraC-treated myotubes and myotubes (Fig. 2c). Critically, the relative compartment changes between the AraC-treated myotubes and myotubes were similar to those observed when these cells were compared to myoblasts (Fig. 2b). Moreover, 2126 genes were significantly differentially expressed between these cell stages despite their gross phenotypic similarity (Fig. 1). Thus, these results indicate that localization within a particular compartment (i.e. A or B; eu- or heterochromatin) does not automatically dictate expression levels.Fig. 2


Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro
Switches between the A and B compartments were observed in pairwise comparisons between the cell populations. a The PC1 values defined using the Hi-C correlation matrices of the three conditions for chr 7 are plotted on the UCSC genome browser. Examples of local changes in the PC1 values between the three conditions are marked with red arrows. b Myogenesis is accompanied by significant changes in chromosome topology evident from the fact that 25% of the genome changed compartment status in at least one of the conditions. Comparisons are done only for bins which have detectable PC1 values in the three conditions (6284 bins in total). c Genes which changed from residing in A compartment to B compartment reduced their average expression levels, whereas genes which changed from residing in B compartment to A compartment increased their average expression levels for myotube-myoblast and AraC-treated myotube-myoblast comparisons. (p values by Wilcoxon test, outliers not plotted). Genes which have expression change of 0 are excluded from the analyses
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig2: Switches between the A and B compartments were observed in pairwise comparisons between the cell populations. a The PC1 values defined using the Hi-C correlation matrices of the three conditions for chr 7 are plotted on the UCSC genome browser. Examples of local changes in the PC1 values between the three conditions are marked with red arrows. b Myogenesis is accompanied by significant changes in chromosome topology evident from the fact that 25% of the genome changed compartment status in at least one of the conditions. Comparisons are done only for bins which have detectable PC1 values in the three conditions (6284 bins in total). c Genes which changed from residing in A compartment to B compartment reduced their average expression levels, whereas genes which changed from residing in B compartment to A compartment increased their average expression levels for myotube-myoblast and AraC-treated myotube-myoblast comparisons. (p values by Wilcoxon test, outliers not plotted). Genes which have expression change of 0 are excluded from the analyses
Mentions: We evaluated the degree of plasticity of the A and B compartments during myotube development and found that 8% of the genome changed compartment residence (Fig. 2a, b; Additional file 9). Switching from an A to B compartment during differentiation was significantly correlated (p < 0.001) with a decrease in gene expression levels (Fig. 2c), consistent with previously published observations in mammalian cells during cell differentiation [38, 42] or de-differentiation [65, 66]. However, while relocating from the B to A compartment was generally associated with an increase in expression, this was only significant in comparisons between the AraC-treated myotubes and myoblasts (Fig. 2c). Notably, changes between A and B compartments did not correlate with changes in expression levels, on the global scale, for comparisons between the AraC-treated myotubes and myotubes (Fig. 2c). Critically, the relative compartment changes between the AraC-treated myotubes and myotubes were similar to those observed when these cells were compared to myoblasts (Fig. 2b). Moreover, 2126 genes were significantly differentially expressed between these cell stages despite their gross phenotypic similarity (Fig. 1). Thus, these results indicate that localization within a particular compartment (i.e. A or B; eu- or heterochromatin) does not automatically dictate expression levels.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Background: The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development.

Methods: In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC.

Results: We observed significant local and global developmental changes despite high levels of correlation between the myotubes and myoblast genomes. Notably, the genes that exhibited the greatest variation in transcript levels between the different developmental stages were predominately within the euchromatic compartment. There was significant re-structuring and changes in the expression of replication-dependent histone variants within the HIST1 locus. Finally, treating terminally differentiated myotubes with AraC resulted in additional changes to the transcriptome and 3D genome organization of sets of genes that were all involved in pyroptosis.

Conclusions: Collectively, our results provide evidence for muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism.

Electronic supplementary material: The online version of this article (doi:10.1186/s13395-017-0122-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus