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Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome.

Libertini E, Lebreton A, Lakisic G, Dillies MA, Beck S, Coppée JY, Cossart P, Bierne H - Front Genet (2015)

Bottom Line: We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed "BAHD1-DMRs"), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX).We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains.Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.

View Article: PubMed Central - PubMed

Affiliation: Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur Paris, France ; Medical Genomics Group, UCL Cancer Institute, University College London London, UK.

ABSTRACT
BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT) to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1). We show that increasing BAHD1 levels induces de novo DNA methylation on autosomes and a marked hypomethylation on the X chromosome (chrX). We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed "BAHD1-DMRs"), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX). Autosomal BAHD1-DMRs were predominantly hypermethylated and located to satellites, interspersed repeats, and intergenic regions. In contrast, BAHD1-DMRs on chrX were mainly hypomethylated and located to gene bodies and enhancers. We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains. Half of these "BAHD1-Associated differentially methylated Domains" (BADs) overlapped with lamina-associated domains (LADs). Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.

No MeSH data available.


Related in: MedlinePlus

BAHD1-specific domains (BADs). Large-scale genomic organization of DMRs present in HEK-BAHD1 cells in comparison to HEK-CT cells is illustrated for an autosome (chr6) and for chrX. Scale indicates the number of DMRs per 0.5 Mb window. Bars represent clusters of DMRs with gain of methylation (hyper-DMRs, in red) or loss of methylation (hypo-DMRs, in blue). BADs (indicated by black boxes) correspond to contiguous domains of DMR clusters where DMR counts are in the top quartile of the genome-wide DMR distribution. The position of genes is shown below. (A) Chromosome-wide representation of hypermethylation and hypomethylation domains on chr6 (top) and chrX (bottom). Arrows indicate the position of pericentromeric regions. (B) Magnification of the domain squared in A, with a chr6 hypermethylation domain (left) and a chrX hypomethylation domain (right). The position of DMRs in introns and enhancers is shown below.
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Figure 5: BAHD1-specific domains (BADs). Large-scale genomic organization of DMRs present in HEK-BAHD1 cells in comparison to HEK-CT cells is illustrated for an autosome (chr6) and for chrX. Scale indicates the number of DMRs per 0.5 Mb window. Bars represent clusters of DMRs with gain of methylation (hyper-DMRs, in red) or loss of methylation (hypo-DMRs, in blue). BADs (indicated by black boxes) correspond to contiguous domains of DMR clusters where DMR counts are in the top quartile of the genome-wide DMR distribution. The position of genes is shown below. (A) Chromosome-wide representation of hypermethylation and hypomethylation domains on chr6 (top) and chrX (bottom). Arrows indicate the position of pericentromeric regions. (B) Magnification of the domain squared in A, with a chr6 hypermethylation domain (left) and a chrX hypomethylation domain (right). The position of DMRs in introns and enhancers is shown below.

Mentions: We previously noticed that high-level overexpression of BAHD1 from a plasmid in HEK293 cells triggers massive compaction of chromatin visible when observed in electron microscopy (Bierne et al., 2009). We hypothesized that BAHD1-mediated heterochromatinization might spread and that this event might coincide with BAHD1-associated DNA methylation changes on large regions. To address this hypothesis, the overall genomic distribution of BAHD1-DMRs was examined at a higher scale by binning DMRs into 0.5 Mb windows (i.e., “BAHD1-DMR clusters”). This analysis revealed that BAHD1-DMRs were non-uniformly distributed along the whole human genome (Figure 4). In order to refine the mapping of regions with high density of DMRs, we defined contiguous domains in DMR clusters where the DMR counts were in the top quartile of the genome-wide DMR distribution. Examples of such “BAHD1–Associated differentially methylated Domains” (BADs) are shown in Figure 5, for chr6 and chrX. Overall, we found 839 BADs with sizes of 0.3–6.5 Mb (median 0.5 Mb), mostly hypermethylated in autosomes (792 “hyper-BADs”) and hypomethylated in chrX (26 “hypo-BADs”).


Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome.

Libertini E, Lebreton A, Lakisic G, Dillies MA, Beck S, Coppée JY, Cossart P, Bierne H - Front Genet (2015)

BAHD1-specific domains (BADs). Large-scale genomic organization of DMRs present in HEK-BAHD1 cells in comparison to HEK-CT cells is illustrated for an autosome (chr6) and for chrX. Scale indicates the number of DMRs per 0.5 Mb window. Bars represent clusters of DMRs with gain of methylation (hyper-DMRs, in red) or loss of methylation (hypo-DMRs, in blue). BADs (indicated by black boxes) correspond to contiguous domains of DMR clusters where DMR counts are in the top quartile of the genome-wide DMR distribution. The position of genes is shown below. (A) Chromosome-wide representation of hypermethylation and hypomethylation domains on chr6 (top) and chrX (bottom). Arrows indicate the position of pericentromeric regions. (B) Magnification of the domain squared in A, with a chr6 hypermethylation domain (left) and a chrX hypomethylation domain (right). The position of DMRs in introns and enhancers is shown below.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664705&req=5

Figure 5: BAHD1-specific domains (BADs). Large-scale genomic organization of DMRs present in HEK-BAHD1 cells in comparison to HEK-CT cells is illustrated for an autosome (chr6) and for chrX. Scale indicates the number of DMRs per 0.5 Mb window. Bars represent clusters of DMRs with gain of methylation (hyper-DMRs, in red) or loss of methylation (hypo-DMRs, in blue). BADs (indicated by black boxes) correspond to contiguous domains of DMR clusters where DMR counts are in the top quartile of the genome-wide DMR distribution. The position of genes is shown below. (A) Chromosome-wide representation of hypermethylation and hypomethylation domains on chr6 (top) and chrX (bottom). Arrows indicate the position of pericentromeric regions. (B) Magnification of the domain squared in A, with a chr6 hypermethylation domain (left) and a chrX hypomethylation domain (right). The position of DMRs in introns and enhancers is shown below.
Mentions: We previously noticed that high-level overexpression of BAHD1 from a plasmid in HEK293 cells triggers massive compaction of chromatin visible when observed in electron microscopy (Bierne et al., 2009). We hypothesized that BAHD1-mediated heterochromatinization might spread and that this event might coincide with BAHD1-associated DNA methylation changes on large regions. To address this hypothesis, the overall genomic distribution of BAHD1-DMRs was examined at a higher scale by binning DMRs into 0.5 Mb windows (i.e., “BAHD1-DMR clusters”). This analysis revealed that BAHD1-DMRs were non-uniformly distributed along the whole human genome (Figure 4). In order to refine the mapping of regions with high density of DMRs, we defined contiguous domains in DMR clusters where the DMR counts were in the top quartile of the genome-wide DMR distribution. Examples of such “BAHD1–Associated differentially methylated Domains” (BADs) are shown in Figure 5, for chr6 and chrX. Overall, we found 839 BADs with sizes of 0.3–6.5 Mb (median 0.5 Mb), mostly hypermethylated in autosomes (792 “hyper-BADs”) and hypomethylated in chrX (26 “hypo-BADs”).

Bottom Line: We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed "BAHD1-DMRs"), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX).We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains.Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.

View Article: PubMed Central - PubMed

Affiliation: Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur Paris, France ; Medical Genomics Group, UCL Cancer Institute, University College London London, UK.

ABSTRACT
BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT) to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1). We show that increasing BAHD1 levels induces de novo DNA methylation on autosomes and a marked hypomethylation on the X chromosome (chrX). We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed "BAHD1-DMRs"), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX). Autosomal BAHD1-DMRs were predominantly hypermethylated and located to satellites, interspersed repeats, and intergenic regions. In contrast, BAHD1-DMRs on chrX were mainly hypomethylated and located to gene bodies and enhancers. We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains. Half of these "BAHD1-Associated differentially methylated Domains" (BADs) overlapped with lamina-associated domains (LADs). Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.

No MeSH data available.


Related in: MedlinePlus