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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 binding domains. (A) Large-scale genomic organization of BAHD1-binding sites (“occupancy domains”) upon induction of BAHD1 expression for 30 h in HPT-BAHD1 cells. Sequencing DNA from NChIP of Protein-C-tagged BAHD1 generated peaks that were clustered in 0.5 Mb windows (black bars). Results are shown for two autosomes (chr6, chr7) and chrX. Scale indicates the number of peaks per bar. (B) Overlap of BAHD1-DMR clusters and BAHD1-occupancy domains on chr6 (hypermethylated DMRs) and chrX (hypomethylated DMRs). The position of XIC and genes is indicated.
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Figure 6: BAHD1-specific binding domains. (A) Large-scale genomic organization of BAHD1-binding sites (“occupancy domains”) upon induction of BAHD1 expression for 30 h in HPT-BAHD1 cells. Sequencing DNA from NChIP of Protein-C-tagged BAHD1 generated peaks that were clustered in 0.5 Mb windows (black bars). Results are shown for two autosomes (chr6, chr7) and chrX. Scale indicates the number of peaks per bar. (B) Overlap of BAHD1-DMR clusters and BAHD1-occupancy domains on chr6 (hypermethylated DMRs) and chrX (hypomethylated DMRs). The position of XIC and genes is indicated.

Mentions: Binning BAHD1-specific peaks into 0.5 Mb windows revealed that they clustered into larger regions, as BAHD1-DMRs. Examples of such “BAHD1–occupancy domains” are shown for chr6, chr7, and chrX on Figure 6A. Surprisingly, overlapping BAHD1–occupancy and–differentially methylated regions revealed a marked difference between autosomes and chrX. On autosomes, BAHD1-binding and–hypermethylated domains often overlapped or were adjacent. In contrast, on chrX, there was an inverse correlation between the location of BAHD1-binding and hypomethylated domains (Figure 6B). Furthermore, BAHD1-occupancy domains were more abundant on the long arm (Xq) than the short arm of chrX (Xp), particularly in the half part of Xq containing the X-inactivation center (XIC) on the Xi. Taken together, these data are in agreement with the hypothesis that BAHD1 plays distinct roles on chrX and autosomes and support a model in which BAHD1-mediated chromatin compaction coincides with binding of BAHD1 on large genomic regions.


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 binding domains. (A) Large-scale genomic organization of BAHD1-binding sites (“occupancy domains”) upon induction of BAHD1 expression for 30 h in HPT-BAHD1 cells. Sequencing DNA from NChIP of Protein-C-tagged BAHD1 generated peaks that were clustered in 0.5 Mb windows (black bars). Results are shown for two autosomes (chr6, chr7) and chrX. Scale indicates the number of peaks per bar. (B) Overlap of BAHD1-DMR clusters and BAHD1-occupancy domains on chr6 (hypermethylated DMRs) and chrX (hypomethylated DMRs). The position of XIC and genes is indicated.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: BAHD1-specific binding domains. (A) Large-scale genomic organization of BAHD1-binding sites (“occupancy domains”) upon induction of BAHD1 expression for 30 h in HPT-BAHD1 cells. Sequencing DNA from NChIP of Protein-C-tagged BAHD1 generated peaks that were clustered in 0.5 Mb windows (black bars). Results are shown for two autosomes (chr6, chr7) and chrX. Scale indicates the number of peaks per bar. (B) Overlap of BAHD1-DMR clusters and BAHD1-occupancy domains on chr6 (hypermethylated DMRs) and chrX (hypomethylated DMRs). The position of XIC and genes is indicated.
Mentions: Binning BAHD1-specific peaks into 0.5 Mb windows revealed that they clustered into larger regions, as BAHD1-DMRs. Examples of such “BAHD1–occupancy domains” are shown for chr6, chr7, and chrX on Figure 6A. Surprisingly, overlapping BAHD1–occupancy and–differentially methylated regions revealed a marked difference between autosomes and chrX. On autosomes, BAHD1-binding and–hypermethylated domains often overlapped or were adjacent. In contrast, on chrX, there was an inverse correlation between the location of BAHD1-binding and hypomethylated domains (Figure 6B). Furthermore, BAHD1-occupancy domains were more abundant on the long arm (Xq) than the short arm of chrX (Xp), particularly in the half part of Xq containing the X-inactivation center (XIC) on the Xi. Taken together, these data are in agreement with the hypothesis that BAHD1 plays distinct roles on chrX and autosomes and support a model in which BAHD1-mediated chromatin compaction coincides with binding of BAHD1 on large genomic regions.

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