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Monoallelic expression of multiple genes in the CNS.

Wang J, Valo Z, Smith D, Singer-Sam J - PLoS ONE (2007)

Bottom Line: We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS.Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci.Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America.

ABSTRACT
The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F(1) (C57BL/6xJF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

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Region of mouse Chr 7 assayed and summary of results.Upper line. The location in Mb of the PWS/AS locus is shown by the turquoise bar, and that of the OlfR clusters by the green bars. Lower line. The location of genes assayed for allele-specific expression is shown. Monoallelically expressed genes are indicated by red triangles; bi-allelically expressed genes by vertical lines (see text).
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pone-0001293-g002: Region of mouse Chr 7 assayed and summary of results.Upper line. The location in Mb of the PWS/AS locus is shown by the turquoise bar, and that of the OlfR clusters by the green bars. Lower line. The location of genes assayed for allele-specific expression is shown. Monoallelically expressed genes are indicated by red triangles; bi-allelically expressed genes by vertical lines (see text).

Mentions: We analyzed the 65 Mb portion of mouse Chr 7 shown in Figure 2, utilizing tiling arrays containing probes for all non-repetitive DNA at 100 bp intervals. While we examined only sequences in the vicinity of genes, we selected tiling arrays rather than promoter or GC-island arrays to include sequences that might be missed by a narrow definition of GC-rich regions or because of incomplete annotation of transcription start sites. For each gene, we scanned up to 16 kb of DNA surrounding the transcription start site(s) to include 8 kb of the 5′ region as well as the first exon and first intron.


Monoallelic expression of multiple genes in the CNS.

Wang J, Valo Z, Smith D, Singer-Sam J - PLoS ONE (2007)

Region of mouse Chr 7 assayed and summary of results.Upper line. The location in Mb of the PWS/AS locus is shown by the turquoise bar, and that of the OlfR clusters by the green bars. Lower line. The location of genes assayed for allele-specific expression is shown. Monoallelically expressed genes are indicated by red triangles; bi-allelically expressed genes by vertical lines (see text).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2100171&req=5

pone-0001293-g002: Region of mouse Chr 7 assayed and summary of results.Upper line. The location in Mb of the PWS/AS locus is shown by the turquoise bar, and that of the OlfR clusters by the green bars. Lower line. The location of genes assayed for allele-specific expression is shown. Monoallelically expressed genes are indicated by red triangles; bi-allelically expressed genes by vertical lines (see text).
Mentions: We analyzed the 65 Mb portion of mouse Chr 7 shown in Figure 2, utilizing tiling arrays containing probes for all non-repetitive DNA at 100 bp intervals. While we examined only sequences in the vicinity of genes, we selected tiling arrays rather than promoter or GC-island arrays to include sequences that might be missed by a narrow definition of GC-rich regions or because of incomplete annotation of transcription start sites. For each gene, we scanned up to 16 kb of DNA surrounding the transcription start site(s) to include 8 kb of the 5′ region as well as the first exon and first intron.

Bottom Line: We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS.Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci.Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America.

ABSTRACT
The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F(1) (C57BL/6xJF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

Show MeSH
Related in: MedlinePlus