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A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies.

Sun J, Li W, Sun Y, Yu D, Wen X, Wang H, Cui J, Wang G, Hoffman AR, Hu JF - Nucleic Acids Res. (2014)

Bottom Line: Using both reverse transcription-associated trap and chromatin conformation capture assays, we demonstrate that this lncRNA interacts with chromatin DNA and is involved in the formation of an intrachromosomal enhancer/promoter loop.In addition, IRAIN was downregulated both in leukemia cell lines and in blood obtained from high-risk AML patients.These data identify IRAIN as a new imprinted lncRNA that is involved in long-range DNA interactions.

View Article: PubMed Central - PubMed

Affiliation: Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.

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Epigenetic regulation of the IRF1R/IRAIN locus. (A) Schematic diagram of CpG islands in the IRAIN promoter. Vertical lines: location of CpG islands. (B) The status of CpG island DNA methylation in the IRAIN promoter. Genomic DNAs were extracted from leukemia cells and AML cells collected from three patients. After treatment with sodium bisulfite, the IRAIN promoter DNA was amplified and sequenced. Open circles: unmethylated CpGs; solid circles: methylated CpGs. (C) Allelic histone codes in the IRAIN promoter. Chromatin complex DNAs were pulled down by immunoprecipitation. After PCR, the two parental alleles were separated by polymorphic restriction enzyme BsaJ1 for histone methylation at H3K4, H3K9 and H3k27. Input: chromatin DNAs collected before antibody immunoprecipitation.
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Figure 3: Epigenetic regulation of the IRF1R/IRAIN locus. (A) Schematic diagram of CpG islands in the IRAIN promoter. Vertical lines: location of CpG islands. (B) The status of CpG island DNA methylation in the IRAIN promoter. Genomic DNAs were extracted from leukemia cells and AML cells collected from three patients. After treatment with sodium bisulfite, the IRAIN promoter DNA was amplified and sequenced. Open circles: unmethylated CpGs; solid circles: methylated CpGs. (C) Allelic histone codes in the IRAIN promoter. Chromatin complex DNAs were pulled down by immunoprecipitation. After PCR, the two parental alleles were separated by polymorphic restriction enzyme BsaJ1 for histone methylation at H3K4, H3K9 and H3k27. Input: chromatin DNAs collected before antibody immunoprecipitation.

Mentions: Imprinted genes are often regulated by differentially methylated regions (DMRs) in an imprinting control region (ICR) (26,47,48). As the IRAIN promoter is very rich in CpG dinucleotides (Figure 3A), we analyzed the status of DNA methylation in the IRAIN promoter. Genomic DNA was treated with sodium bisulfite to convert unmethylated cytosines into uracils while methylated cytosines are left unchanged. The treated DNA was amplified with methylation-specific primers, cloned in pJet vector and sequenced.


A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies.

Sun J, Li W, Sun Y, Yu D, Wen X, Wang H, Cui J, Wang G, Hoffman AR, Hu JF - Nucleic Acids Res. (2014)

Epigenetic regulation of the IRF1R/IRAIN locus. (A) Schematic diagram of CpG islands in the IRAIN promoter. Vertical lines: location of CpG islands. (B) The status of CpG island DNA methylation in the IRAIN promoter. Genomic DNAs were extracted from leukemia cells and AML cells collected from three patients. After treatment with sodium bisulfite, the IRAIN promoter DNA was amplified and sequenced. Open circles: unmethylated CpGs; solid circles: methylated CpGs. (C) Allelic histone codes in the IRAIN promoter. Chromatin complex DNAs were pulled down by immunoprecipitation. After PCR, the two parental alleles were separated by polymorphic restriction enzyme BsaJ1 for histone methylation at H3K4, H3K9 and H3k27. Input: chromatin DNAs collected before antibody immunoprecipitation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150754&req=5

Figure 3: Epigenetic regulation of the IRF1R/IRAIN locus. (A) Schematic diagram of CpG islands in the IRAIN promoter. Vertical lines: location of CpG islands. (B) The status of CpG island DNA methylation in the IRAIN promoter. Genomic DNAs were extracted from leukemia cells and AML cells collected from three patients. After treatment with sodium bisulfite, the IRAIN promoter DNA was amplified and sequenced. Open circles: unmethylated CpGs; solid circles: methylated CpGs. (C) Allelic histone codes in the IRAIN promoter. Chromatin complex DNAs were pulled down by immunoprecipitation. After PCR, the two parental alleles were separated by polymorphic restriction enzyme BsaJ1 for histone methylation at H3K4, H3K9 and H3k27. Input: chromatin DNAs collected before antibody immunoprecipitation.
Mentions: Imprinted genes are often regulated by differentially methylated regions (DMRs) in an imprinting control region (ICR) (26,47,48). As the IRAIN promoter is very rich in CpG dinucleotides (Figure 3A), we analyzed the status of DNA methylation in the IRAIN promoter. Genomic DNA was treated with sodium bisulfite to convert unmethylated cytosines into uracils while methylated cytosines are left unchanged. The treated DNA was amplified with methylation-specific primers, cloned in pJet vector and sequenced.

Bottom Line: Using both reverse transcription-associated trap and chromatin conformation capture assays, we demonstrate that this lncRNA interacts with chromatin DNA and is involved in the formation of an intrachromosomal enhancer/promoter loop.In addition, IRAIN was downregulated both in leukemia cell lines and in blood obtained from high-risk AML patients.These data identify IRAIN as a new imprinted lncRNA that is involved in long-range DNA interactions.

View Article: PubMed Central - PubMed

Affiliation: Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.

Show MeSH
Related in: MedlinePlus