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HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [RNA-seq]

ABSTRACT: HMGN5 is a member of the HMGN family that de-compacts chromatin and regulates gene expression. Chromatin-associated RNAs are known to play a major role in controlling gene expression and chromatin architecture. We recently showed that RNA is required to open chromatin structure in Drosophila. A potential involvement of RNA in the HMGN5-dependent opening of chromatin has not been studied so far. Here we revealed that HMGN5 has a novel and specific RNA binding activity, which is extended to the HMGN family. HMGN5 is associated preferentially with active regulatory regions and binds co-transcriptionally to the nascent RNA. Additionally, we showed that HMGN5 co-localizes and interacts with CTCF, which suggests a cooperative role of both proteins in organizing higher order structures of chromatin. We showed that HMGN5 forms mutually exclusive complexes with chromatin and RNA in vitro, altogether suggesting a dual role for HMGN5 in gene regulation, switching from nucleosome to RNA binding during gene activation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE166091 | GEO | 2024/05/08

REPOSITORIES: GEO

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Project description:In most metazoan nuclei, heterochromatin is located at the nuclear periphery in contact with the nuclear lamina, which provides mechanical stability to the nucleus. We show that in cultured cells, chromatin de-compaction by the nucleosome binding protein HMGN5 decreases the sturdiness, elasticity, and rigidity of the nucleus. Mice overexpressing HMGN5, either globally or only in the heart, are normal at birth but develop hypertrophic heart with large cardiomyoctyes, deformed nuclei and disrupted lamina, and die of cardiac malfunction. Chromatin de-compaction is seen in cardiomyocytes of newborn mice but misshaped nuclei with disrupted lamina are seen only in adult cardiomyocytes, suggesting that loss of heterochromatin diminishes the ability of the nucleus to withstand the mechanical forces of the contracting heart. Thus, heterochromatin enhances the ability of the nuclear lamina to maintain the sturdiness and shape of the eukaryotic nucleus; a structural role for chromatin that is distinct from its genetic functions. The full length mouse Hmgn5 cDNA, containing the entire 5’ UTR and FLAG tag on the 3’ end was amplified by PCR and inserted between BglII and XhoI sites of the pCALL vector (Novak et al., 2000). This vector contains a floxed LacZ cDNA driven by the CAG (a hybrid CMV enhancer and chicken beta–actin) promoter which is highly active in early mouse embryos. The vector was linearized by NotI digestion and injected into fertilized oocytes of C57BL/6 mice. Total embryonic excision of LacZ sequence was done by breeding floxed HMGN5-TG mice with SoxCre mice (Hayashi et al., 2002). Heart-specific excision was performed by breeding floxed HMGN5-TG mice with alphaMHC-cre mice (Oka et al., 2006).Total RNA from the left ventricle of newborn and adult Hmgn5-hTG mice which overexpress HMGN5 only in the heart as well as control mice was collected from biological triplicates (duplicates, in the case of newborn wild-type mice) and analyzed by Affymetrix expression arrays.

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HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [RNA-seq]

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