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Effects of HMGN variants on the cellular transcription profile.

Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M - Nucleic Acids Res. (2011)

Bottom Line: Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation.Analysis of point and swap HMGN mutants revealed that the transcriptional specificity is determined by a unique combination of a functional nucleosome-binding domain and C-terminal domain.The results reveal an HMGN-variant-specific effect on the fidelity of the cellular transcription profile, indicating that functionally the various HMGN subtypes are not fully redundant.

View Article: PubMed Central - PubMed

Affiliation: Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

ABSTRACT
High mobility group N (HMGN) is a family of intrinsically disordered nuclear proteins that bind to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here, we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. We find that both up- and downregulation of HMGN expression altered the cellular transcription profile. Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation. Analysis of point and swap HMGN mutants revealed that the transcriptional specificity is determined by a unique combination of a functional nucleosome-binding domain and C-terminal domain. Doubling the amount of HMGN had a significantly larger effect on the transcription profile than total deletion, suggesting that the intrinsically disordered structure of HMGN proteins plays an important role in their function. The results reveal an HMGN-variant-specific effect on the fidelity of the cellular transcription profile, indicating that functionally the various HMGN subtypes are not fully redundant.

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Effects of HMGNs knock out on transcription in primary MEFs. (A) Venn diagrams of down- and upregulated genes in primary MEFs. (B) GO analysis of affected genes (P <0.05).
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Figure 2: Effects of HMGNs knock out on transcription in primary MEFs. (A) Venn diagrams of down- and upregulated genes in primary MEFs. (B) GO analysis of affected genes (P <0.05).

Mentions: To investigate the transcriptional specificity of HMGN variants we first analyzed the transcriptional profile of primary MEFs isolated form Hmgn1−/−, Hmgn3−/− and Hmgn5−/− mice using mouse 430.2 Affymetrix expression arrays. Hmgn2−/− are not available because these mice are embryonic lethal (M.B. unpublished data). The results reveal variant-specific changes in gene expression profile; no overlap was observed for the genes affected by the knockout of different HMGN variants (Figure 2A). The changes involved both up- and downregulation of transcript levels, a finding that is fully compatible with the notion that HMGNs enhance transcriptional fidelity by affecting chromatin structure and optimizing the fidelity of transcription. Even though transcription of a relatively small number of genes was affected, Gene Ontology (GO) analysis revealed significant enrichment in a few non-overlapping pathways for Hmgn1−/−, Hmgn3−/− MEFs (Figure 2B). These results are in agreement with our previous observations that the phenotypes of Hmgn1−/− and Hmgn3−/− mice are distinct but not severe (19,49).Figure 2.


Effects of HMGN variants on the cellular transcription profile.

Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M - Nucleic Acids Res. (2011)

Effects of HMGNs knock out on transcription in primary MEFs. (A) Venn diagrams of down- and upregulated genes in primary MEFs. (B) GO analysis of affected genes (P <0.05).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105402&req=5

Figure 2: Effects of HMGNs knock out on transcription in primary MEFs. (A) Venn diagrams of down- and upregulated genes in primary MEFs. (B) GO analysis of affected genes (P <0.05).
Mentions: To investigate the transcriptional specificity of HMGN variants we first analyzed the transcriptional profile of primary MEFs isolated form Hmgn1−/−, Hmgn3−/− and Hmgn5−/− mice using mouse 430.2 Affymetrix expression arrays. Hmgn2−/− are not available because these mice are embryonic lethal (M.B. unpublished data). The results reveal variant-specific changes in gene expression profile; no overlap was observed for the genes affected by the knockout of different HMGN variants (Figure 2A). The changes involved both up- and downregulation of transcript levels, a finding that is fully compatible with the notion that HMGNs enhance transcriptional fidelity by affecting chromatin structure and optimizing the fidelity of transcription. Even though transcription of a relatively small number of genes was affected, Gene Ontology (GO) analysis revealed significant enrichment in a few non-overlapping pathways for Hmgn1−/−, Hmgn3−/− MEFs (Figure 2B). These results are in agreement with our previous observations that the phenotypes of Hmgn1−/− and Hmgn3−/− mice are distinct but not severe (19,49).Figure 2.

Bottom Line: Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation.Analysis of point and swap HMGN mutants revealed that the transcriptional specificity is determined by a unique combination of a functional nucleosome-binding domain and C-terminal domain.The results reveal an HMGN-variant-specific effect on the fidelity of the cellular transcription profile, indicating that functionally the various HMGN subtypes are not fully redundant.

View Article: PubMed Central - PubMed

Affiliation: Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

ABSTRACT
High mobility group N (HMGN) is a family of intrinsically disordered nuclear proteins that bind to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here, we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. We find that both up- and downregulation of HMGN expression altered the cellular transcription profile. Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation. Analysis of point and swap HMGN mutants revealed that the transcriptional specificity is determined by a unique combination of a functional nucleosome-binding domain and C-terminal domain. Doubling the amount of HMGN had a significantly larger effect on the transcription profile than total deletion, suggesting that the intrinsically disordered structure of HMGN proteins plays an important role in their function. The results reveal an HMGN-variant-specific effect on the fidelity of the cellular transcription profile, indicating that functionally the various HMGN subtypes are not fully redundant.

Show MeSH