Histone acetylation and heterochromatin content of cultured Peromyscus cells

Structural insights into the binding mechanism of Clr4 methyltransferase to H3K9 methylated nucleosome

The establishment and maintenance of heterochromatin, a specific chromatin structure essential for genomic stability and regulation, rely on intricate interactions between chromatin-modifying enzymes and nucleosomal histone proteins. However, the precise trigger for these modifications remains unclear, thus highlighting the need for a deeper understanding of how methyltransferases facilitate histone methylation among others. Here, we investigate the molecular mechanisms underlying heterochromatin assembly by studying the interaction between the H3K9 methyltransferase Clr4 and H3K9-methylated nucleosomes. Using a combination of liquid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy, we elucidate the structural basis of Clr4 binding to H3K9-methylated nucleosomes. Our results reveal that Clr4 engages with nucleosomes through its chromodomain and disordered regions to promote de novo methylation. This study provides crucial insights into the molecular mechanisms governing heterochromatin formation by highlighting the significance of chromatin-modifying enzymes in genome regulation and disease pathology.

Gene regulation and epigenetics in Friedreich's ataxia

This is an exciting time in the study of Friedreich's ataxia. Over the last 10 years much progress has been made in uncovering the mechanisms, whereby the Frataxin gene is silenced by (GAA)n repeat expansions and several of the findings are now ripe for testing in the clinic. The discovery that the Frataxin gene is heterochromatinised and that this can be antagonised in vivo has led to the tantalizing possibility that the disease might be amenable to a more radical therapeutic approach involving epigenetic modifiers. Here, we set out to review progress in the understanding of the fundamental mechanisms whereby genes are regulated at this level and how these findings have been applied to achieve a deeper understanding of the dysregulation that occurs as the primary genetic lesion in Friedreich's ataxia.

High-performance liquid chromatography of chromatin histones

A method is described for the rapid analysis of histones by high-performance liquid chromatography on reversed-phase muBondapak columns, containing either octadecylsilane (C18) or cyanopropylsilane (CN) bonded to silica particles packed in either steel columns or Radial-Pak cartridges. A linear gradient progressing from water-acetonitrile (80:20) to water-acetonitrile (40:60) and increasing in acetonitrile concentration at the rate of 10%/h was used to elute the histones at a flow-rate of 1 ml/min for steel columns or 2 ml/min for Radial-Pak cartridges. Two conditions were found to be necessary to achieve histone fractionation: (1) silylation of the active silanol groups on the silica matrix, and (2) 0.1-0.3% trifluoroacetic acid in the eluting solvent. More than 95% of the total [3H]lysine-labeled protein applied to the CN column was eluted. The histone fractions were identified by their electrophoretic mobilities in both acid-urea and Triton DF-16 polyacrylamide gels. Histones were eluted from the columns in the following order: H1, H2B, (LHP)H2A, (MHP)H2A, H4, (LHP)H3, and (MHP)H3 (where LHP and MHP refer to the less-hydrophobic and more-hydrophobic histone variants). Phosphorylated and acetylated histone molecules were not separated from their unmodified parent molecules. The volatile nature of the water-acetonitrile-trifluoroacetic acid eluting solvent facilitated recovery of salt-free histones from the fractions by direct lyophilization of the column effluents. The best resolution of histone fractions was obtained with the Radial-Pak muBondapak C18 cartridge using 0.3% TFA. However, for analytical studies, the best detection was obtained by using the muBondapak CN steel column. Poorer resolution was obtained by using the non-silica based PRP-1 reversed-phase column, containing a polystyrene-divinylbenzene resin under the same conditions.

Histone fractionation by high-performance liquid chromatography on cyanoalkysilane (CN) reverse-phase columns

Previous work in our laboratory [Gurley et al. Anal. Biochem. 129, 132-144 (1983)] described conditions for the rapid fractionation of histones by high-performance liquid chromatography (HPLC) using a reverse-phase muBondapak C18 column. That procedure resolved the major classes of histones with one exception: the more hydrophobic H2A variant, (MHP)H2A, was not resolved from the H4 histone class. This report extends that work describing experiments using a muBondapak CN column which better resolves the classes of histones from each other including the resolution of (MHP)H2A from the H4. In addition, the less hydrophobic H2A variant, (LHP)H2A, is partially resolved from the (MHP)H2A, and the less hydrophobic H3 variant, (LHP)H3, is resolved from the more hydrophobic H3 variant, (MHP)H3. Lower trifluoroacetic acid (TFA) concentrations (0.1%) in the eluting water/acetonitrile solvent were used with the CN column than were used with the C18 column which increased the sensitivity of histone detection by ultraviolet absorption at 206 nm. Greater than 95% of the total [3H]lysine-labeled protein applied to the CN column was eluted from the column. Contaminating nonhistone proteins were found to chromatograph in the region of histone elution. These were greatly reduced by isolating nuclei prior to histone preparation. The fractionation of the histones appears to be based on the hydrophobic properties of the proteins. The histone fractions (identified by their electrophoretic mobilities) were eluted from the CN column in the following order: H1, H2B, (LHP)H2A, (MHP)H2A, H4, (LHP)H3, and (MHP)H3. Phosphorylated and acetylated histone species were not resolved from their unmodified parental species.

Preferential alkaline phosphatase isoenzyme induction by sodium butyrate

SW-620, a continuous cell line derived from a poorly differentiated human colon carcinoma, produces two alkaline phosphatases. Under basal conditions the heat-stable, term-placental is the major isoenzyme and the heat-labile, liver/bone/kidney form represents a minor component. Exposing SW-620 cells to sodium butyrate causes induction of increased levels of activity accompanied by a striking shift in isoenzyme distribution not observed heretofore. The activity increase is accounted for entirely by augmentation of the liver/bone/kidney isoenzyme, with the term-placental form not being affected. Two other known alkaline phosphatase inducers, prednisolone and hyperosmolality, do not influence specific activity and isoenzyme distribution. The preferential induction of the liver/bone/kidney form of alkaline phosphatase in SW-620 cells may reflect a butyrate-elicited expression of a more differentiated state.

Histone fractionation by high-performance liquid chromatography

A method for the rapid chromatography of histones by high-performance liquid chromatography (HPLC) using a reverse-phase mu Bondapak C18 column containing a packing of octadecylsilane chemically bonded to silica and a linear elution gradient running from water to acetonitrile is described. Two conditions were found to be necessary to achieve histone fractionation: (i) silylation of the active groups of the silica solid support, and (ii) trifluoroacetic acid (TFA) in the eluting solvents. Greater than 90% of the total [3H]lysine-labeled protein applied to the column was eluted from the column. The fractionation of the histones appears to be based on the hydrophobic properties of the proteins. The HPLC histone fractions (identified by their electrophoretic mobilities) were eluted from the column in the following order: H1, H2B, (LHP)H2A, (MHP)H2A + H4, (LHP)H3, and (MHP)H3 (where LHP and MHP refer to the less hydrophobic and more hydrophobic histone variants). Phosphorylated histone species were not resolved from their unmodified parental species. The volatile nature of the water/acetonitrile/TFA eluting solvent facilitated the recovery of salt-free histones from the eluted HPLC fractions by simple lyophilization. This system is very useful for the rapid isolation of the lysine-rich histones, H1 and H2B, and the variants of histone H3. With further development, this system is expected to extend the advantages of HPLC to the fractionation of histone H4 and the variants of histone H2A as well.

Synergistic induction of alkaline phosphatase in colonic carcinoma cells by sodium butyrate and hyperosmolality

Exposing HT-29 cells to the combination of two inducers of intestinal alkaline phosphatase, sodium butyrate and hyperosmolality, causes a synergistic (over 1000-fold) increase in specific activity. Evidence is presented showing that enzyme induction is reversible; the half-life of the induced activity is approximately 30 h. Preinduction by butyrate or by hyperosmolality does not prime the cells so as to respond synergistically when subsequently exposed to hyperosmolality or butyrate, respectively. This study demonstrates that when applied in combination, the effect on gene expression by one alkaline phosphatase inducer is amplified by the other.