Exercise 10.5 - Extraction and Electrophoresis of Histones

LEVEL II

Materials

• Saline Citrate (1/10 SSC)
  
• 1.0 N HSO
  
• Refrigerated preparative centrifuge
  
• Absolute ethanol
  
• -mercaptoethanol
  
• 0.01 M Sodium phosphate buffer, pH 7.0 + 1% (w/v) SDS + 0.1% (v/v) -mercaptoethanol
  
• 10% acrylamide gels (10%T:5%C) with 0.1% (w/v) SDS
  
• 7% (w/v) Acetic acid
  
• 0.25% Coomasie blue

Procedure 5

1. Dissolve crude chromatin in cold dilute saline citrate (0.015 M NaCl + 0.001 M Sodium Citrate) to a final DNA concentration of 500 µg/ml.

2. Stir the solution on ice and slowly add 1/4 volume of cold 1.0 N HSO. Continue stirring for 30 minutes.

3. Centrifuge the suspension at 12,000 xg for 20 minutes at 4° C. Save the supernatant. For maximum yield, break up the pellet, resuspend in fresh, cold 0.4 N HSO, re-extract, centrifuge, and add the resulting supernatant to the first.

4. Add 4 volumes of cold absolute ethanol to the supernatant and store for 24 hours at -10° C to precipitate the histone-sulfates.

5. Collect the precipitate by centrifugation at 2,000 xg for 30 minutes.

6. Decant as much of the alcohol as possible, and resuspend the pellet in cold absolute ethanol.

7. Centrifuge at 10,000 xg for 15 minutes.

8. Collect the pellet and freeze dry for later analysis.
   To continue with the electrophoresis, carefully weigh the histone protein sample and dissolve in 0.01 M sodium phosphate buffer, with a pH 7.0 and containing 1% sodium dodecyl sulfate and 0.1% -mercaptoethanol; final volume should contain approximately 300 µg of protein in 100 µl of buffer.

9. Prepare the electrophoresis chamber with a 10% acrylamide gel with 0.1% SDS.

10. Add separately 25 µl of the dissolved protein and 25 µl of protein standards to:
    50 µl of 0.1% SDS, 0.1% -mercaptoethanol in Buffer
    5 µl of -mercaptoethanol
    1 µl of 0.1% bromophenol blue in water

11. Mix thoroughly and apply the histone extract and protein standards to separate wells of the electrophoresis gel.

12. Separate the proteins in the anode direction (Anionic system). 6
    • The addition of SDS anions to the proteins results in negatively charged proteins which will separate according to molecular weight.

    • Electrophoresis is carried out in the standard manner following the basic steps given in Chapter Four. The buffer utilized is that of Laemmli, 7 0.025 M Tris-0.192 Glycine and 0.1% SDS, pH 8.3.

    • Proteins are separated by a current of 3-4 mA per gel until the bromophenol marker reaches the bottom of the tube (about 7 hours at 3 mA, and 4 hours at 4 mA).

13. Stain the gels with 0.25% Coomasie Blue for 2 hours.

14. Destain and store in 7% acetic acid.

15. Scan the gels and determine the molecular weights of each component.

Notes

Preparation of a total histone fraction from nuclei is normally accomplished by extraction with a dilute acid or a high molarity salt solution. The acidic extraction removes histones from DNA and non-histones immediately, while the dissociation of chromatin in salt solutions will require further purification. In either event, the histones themselves are subdivided into five major types, designated as H1, H2, H3, H4 and H5. H2 dissociates into two peptides, which are thus designated as H2A and H2B. The classification of histones is based on their electrophoretic mobility.

Non-histone proteins can also be extracted and separated by electrophoresis. Whereas histones have only 5 major types, non- histones are extremely heterogeneous and up to 500 different proteins have been identified from one cell type, while the major proteins comprise less than 20 types.

The extraction of chromatin DNA was possible with the 7 M urea - 3 M NaCl extraction performed in Exercise 10.4. Further analysis of DNA will be undertaken as part of a later lab exercise (on Transcription), and the DNA sample from this lab may be kept lyophilized and frozen until that time.

For our current needs it is sufficient to note that the genes are composed of DNA, and that various specific regions of the DNA/Genetic information can be physically isolated to a specific locus on a chromosome. This in turn is readily observed and correlated with banding patterns, such as those in the fruit fly poltytene chromosomes.

Return to Table of Contents