Digestion of chromosomal proteins in formaldehyde treated chromatin

Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin

Epigenetic modifications of chromatin serve an important role in regulating the expression and accessibility of genomic DNA. We report here a genomewide approach for fractionating yeast chromatin into two functionally distinct parts, one containing RNA polymerase II transcribed sequences, and the other comprising noncoding sequences and genes transcribed by RNA polymerases I and III. Noncoding regions could be further fractionated into promoters and segments lacking promoters. The observed separations were apparently based on differential crosslinking efficiency of chromatin in different genomic regions. The results reveal a genomewide molecular mechanism for marking promoters and genomic regions that have a license to be transcribed by RNA polymerase II, a previously unrecognized level of genomic complexity that may exist in all eukaryotes. Our approach has broad potential use as a tool for genome annotation and for the characterization of global changes in chromatin structure that accompany different genetic, environmental, and disease states.

Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking

By using formaldehyde cross-linking of histones to DNA and gel retardation assays we show that formaldehyde fixation, similar to previously established psoralen photocross-linking, discriminates between nucleosome- packed (inactive) and nucleosome-free (active) fractions of ribosomal RNA genes. By both cross-linking techniques we were able to purify fragments from agarose gels, corresponding to coding, enhancer and promoter sequences of rRNA genes, which were further investigated with respect to DNA methylation. This approach allows us to analyse independently and in detail methylation patterns of active and inactive rRNA gene copies by the combination of Hpa II and Msp I restriction enzymes. We found CpG methylation mainly present in enhancer and promoter regions of inactive rRNA gene copies. The methylation of one single Hpa II site, located in the promoter region, showed particularly strong correlation with the transcriptional activity.

Analysis of protamines isolated from alcohol preserved epididymides

Protamines 1 and 2 have been isolated from the sperm of frozen and isopropanol preserved Syrian hamster (Mesocricetus auratus) epididymides and analyzed by gel electrophoresis, high-performance liquid chromatography (HPLC), and amino acid analysis and sequencing. The results show that alcohol preservation does not alter the primary structure of the two sperm nuclear proteins and that the preservation of mammalian reproductive organs in alcohol is a viable alternative to freezing tissues collected in the field. Sperm were isolated from tissues fixed in isopropanol for as long as 7 months without detectable adverse effects on either the isolation of sperm or the primary structure of the protamines.

Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures

Formaldehyde (HCHO) produces DNA-protein crosslinks both in vitro and in vivo. Simian virus 40 (SV40) chromosomes that have been fixed by prolonged incubation with HCHO either in vitro or in vivo (within SV40-infected cells) can be converted to nearly protein-free DNA by limit-digestion with Pronase in the presence of NaDodSO4. The remaining Pronase-resistant DNA-peptide adducts retard the DNA upon gel electrophoresis, allowing resolution of free and crosslink-containing DNA. Though efficiently crosslinking histones to DNA within nucleosomes both in vitro and in vivo, HCHO does not crosslink either purified lac repressor to lac operator-containing DNA or an (A + T)-DNA-binding protein (alpha-protein) to its cognate DNA in vitro. Furthermore, a protein that does not bind to DNA, such as serum albumin, is not crosslinked to DNA by HCHO even at extremely high protein concentrations. These properties of HCHO as a DNA-protein crosslinker are used to probe the distribution of nucleosomes in vivo. We show that there are no HCHO-crosslinkable DNA-protein contacts in a subset of SV40 chromosomes in vivo within a 325-base-pair stretch that spans the "exposed" (nuclease-hypersensitive) region of the SV40 chromosome. This replication origin-proximal region has been found previously to lack nucleosomes in a subset of isolated SV40 chromosomes. We discuss other applications of the HCHO technique, including the possibility of obtaining base-resolution in vivo nucleosome "footprints."

Effects of formaldehyde exposure on the extractability of DNA from proteins in the rat nasal mucosa

Reaction of an homogenate of the rat nasal mucosa with formaldehyde (CH2O) followed by solubilization and extraction in a strongly denaturing aqueous-immiscible organic solvent mixture decreased the quantity of nucleic acids that remained in aqueous solution in comparison with a control homogenate untreated with CH2O. The absent DNA and RNA were located in the interface between the aqueous and organic phases, from which they could be recovered only after enzymatic proteolysis. It is concluded that interfacial nucleic acids were cross-linked to proteins by CH2O. The concentration of cross-links was estimated with 14CH2O; under conditions that rendered 48% of the DNA nonextractable from proteins, there was less than one cross-link per 28,000 nucleotide residues. Exposure of rats to airborne CH2O at concentrations of 0, 2, 6, 15, and 30 ppm (6 hr/day for 2 days) resulted in a statistically significant increase in the percentage of the total DNA from the respiratory mucosa that was located in the interface at concentrations of 6 ppm and higher. However, the percentage of DNA from the olfactory mucosa located in the interface was not increased by CH2O exposure. Analysis of nasal mucosal DNA by ultracentrifugation in CsCl density gradients provided no evidence of a change in the buoyant density of the DNA caused by reaction with CH2O. The results indicate that CH2O may induce DNA-protein cross-links in the respiratory but not in the olfactory mucosa at concentrations equal to or greater than 6 ppm.