Separation of lymphocyte chromatin into template-active fractions with specificity for eukaryotic RNA polymerase II or prokaryotic RNA polymerase

Mapping physical interactions within chromatin by proteomic approaches

Our ability to study protein-protein interactions has grown by leaps and bounds in recent years, enabling numerous large-scale studies to be performed in a variety of organisms. Despite this success, some classes of proteins, including those bound to chromatin, remain difficult to characterize through proteomic approaches. Some of the problems faced by researchers studying chromatin-bound proteins include low complex solubility, heterogeneous sample composition, and numerous transient interactions, which can be further complicated by the presence of DNA itself. To tackle these issues, a number of innovative protocols have been developed to better study the various facets of chromatin biology. In this review, we will discuss novel approaches to study protein-DNA interactions as well as protein complexes affecting chromatin.

Chromatin conformation modulates repair of single strand interruptions by polynucleotide ligase-[3H] AMP

Conformationally distinct chromatin populations were utilized as substrates to quantitate the relative amount of and accessibility of internal 5'-phosphomonoester breaks in DNA-chromatin. In these studies, a constant amount of chromatin as well as deproteinized DNA derived from the respective chromatin sample was titrated with increasing quantities of adenylated polynucleotide ligase intermediate. This enzyme intermediate releases its AMP moiety while repairing a DNA single strand interruption, release of AMP being directly proportional to the number of internal 5'-phosphomonoester breaks repaired. Results of this study indicate that the ability of polynucleotide ligase to repair DNA breaks within chromatin was affected by the conformational state of the chromatin. The degree of conformational constraint present in a given chromatin, therefore, determined the capacity of the enzyme to repair internal DNA 5'-phosphomonoester breaks.

Uptake and early fate of metaphase chromosomes ingested by the Wi-L2 human lymphoid cell line

Aspects of the ingestion and early intracellular fate of homologous. [3H]-thymidine-labeled chromosomes (donor) were studied in recipient Wi-L2 cells in the absence of reutilized radioactivity. As much as 67% of the cell-associated radioactivity was resistant to hydrolysis by DNase I after 4 h of incubation. Cell fractionation and electron microscope autoradiography indicated that chromosome uptake was rapid, into both cytoplasmic and nuclear fractions and was facilitator and dose dependent. Sedimentation analysis demonstrated that at 4 h donor DNA of approximate single-strand mol wt of 1--6 X 10(6), as compared to 6--12 X 10(6) for chromosomal DNA, was recoverable in cell fractions. By 6 h, a significant portion of the nucleus-associated donor DNA was converted into material of higher mol wt, although no evidence was found for integration into recipient DNA. Cytoplasmic donor DNA continued to be degraded. An average number of chromosome equivalents of nucleus-associated donor DNA to recipient cell nuclei of 1--4 was obtained and its relationship to the lower frequency of chromosome-mediated gene transfer is discussed.

Changes of Template Activity and Proteins of Chromatin during Wheat Germination

Relationships between changes in template activity and composition of chromatin during germination of wheat embyros (Triticum aestivum L.) were investigated. The template activity of chromatin was determined with exogenous DNA-dependent RNA polymerase II (EC 2.7.7.6) prepared from wheat embryos. It was essentially constant for 18 hours of germination, corresponding to 2.5% of that of a native calf thymus DNA. Thereafter, the activity increased 2-fold and 5-fold at 24 and 60 hours of germination, respectively.Chromatin-associated proteins were separated into at least 22 distinct bands by sodium dodecyl sulfate gel electrophoresis throughout 60 hours of germination. Significant changes were observed in two nonhistone proteins, approximate molecular weights 59,000 and 39,000: the amount of the former was constant up to 18 hours, reduced for the period from 18 to 60 hours, and that of the latter was decreased for the period from 18 to 60 hours of germination. No change was observed in the number of histone components by acid-urea gel electrophoresis.