Evidence from several model systems suggests that nonhistone chromosomal proteins may regulate gene expression in eukaryotic cells. The data indicate that the synthesis of new species of nonhistone chromosomal proteins as well as modifications of preexisting nonhistone chromosomal proteins are involved in the control of transcription. However, from the vast number of proteins included in this class, it is apparent that, in addition to regulating the transcription of defined genome loci, the nonhistone chromosomal proteins include enzymes that have a general function, proteins that are involved in determining the structure of chromatin, as well as proteins that serve as recognition sites for binding of regulatory macromolecules. The presence of a nucleoplasmic pool of nonhistone chromosomal proteins which may exchange with the chromatin has also been reported (89). While it is clear that the nonhistone chromosomal proteins play a key role in the regulation of gene expression, the exact manner in which they interact with the genome to initiate, modify, or augment the transcription of specific RNA molecules remains to be resolved.

http://science.sciencemag.org/content/sci/183/4127/817.full.pdf

Nonhistone Chromosomal Proteins and Gene Regulation

Biochemical and genetic studies have produced a vast fund of knowledge concerning gene action and regulation in prokaryotes In these organisms the DNA is exposed rather nakedly to the world, protected primarily by the cell membrane In eukaryotes the DNA seems far better shielded, being enmeshed in histone and nonhistone proteins and sequestered behind both the cell and the nuclear membrane These differences have led to a considerable degree of caution in the application of this knowledge of prokaryotes to problems of gene regulation in eukaryotes, and rightly so There are, however, several observations which suggest that higher organisms may have picked up a number of fundamental genetic tricks from their lowly predecessors It has frequently been suggested that eukaryotes must do things differently from prokaryotes, until proven otherwise It may be prudent to reverse this line of thought and suggest that they do things the came until proven different The following similarities suggest this (1) T he basic genetic dogmas concerning DNA replication, transcription, andlation are similar, (2) The genetic code is the same (3) Both systems appear to make use of cyclic AMP as a basic mediator for, humoral or diffusible, signals (4) In both systems DNA synthesis may be controlled at membranes (5) Both make use of different types of RNA polymerase and RNA polymerase cofactors (6) Recent studies of polylysine binding to chromatin suggest the eukaryotic DNA may not be so thoroughly enmeshed in Protein as once thought (7) The visualization of genes in action by electron microscopic techniques intimates that genes are spaced and read in a similar manner And finally, (8) merely because the clustering of related genes is unusual in higher organisms is no reason in itself to totally discard the promoter-operator-repressor concept as a way of regulating single structural genes This system has provided an immense amount of data concerning the manner in which proteins interact with specific DNA sequences to control the attachment and utilization of RNA polymerase It is hard to imagine that eukaryotes, being presented with such a superb mechanism for controlling DNA transcription, would totally discard it and opt for something different It is far more likely that they would build on to this solid foundation

The structure and function of chromatin.

Nuclear proteins. III. The fibrillar nature of the nuclear matrix.

Publisher Summary This chapter describes the classification and the types of proteins of the cell nucleus. The cell nucleus is a well-delineated functional structure, containing mainly deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and proteins. The classification of the nuclear proteins, according to their solubility in buffered salt solutions, dilute acids, bases, is the conventional system, as it follows the initial steps in the separation of fractions. The alkali-soluble nuclear protein fraction is a mixture of DNA, RNA, lipoprotein, and proteins containing sulfur and tryptophan. This fraction, which is also referred to as the nuclear residual protein fraction, contains alkali-soluble proteins of nucleoli, chromatin, and nuclear membranes. The amino acid composition of acidic nuclear proteins differs slightly from that of the saline- and tri-soluble proteins. The NH2-terminal amino acids of acidic nuclear proteins are alanine, glycine, serine, aspartic and glutamic acid, valine, and the leucine, again, indicating the great heterogeneity of this protein mixture. It is found that the amino acid composition of nucleolar proteins from the mammalian tissues is similar to the composition of the corresponding fractions isolated from the whole nuclei.

Proteins of the Cell Nucleus

The transcription of rat-liver chromatin has been studied using partially purified from AI and highly purified form B DNA-dependent RNA polymerases isolated from rat liver. Chromatin contains endogenous RNA polymerase activity. This activity is evident only when the RNA polymerase assays are carried out at high ionic strength and its appearance as the ionic-strenght increases is thought to be due to the removal of chromatin-associated proteins which block further transcription by the bound enzyme. This activity is insensitive to the rifampicin derivative AF/0-13 which is shown to inhibit initiation of RNA synthesis by mammalian RNA polymerases. From AI polymerase is virtually inactive in the transcription of chromatin whereas the from B RNA polymerase (α-amanitin sensitive) actively transcibes chromatin. This activity has two salt concentration optima: (a) 0.01 M (NH4)2SO4 or 0.03 M KCI; (b) 0.16 M (NH4)2SO4 or 0.25 MKCI. Both these activities are inhibited by rifampicin AF/0-13. A comparison of the activity of the rat-liver from B polymerase and the Micrococcus lysodeikticus RNA polymerase demonstrates that chromatin is a more efficent template for the rat-liver enzyme. Evidence is presented that the rat-liver form B and the Micrococcus lysodeikticus RNA polymerases bind to and transcribe from different sites on the chromatin DNA.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1971.tb01613.x

Transcription of Mammalian Chromatin by Mammalian DNA-Dependent RNA Polymerases

Activated transcription from rat liver chromatin by non-histone proteins.

Differential activation of transcription of chromatin by non-histone fractions

Nonhistone proteins fractionated from normal rat liver and Walker carcinosarcoma can stimulate chromatin-templated RNA synthesis in vitro . This has been demonstrated by using RNA polymerase prepared from rat liver, Walker tumor, or Micrococcus luteus . The RNA isolated from these fractionated nonhistone proteins does not activate transcription from chromatin. As judged by DNA-RNA hybridization studies, the altered transcription of chromatin effected by the nonhistone proteins reflects the characteristic transcription from chromatin homologous to the nonhistone proteins. Thus, when rat liver nonhistone proteins were used to activate transcription from Walker tumor chromatin, the activated transcript was found to contain RNA species similar to that synthesized in vitro from rat liver chromatin. Conversely, Walker tumor nonhistone proteins can activate the synthesis of RNA from rat liver chromatin to that partly characteristic of Walker tumor chromatin transcript. It is concluded that the nonhistone proteins are tissue specific in the alteration of transcription of chromatin.

/pdf/transcriptional-transformation-of-walker-tumor-chromatin-by-57qtypqevg.pdf

Transcriptional transformation of Walker tumor chromatin by nonhistone proteins.

Protein synthesis in nuclear residual protein

Summary The in vitro transcriptions from chromatins of Walker 256 carcinosarcoma, rat mammary gland, and rat liver were compared with respect to template activities and reciprocal double saturation hybridization of the transcribed RNA9s. Walker tumor chromatin was found to have the least template activity in RNA synthesis in vitro , and the synthesized RNA, when annealed with DNA, also showed the least saturation hybridization plateau. Hybridization studies further showed the presence of new RNA species in transcripts from Walker tumor chromatin which were not detected in normal in vitro chromatin transcription. These results indicate that in the transformation from normal to neoplastic state both repression and derepression of normal transcribable DNA sequences occur.

https://cancerres.aacrjournals.org/content/canres/31/11/1663.full.pdf

T. Y. Wang

Papers

Activated transcription from rat liver chromatin by non-histone proteins.

Differential activation of transcription of chromatin by non-histone fractions

Transcriptional transformation of Walker tumor chromatin by nonhistone proteins.

Protein synthesis in nuclear residual protein

Transcription of Walker 256 carcinosarcoma chromatin.