Dynamics of interaction of RNA polymerase II with nucleosomes. II. During read‐through and elongation

1993

Protein Science

Self Cite

Mononucleosomes were labeled with the sulfhydryl-specific fluorescence probe 1,5-IAEDANS (5-(2-((iodoacety1)amino)ethyl)amino-naphthalene-1-sulfonic acid) by attaching the dye to the single cysteine of H3 through a covalent linkage. The enzyme RNA polymerase I1 (pol 11) utilized the native and the reconstituted fluorescent nucleosomes as templates with greatest efficiency when 0.2 M potassium acetate (AcOK) was used as the supporting salt; 0.2 M NaCl was found to be very much inhibitory. Measurement of polarity of the microenvironment of the dye at its binding site in the nucleosome showed the conformation to be more open in the presence of AcOK, compared to that in 0.1 or 0.2 M NaCl. The binding of pol I1 to the nucleosome resulted in a relatively more compact structure when measured in terms of the polarity of the microenvironment of the dye in various salt-dependent conformations of the nucleosomes. Time-resolved fluorescence spectroscopy showed that the probe molecule at its binding site undergoes certain excited-state processes, and the presence/absence or rate of these excited-state processes depends on the conformation of nucleosomes, which in turn depends on the type and concentration of the ion present in the medium. Time-resolved emission spectra showed that binding of nucleosomes by pol 11 established some new contacts that resulted in inaccessibility of the dye to the bulk solvent, reflecting a more hydrophobic environment for the dye in the steady-state spectra. Thus, binding or transcription of nucleosomes by pol I1 did not break open their structure. Rather, some transient internal adjustments within the histone octamer may take place to accommodate the bulky pol I1 molecule.

Section: Binding Of Pol I1 To Nucleosomes Results In a More Compact Ssupporting

confidence: 75%

Section: Binding and Transcription Of Nucleosomes By Pol II Is Facilimentioning

confidence: 98%

Section: Mononucleosomes As Templates For Pol II In Vitromentioning

confidence: 99%

See 1 more Smart Citation

Dynamics of interaction of RNA polymerase II with nucleosomes. I. Effect of salts

1993

Protein Science

Self Cite

“…Histone replacement/exchange by RI assembly on transcribed templates suggests a possible mechanism for read‐through of a nucleosomal template by the enzyme RNA polymerase. It was found in an in vitro study that RNA polymerase II (pol II) can transcribe through a nucleosome without completely displacing histones from it [87]. The protein complex facilitates chromatin transcription (FACT) facilitates read‐through of the nucleosomal template by RNA polymerase II during transcription elongation [88].…”

Section: Variants Of Core Histones In Various Nuclear Processesmentioning

confidence: 99%

Histones in functional diversification

Pusarla

2005

The FEBS Journal

Self Cite

Recent research suggests that minor changes in the primary sequence of the conserved histones may become major determinants for the chromatin structure regulating gene expression and other DNA‐related processes. An analysis of the involvement of different core histone variants in different nuclear processes and the structure of different variant nucleosome cores shows that this may indeed be so. Histone variants may also be involved in demarcating functional regions of the chromatin. We discuss in this review why two of the four core histones show higher variation. A comparison of the status of variants in yeast with those from higher eukaryotes suggests that histone variants have evolved in synchrony with functional requirement of the cell.

“…It is generally considered repressive for gene expression as wrapping of DNA into nucleosomes may block the accessibility of the promoter sequences. Nevertheless, RNA polymerase can read through a nucleosome, which can also promote the interaction between two DNA‐binding proteins by bringing them closer together in space 55, 56. Thus, it is established now that the relative positions of the nucleosomes with reference to the underlying DNA sequences of the genome have a profound effect on the activity status of the genome.…”

Section: Nucleosome Positioning and Chromatin Dynamics In Gene Regumentioning

confidence: 99%

Epigenetics to proteomics: From yeast to brain

2010

Proteomics

Self Cite

Brain is the most complex and least understood organ of the body. Recent research suggests that epigenetics of the brain may be behind the complex functions of this master organ. Yeast, the simplest eukaryote, had been the model for studying the complex physiology of higher eukaryotes, including humans. Current depth in understanding of mechanisms of gene regulation has been possible mainly because of the knowledge acquired by epigenetic studies on yeast while the research on the biochemistry and physiology of the brain has been tremendously benefitted by proteomic studies. The independent advances of research in both these fields are now converging. As the current understanding of epigenetics can be applied to understand the mysteries of normal brain function as well as various diseases, modern proteomic approaches can help find new therapeutic targets.