Module -3 Discussion Forum

Chromatin opening and closing:

• Nucleosomes package DNA into units with about 150 bp DNA and eight histones, two each of H2A, H2B, H3, and H4. The positively charged histone proteins bind tightly to the negatively charged phosphate groups of the DNA. This binding gets in the way of protein binding. RNA polymerase II is a big, complex protein and it has to bind to promoters to start up transcription. 

•  How can it get in? Do you have to get rid of nucleosomes to turn on a gene?

• Several studies have shown that in the test tube, chromatin can’t be transcribed when it is in the usual tight structure. Experiments catching chromatin in different states in the cell have shown that when genes are being expressed, the nucleosome structure is different. Sometimes the nucleosome slides along to free the promoter where RNA polymerase II needs to bind to start the transcription of a gene. Sometimes, the only thing we know is that DNase I, added to isolated chromatin, cuts more in the promoter and/or enhancer region, implying some undefined looseness (DNase I hypersensitivity). It can be shown using ChIP (chromatin immunoprecipitation) that sites of DNase I hypersensitivity are sites where RNA polymerase complex and transcription factors bind to turn on genes.
• Chromatin remodeling complexes such as Swi/Snf and SAGA (In molecular biology, SWI/SNF (SWItch/Sucrose Non-Fermentable), is a subfamily of ATP-dependent chromatin remodeling complexes, which is found in eukaryotes. In other words, it is a group of proteins that associate to remodel the way DNA is packaged) can rearrange the chromatin components in vitro so that transcription factors can bind and transcription can begin, or if they contain histone deacetylases, they can compact and silence the chromatin. These complexes interact with non-coding RNAs in some systems.