If I understand this correctly during interphase most of the DNA strand is tightly wound around histones in the form of nucleosomes, to conserve space in the nucleus. Yet RNA polymerase in order to work needs a part of DNA to be temporarily unwound. How does the polymerase find the particular part of the DNA (and especially the promoter for a gene coding the protein needed to be synthesised) in this mass of tightly wound DNA?
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1$\begingroup$ I was told that during interphase the DNA is actually looser and more accessible to RNA polymerase, and that it is wound up in chromosomes only during mitosis? $\endgroup$– alpha-tetramerCommented Aug 2, 2017 at 22:31
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1$\begingroup$ Though this publication doesn't directly answer your question of how RNA finds a particular portion of DNA, it does address how DNA is unraveled from a previous, tighly wound conformation. pdfs.semanticscholar.org/64b4/… $\endgroup$– user22020Commented Aug 3, 2017 at 16:49
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3 Answers
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This answer will be a very broad overview and is based largely on information from the textbook "Molecular Biology of the Gene" by Watson et al. (which I highly recommend).
Nucleosomes are dynamic structures.
The interactions between DNA and histones are non-specific and dynamic. Regions of DNA can be transiently unwrapped from the nucleosome and thus recognized by DNA binding proteins. In fact, because of the non-specific nature of the interaction, DNA can slide relative to the histone core and expose different sections of DNA. This can be facilitated by nucleosome remodelling complexes which can also catalyze complete ejection of histone octamers to expose even more DNA.
Nucleosomes can be positioned specifically.
The association of DNA binding proteins with specific sequences can prevent or control nucleosome formation at specific loci and leave tracts of exposed DNA accessible to the transcription machinery. Additionally, certain DNA sequences that form bent helices are preferentially bound by nucleosomes.
Chromatin compaction is highly regulated.
Two broad classes of chromatin are present in the interphase nucleus: highly condensed, transcriptionally inactive heterochromatin and less condensed, transcriptionally active euchromatin. Chromatin compaction is regulated by post-translational modification of histone tails, and modifications such as acetylation and phosphorylation, especially of the N-terminal tails, can prevent higher order, repressive chromatin compaction. The specific pattern of histone modification is referred to as the histone code and certain modifications are associated with gene expression. These modifications can be recognized by remodelling complexes and even transcription factors.
Further Reading:
answered Aug 4, 2017 at 5:42
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There are a number of different ways. The histone may be marked through some histone modification (a form of epigenetic modification) that relaxes the DNA and makes it more accessible.
For example certain forms of acetylation "remove the positive charge on the histones and decreases the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure" this then makes it easier for RNA polymerase to access it and find the promoter for example
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Nucleosome is a structure formed when negatively charged DNA is wrapped around positively charged histone octamer. Now, for transcription only one strand of DNA is copied to RNA having polarity 3'-->5' known as Template strand, the other strand known as Coding strand (5'-->3') has same sequence as RNA (except thymine at place of uracil) Promoter is located towards 5' end(all references are made with coding strand) while terminator end is at 3' end.
The presence of PROMOTER in transcription unit defines the template and coding strand. In transcription only a segment of DNA is copied.
For unwrapping of DNA there are special enzymes like helicases(for unwinding helix), DNA Gyrase(for relaxing strain and supercoiling), Telomerase and holoenzyme.
