Question

A protein called __________ usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around ___________

Answer 1

A transcription factor usually cleaves DNA at regulatory sites but does not cleave DNA wrapped around histones, influencing gene expression through DNA-protein interactions and epigenetic modifications.

Step-by-step explanation:

A protein called transcription factor usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around histones. These proteins play a crucial role in gene expression by recognizing and binding to specific DNA sequences in the regulatory regions of genes, such as enhancers or silencers. The interaction between transcription factors and DNA is essential for the control of gene expression, as they can activate or repress transcription, depending on whether they function as activators or repressors.

Transcription factors bind to the major grooves of the DNA double helix and often induce conformational changes that facilitate the assembly of a transcription initiation complex. Enhancer regions, which can be located far from the promoter sites, bind transcription factors that are brought in close proximity to promoter-bound factors by the bending of DNA, mediated by DNA bending proteins. This dynamic structural change in the DNA allows the recruitment of RNA polymerase II and initiates transcription.

Epigenetic mechanisms, including DNA methylation and histone modification, also play significant roles in gene regulation. These modifications alter the accessibility of chromatin to various molecular machinery without changing the DNA sequence itself, thereby influencing the patterns of gene expression in response to various signals.

Answer 2

A protein called DNase I usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around histones.

DNase I is an endonuclease enzyme that can hydrolyze phosphodiester linkages in DNA, and it is often used in experiments to assess chromatin accessibility. Regulatory transcription factors often bind to specific regions of DNA, making those regions more susceptible to cleavage by DNase I.

DNase I is a non-specific endonuclease that can break both single- and double-stranded DNA. However, its activity is significantly hindered by the presence of histones, which tightly package and protect the DNA within chromatin fibers.