Both cis-acting sequences and trans-acting proteins affect gene expression in eukaryotic chromosomes

Question

What are the three basic mechanisms by which trans-acting proteins access specific regulatory DNA sequences in eukaryotic chromosomes? Describe how chromatin is altered in each of these processes.

Answer 1

1. Some regulatory sequences are not tightly bound by histones, allowing open access to the regulatory DNA. These sequences include the "linker" sequences between nucleosomes and sequences with specific characteristics that prevent histones from binding efficiently.
2. Chromatin remodelers can enzymatically change the distribution or composition of nucleosomes. These remodeler enzymes can act by reorganizing nucleosomes to repress transcription, sliding nucleosomes along the chromosome or removing them to activate transcription, or changing histone composition to activate genes.
3. Chromatin modifiers can enzymatically modify histones by adding or removing methyl or
acetyl groups at specific amino acid residues. Adding acetyl groups is associated with gene activation (euchromatin), while removing acetyl groups and/or adding methyl groups are associated with gene repression (heterochromatin). These chromatin-modifying enzymes are recruited to specific sites in chromatin by trans-acting factors that bind to specific DNA sequences.
This combination of activities determines the relative access of trans-acting transcription factors to cis-acting DNA sequences in particular cells, at different times of organismal development, and under certain physiological conditions. Thus chromatin remodelers and chromatin modifiers mediate the reversible transition from inactive heterochromatic DNA to active euchromatic DNA.