What role does chromatin play in gene expression?

Chromatin is a highly structured complex in which DNA is stored. Epigenetic processes regulate gene expression by altering the structure of chromatin. Actively transcribed genes are found in chromatin regions that are accessible, whereas transcriptionally silent genes are found in inaccessible chromatin regions.

Whether it is a blessing or a curse, chromatin adds an extra layer of control over gene expression. This control is exercised via a slew of chemical modifications to histones and DNA known as epigenetic marks, which alter chromatin structure and provide specific recognition sites for regulatory factors.

In response to environmental stimuli, the epigenome undergoes biochemical changes, which result in chromatin structure remodeling. The term "chromatin remodeling" primarily refers to the ATP-dependent process of genomic transformation by nucleosome-shifting enzymes such as the SWI/SNF complex.

Epigenetics heavily relies on chromatin remodeling. Epigenetic modifications to histone proteins, such as methylation/demethylation and acetylation/deacetylation, can alter the structure of chromatin, resulting in transcriptional activation or repression. Epigenetic mechanisms are important regulators of gene expression that establish potentially heritable changes in gene expression without changing the underlying nucleotide sequence. These mechanisms include CpG methylation, chromatin remodeling, and regulatory ncRNAs.

Dynamic changes in chromatin conformation can either activate or suppress gene expression by facilitating interactions between enhancers or other cis-regulatory elements and their target genes. All aspects of transcription that are mediated by RNA polymerase II are hampered by chromatin structure. Multiple mechanisms control the dynamics of chromatin structure, including histone modification, chromatin remodeling, histone variant incorporation, and histone eviction.

To activate transcription, some of the specific transcription factors must be able to bind to their binding sites when organized into nucleosomes. The promoter's chromatin structure must then be decondensed in order for the basal transcription machinery to bind.