Present an overview of the manner in which chromatin can be remodeled. Describe the manner in which these remodeling processes influence transcription.

Imagine a bustling city where buildings (nucleosomes) frequently change location or even their structure to make room for different events. In the same way, ATP-dependent chromatin remodeling acts as an urban development team, shifting and reshaping the chromatin landscape. These complexes use energy from ATP to slide nucleosomes along the DNA, remove them altogether, or replace parts of them. This process allows for precise control over which genes are turned on or off by making the underlying DNA more or less available to the transcription machinery.

For example, during times of active gene expression, ATP-dependent remodelers can clear the way for transcription factors to access specific DNA regions, similar to opening a gate to let people through for a concert. In essence, these remodelers are the keymasters to the kingdom of genetic information, playing a pivotal role in orchestrating the symphony of gene expression.

Histones, much like individuals, can change their character by adding or removing various molecular accessories. These changes are known as post-translational histone modifications and involve adding chemical groups such as acetyl, methyl, or phosphate to amino acids in histone proteins.

Let's take acetylation as an example—it's akin to loosening the grip of histones on DNA, promoting a relaxed chromatin state that encourages transcriptional activity. It’s as if histones are putting on a pair of sunglasses, assuming a cool posture that says, 'DNA is free to be read.' Other modifications can act as signals to recruit additional proteins that further remodel the chromatin or directly impact transcription. Taken together, these modifications form a complex 'histone code' that determines the overall landscape of chromatin accessibility.

DNA methylation is a significant epigenetic event where a methyl group is added to cytosine bases in DNA. This is not a flamboyant decoration but a subtle mark that usually whispers 'silence' to gene activity. Imagine a librarian applying a 'quiet' sign on certain books; similarly, DNA methylation tamps down the 'noise' of gene expression.

It commonly occurs in regions rich with C and G nucleotides (CpG islands) often found near gene promoters. When these islands are methylated, it's like putting up a 'Do Not Enter' sign that keeps transcription machinery at bay. This quieting of the gene can be perpetuated across cell divisions, thereby having long-term effects on cell function and identity. Importantly, DNA methylation patterns are dynamically rewritten during development and in response to environmental changes.

Histones come in different flavors, and these variants can have profound effects on the structure and stability of nucleosomes. These are not your standard histones; they offer a customized approach to organizing the chromatin and can mix-and-match within nucleosomes to confer distinct characteristics.

Consider a histone variant as a specially designed brick in a building; it might make the structure sturdier or give it a unique appearance. By swapping out the regular histones for these specialized versions, the cell can mark certain genes for rapid activation or form chromatin that's robust against disturbances. This nuanced layer of chromatin remodeling plays a crucial role in gene regulation, ensuring that each cell executes its unique program and responds appropriately to internal and external cues.