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

Chromatin remodeling is the dynamic process by which the structure and composition of chromatin is altered to provide access to the underlying DNA. Chromatin is made up of DNA, histones, and other proteins. Remodeling allows for the regulation of DNA-related processes, like transcription, replication, and repair, by changing the accessibility of DNA to different proteins within the cell.

There are several ways in which chromatin can be remodeled: 1. Histone Modification: This involves the addition or removal of functional groups (e.g., acetyl, methyl, or phosphate) to specific amino acids in histones. These modifications can change the interaction of the histones with DNA, allowing for gene activation or repression. 2. ATP-dependent Remodeling: This process uses the energy from ATP hydrolysis to move, evict, or replace histones. This can loosen or tighten the chromatin structure, affecting the accessibility of DNA. 3. Histone Variants: Replacement of standard histones with histone variants can change the properties of the nucleosome and influence how the chromatin interacts with regulatory proteins. 4. Chromatin Looping: This occurs when distant regions of chromatin are brought together through protein complexes, forming 3D structures that can either activate or repress gene expression.

Chromatin remodeling plays a crucial role in the regulation of transcription (the process whereby RNA is synthesized from a DNA template). During transcription, an enzyme called RNA polymerase, along with other transcription factors, must have access to the DNA template. The remodeling processes mentioned above can either increase or decrease the accessibility of the DNA, thus influencing transcription. 1. Histone Modification: The addition of acetyl groups can loosen the interaction between histones and DNA, making the DNA more accessible for transcription. The removal of acetyl groups can have the opposite effect, tightening the chromatin structure and inhibiting transcription. 2. ATP-dependent Remodeling: The remodeling complexes can expose or hide specific DNA sequences, effectively activating or repressing the transcription of nearby genes. 3. Histone Variants: Inclusion of specific histone variants can lead to a more open or closed chromatin configuration, influencing the transcription of nearby genes. 4. Chromatin Looping: Bringing together distant regions of chromatin can allow for the recruitment of transcription factors and enhance gene expression. In contrast, looping can also block the access of transcription factors and repress gene expression.

Several chromatin remodeling complexes have been discovered, and they play vital roles in various cellular processes. Some examples include: 1. SWI/SNF (switch/sucrose non-fermentable) complexes: These ATP-dependent remodeling complexes are involved in the control of gene expression. 2. ISWI (imitation SWI) complexes: These complexes are also ATP-dependent and are involved in several processes like transcription, DNA replication, and DNA repair. 3. NuRD (nucleosome remodeling and deacetylase) complexes: These contain both histone deacetylase and ATP-dependent remodeling activities and are involved in transcriptional repression. In conclusion, chromatin remodeling processes play a significant role in controlling gene expression by influencing the accessibility of DNA to the transcription machinery.