12 Mnemogenic reactions, such as de novo protein synthesis and DNA-histone modifications, chemically alter the biological system so that the acquired information is stably protected from protein turnover.13 Another important aspect of memory is the change in synaptic connection strength. This ...
1976). Another clue came from chemically cross-linking (i.e., joining) histones in chromatin (Thomas & Kornberg, 1975). This experiment demonstrated that H2A, H2B, H3, and H4 form a discrete protein octamer, which is fully consistent with the presence of a repeating histone-containing unit ...
The Collepardo group develops a bottom-up multiscale model of chromatin—integrating atomistic descriptions of nucleosomes, a chemically-specific chromatin model and a minimal coarse-grained model of sub-Mb scale chromatin—and a Debye-length replica exchange enhanced sampling technique. With this appro...
their complexes like chromatin. Phase separation is a thermodynamic process in which a mixture reaches its lowest free energy state by partitioning into a concentrated phase and a dilute phase [1,2,3]. The concentrated phase consists of aggregates of the solute(s), which are termed condensates....
By chemically ligating modified tail peptides onto recombinant histone core preparations, it has been possible to show that acetylation of H4K16 has a negative effect on the formation of a 30-nanometer fiber and the generation of higher-order structures (Shogren-Knaak et al., 2006; also see ...
In addition, active demethylation can be direct, erasing DNAmethylation through a base excision repair pathway by aDNA demethylase, or indirect, in which methyl-cytosine isfirst chemically converted to an intermediate product beforeDNA glycosylase acts (64).The identity of enzymes that promote active...
The asterisk indicates the lysine residue in H3 that is known to be targeted for acetylation as well as for methylation; lysine 9 in CENP-A (bold) may also be chemically modified (see text). The above depictions of chromatin structure and H3 are schematic; no attempt has been made to ...
On the other hand, GO analysis of genes bound by p38α and upregulated when p38α activity was chemically inhibited showed enrichment for transcription factors and nuclear receptor coactivators (Fig. 6c). Interestingly, DAVID analysis of canonical pathways enriched in genes bound by p38α ...
Histones were acid extracted from nuclei and ~10 µg of material per sample was chemically derivatized, followed by digestion to tryptic peptides43. Prior to LC-MS analysis, derivatized samples were desalted using C18 stage-tips. Using a 75 µm ID x 17 cm, in-house packed ...
Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating ...