Nucleosomes and Histone Proteins | amsbio
The fundamental unit of chromatin, termed the nucleosome, is composed of DNA and The core histones, H3, H4, H2A and H2B, are small, basic proteins highly . link between the assembly of chromatin and the processes of replication and. HistoneDB - Database of histones and variants at NCBI · Chromatin, Histones & Cathepsin; PMAP The Proteolysis Map-. Like proteins, these RNA molecules perform a a correlation exists between the complexity of an.
Arginine citrullination[ edit ] Enzymes called peptidylarginine deiminases PADs hydrolyze the imine group of arginines and attach a keto group, so that there is one less positive charge on the amino acid residue. This process has been involved in the activation of gene expression by making the modified histones less tightly bound to DNA and thus making the chromatin more accessible.
This reduces electrostatic attraction between the histone and the negatively charged DNA backbone, loosening the chromatin structure; highly acetylated histones form more accessible chromatin and tend to be associated with active transcription. Lysine acetylation appears to be less precise in meaning than methylation, in that histone acetyltransferases tend to act on more than one lysine; presumably this reflects the need to alter multiple lysines to have a significant effect on chromatin structure.
The modification includes H3K27ac. It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification, and binding domains such as BRCT have been characterised.
Functions in transcription[ edit ] Most well-studied histone modifications are involved in control of transcription. Actively transcribed genes[ edit ] Two histone modifications are particularly associated with active transcription: However, it is an excellent mark of active promoters and the level of this histone modification at a gene's promoter is broadly correlated with transcriptional activity of the gene.
The formation of this mark is tied to transcription in a rather convoluted manner: The same enzyme that phosphorylates the CTD also phosphorylates the Rad6 complex,   which in turn adds a ubiquitin mark to H2B K K in mammals. This process therefore helps ensure that transcription is not interrupted. Three histone modifications are particularly associated with repressed genes: The formation of heterochromatin has been best studied in the yeast Schizosaccharomyces pombewhere it is initiated by recruitment of the RNA-induced transcriptional silencing RITS complex to double stranded RNAs produced from centromeric repeats.
This mark is placed by the Suvh methyltransferase, which is at least in part recruited by heterochromatin protein 1. This peculiar combination of modifications marks genes that are poised for transcription; they are not required in stem cells, but are rapidly required after differentiation into some lineages. Once the cell starts to differentiate, these bivalent promoters are resolved to either active or repressive states depending on the chosen lineage.
It also protects DNA from getting destroyed by ultraviolet radiation of sun. H3K56 acetylation is also required to stabilise stalled replication forks, preventing dangerous replication fork collapses. Salt links and hydrogen bonding between both side-chain basic and hydroxyl groups and main-chain amides with the DNA backbone phosphates form the bulk of interactions with the DNA.
Nucleosome - Wikipedia
This is important, given that the ubiquitous distribution of nucleosomes along genomes requires it to be a non-sequence-specific DNA-binding factor. Although nucleosomes tend to prefer some DNA sequences over others,  they are capable of binding practically to any sequence, which is thought to be due to the flexibility in the formation of these water-mediated interactions.
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In addition, non-polar interactions are made between protein side-chains and the deoxyribose groups, and an arginine side-chain intercalates into the DNA minor groove at all 14 sites where it faces the octamer surface. The distribution and strength of DNA-binding sites about the octamer surface distorts the DNA within the nucleosome core.
The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is However, the overall twist of nucleosomal DNA is only The N-terminal tail of histone H4, on the other hand, has a region of highly basic amino acidswhich, in the crystal structure, forms an interaction with the highly acidic surface region of a H2A-H2B dimer of another nucleosome, being potentially relevant for the higher-order structure of nucleosomes.
This interaction is thought to occur under physiological conditions also, and suggests that acetylation of the H4 tail distorts the higher-order structure of chromatin.
Higher order structure[ edit ] The current chromatin compaction model. The organization of the DNA that is achieved by the nucleosome cannot fully explain the packaging of DNA observed in the cell nucleus. Further compaction of chromatin into the cell nucleus is necessary, but is not yet well understood.
The current understanding  is that repeating nucleosomes with intervening "linker" DNA form a nm-fiber, described as "beads on a string", and have a packing ratio of about five to ten. Further compaction leads to transcriptionally inactive heterochromatin. Dynamics[ edit ] Although the nucleosome is a very stable protein-DNA complex, it is not static and has been shown to undergo a number of different structural re-arrangements including nucleosome sliding and DNA site exposure.
Depending on the context, nucleosomes can inhibit or facilitate transcription factor binding. Nucleosome positions are controlled by three major contributions: First, the intrinsic binding affinity of the histone octamer depends on the DNA sequence. Second, the nucleosome can be displaced or recruited by the competitive or cooperative binding of other protein factors. Third, the nucleosome may be actively translocated by ATP-dependent remodeling complexes.
Init was further revealed that CTCF binding sites act as nucleosome positioning anchors so that, when used to align various genomic signals, multiple flanking nucleosomes can be readily identified. InBeena Pillai's laboratory has demonstrated that nucleosome sliding is one of the possible mechanism for large scale tissue specific expression of genes.
The work shows that the transcription start site for genes expressed in a particular tissue, are nucleosome depleted while, the same set of genes in other tissue where they are not expressed, are nucleosome bound. Measurements of these rates using time-resolved FRET revealed that DNA within the nucleosome remains fully wrapped for only ms before it is unwrapped for ms and then rapidly rewrapped.
Nucleosomes and Histone Proteins
Indeed, this can be extended to the observation that introducing a DNA-binding sequence within the nucleosome increases the accessibility of adjacent regions of DNA when bound. This allows for promoter DNA accessibility to various proteins, such as transcription factors.
Nucleosome free region typically spans for nucleotides in S. In order to achieve the high level of control required to co-ordinate nuclear processes such as DNA replication, repair, and transcription, cells have developed a variety of means to locally and specifically modulate chromatin structure and function.
This can involve covalent modification of histones, the incorporation of histone variants, and non-covalent remodelling by ATP-dependent remodeling enzymes. Histone post-translational modifications[ edit ] Since they were discovered in the mids, histone modifications have been predicted to affect transcription. Later it was proposed that combinations of these modifications may create binding epitopes with which to recruit other proteins.
Modifications such as acetylation or phosphorylation that lower the charge of the globular histone core are predicted to "loosen" core-DNA association; the strength of the effect depends on location of the modification within the core. Common modifications include acetylationmethylationor ubiquitination of lysine ; methylation of arginine ; and phosphorylation of serine.