Memory is commonly referred to as the ability to encode, store, retain and subsequently recall information and past experiences in the human brain. This process involves many proteins, one of which is the Histone-binding protein RbAp48 (also known as RBBP4 or NURF55), encoded by the RBBP4 gene in humans. [1]
RbAp48, also known as RBBP4 gene, encodes a nuclear protein, which belongs to a highly conserved family of WD40 repeat. This gene is present in many protein complexes that are involved in histone acetylation and deacetylation processes as well as chromatin assembly. [2] This gene also belongs to the Mi-2/NuRD complex, also known as nucleosome remodeling deacetylase complex which plays a role in both ATP-dependent chromatin remodeling and histone deacetylase activities. [3] This protein is also part of a co-repressor complex which is an important component of transcriptional silencing. This gene is widely available and can be found in several cellular proteins which bind directly to the retinoblastoma protein to regulate growth and cell proliferation. [4] This protein also found in the transcriptional repression of E2F-responsive genes, which are a group of genes that encode for a family of transcription factors. [2]
To further distinguish age-related memory loss from Alzheimer's disease (AD), a subregion of the hippocampal formation called the dentate gyrus (DG) was further studied, since it is thought to be targeted by aging. Human postmortem tissue was collected from both DG and entorhinal cortex (EC). Entorhinal cortex is a neighboring subregion unaffected by aging and known to be implicated in age-related memory loss. After normalizing the expression of EC, 17 genes were manifested due to age-related changes in the DG. Mice were used as the experimental subjects to test whether the decline of RbAp48 was also related to age-related memory loss. The results were consistent with the human studies, where the level of RbAp48 protein was much lower in adults as compared to the young. To solidify these findings, magnetic resonance imaging (MRI) was performed which revealed that dysfunction occurred in the DG, corresponding to the regionally selective decreases in histone acetylation. [4]
The hippocampus is a brain region which has many interconnected subregions, with each region having its own distinct neuron populations playing an important role in encoding memory. Many studies showed that Alzheimer's disease (AD) ameliorates memory by first acting on the entorhinal cortex (EC) which is the region providing the main input conduit from the external sensors to the hippocampus. Scientists initially identified memory loss associated with aging as an early manifestation of Alzheimer's; however, more recent evidence suggests that a distinct process affects the dentate gyrus (DG), which is a subregion of the hippocampus, and causes memory deterioration. [5] The hippocampal formation is made up of many interconnected subregions and plays a vital role in retaining memory. Each subregion contains a specific population of neurons which have distinct molecular expression and physiological properties. As a result, these regions are vulnerable to various pathogenic mechanisms. [6] Although both AD and the normal aging process affect the hippocampus, studies showed that these two processes can be distinguished by two anatomical patterns of hippocampal dysfunctions. Postmortem studies suggest that the entorhinal cortex (EC) and the subiculum are the hippocampal subregions most affected by AD, [7] whereas the dentate gyrus is relatively preserved in most cases. In contrast to AD, the normal aging process does not cause cell death or other pathognomonic abnormalities that result in memory loss. Rather, age-related memory loss is characterized by dysfunctioning neurons. [4] These results from MRI and other studies suggest that the primary initial target of normal aging is the DG, whereas the EC is relatively preserved. [6]
Guided by the pattern that distinguishes age-related hippocampal dysfunction from AD, scientists from Columbia University Medical Center collected the dentate gyrus (DG) from postmortem human brains. These DG were free from any detectable brain pathology. These experimental subjects from which the DG was taken ranged from 33 to 88 years of age. Scientist also harvested the EC from each brain and generated gene expression profiles with Affymetrix microarray chips, where each microarray was customized to each individual's brain area. [8] Their hypothesis was driven by the analysis that the DG is preferentially affected by aging rather than AD. The gene expression in the DG was normalized to their expression in EC; the normalized values of DG were then analyzed to find the correlation between age of the experimental subjects. Scientists found that 17 normalized profiles showed an increase and decrease with correlation to age. With a P ≤ 0.005, scientists confirmed that the observed changes were not the product of age-related change but rather the product of their relative abundance in the EC. One of the biggest change in terms of gene expression was the expression of gene RbAp48, where the p value conformed to the pattern of normal age-associated hippocampal dysfunction. To further advance their studies, scientists collected EC and DG from an additional 10 healthy human brains with ages ranging from 49 to 81 years. After the level of RbAp48 and actin in every single tissue was measured using Western blot, they discovered that the level of RbAp48 decreased with the increasing age. The level of mRNA also decreased as the age of the subject increased in DG; however, the level of RbAp48 remained unchanged in the EC. [4]
In mice, the RbAp48 protein is key component in histone acetylation, transcriptional regulation and in cyclic adenosine monophosphate (cAMP)-protein kinase element-binding protein CREB1 path way. [9] Since histone acetylation and the cAMP-PKA-CREB1 pathway are extremely important for normal hippocampal function and aging in mice, [10] scientists further investigate RbAp48 to test whether its modulation was the cause of age-related memory losses in animals, especially mice. By studying wild-type mice, Scientists discovered that RbAp48 was expressed at a much higher level in the hippocampus, particularly in the dentate gyrus (DG). This finding was consistent with what they found in mice tissue because RbAp48 protein was less abundant in the DG of adult mice, as compared to a lower expression level in adult. In addition, the age-related reduction of RbAp48 was only detected in the DG, whereas the region of EC was preserved. [4] This finding further solidifies the previous discovery that aging only affects the DG and does not cause the dysfunction of EC.
In eukaryotic cells, DNA is wrapped around an octamer of histone proteins to form nucleosomes, which fold into higher-order chromatin structures. The nucleosome comprises two copies of histone H3 and histone H4. These nucleosomes form a heterotetramer and bind to DNA in the first step of nucleosome assembly. When DNA is replicated, nucleosomes need to be disassembled in front of the fork and the histones must then be transferred to the newly duplicated strands for reassembly. Studies of the in- vivo composition of histone H3 complexes, as well as the structural of the ASF1-H3-H4 complex, have shown that histone H3-H4 complexes are handled as a protein dimer. [11]
Proteins RbAp48 is a key player in the assembly of nucleosomes. [12] RbAp48 protein is a subunit of the chromatin-assembly factor-1 (CAF-1) complex, which assembles histones H3 and H4 onto newly replicated DNA to initiate nucleosomes assembly. [13] RbAp48 protein is also found in numerous other protein complexes for regulation of chromatin structure. Studies show that RbAp48 interacts with H3-H4 dimers and imply that the function of RbAp48 is involved in numerous process such as chromatin assembly, remodeling and modifications; therefore, in many other chromatin-related processes, histones H3-H4 might be handled as a dimer. More generally, it seems plausible that the presence of RbAp48 may reflex the post-translational modifications of the nucleosome. As a result, this can affect the activities of neurons and ultimately impact the memory encoding ability [12]
CREB-binding protein, also known as CREBBP or CBP, is a protein that is encoded by the CREBBP gene in humans. [15] [16] The CREB protein carries out its function by activating transcription, where interaction with transcription factors is managed by one or more CREB domains: the nuclear receptor interaction domain (RID), the CREB and MYB interaction domain (KIX), the cysteine/histidine regions (TAZ1/CH1 and TAZ2/CH3) and the interferon response binding domain (IBiD). The CREB protein domains, KIX, TAZ1 and TAZ2, each bind tightly to a sequence spanning both transactivation domains 9aaTADs of transcription factor p53. [17] [18] [19] [20] [21] [22]
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.
Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-N-acetyllysine. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression.
In molecular biology, a histone octamer is the eight-protein complex found at the center of a nucleosome core particle. It consists of two copies of each of the four core histone proteins. The octamer assembles when a tetramer, containing two copies of H3 and two of H4, complexes with two H2A/H2B dimers. Each histone has both an N-terminal tail and a C-terminal histone-fold. Each of these key components interacts with DNA in its own way through a series of weak interactions, including hydrogen bonds and salt bridges. These interactions keep the DNA and the histone octamer loosely associated, and ultimately allow the two to re-position or to separate entirely.
S phase (Synthesis phase) is the phase of the cell cycle in which DNA is replicated, occurring between G1 phase and G2 phase. Since accurate duplication of the genome is critical to successful cell division, the processes that occur during S-phase are tightly regulated and widely conserved.
Histone H4 is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H4 is involved with the structure of the nucleosome of the 'beads on a string' organization. Histone proteins are highly post-translationally modified. Covalently bonded modifications include acetylation and methylation of the N-terminal tails. These modifications may alter expression of genes located on DNA associated with its parent histone octamer. Histone H4 is an important protein in the structure and function of chromatin, where its sequence variants and variable modification states are thought to play a role in the dynamic and long term regulation of genes.
Histone H2B is one of the 5 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and long N-terminal and C-terminal tails, H2B is involved with the structure of the nucleosomes.
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.
Histone-modifying enzymes are enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression. To safely store the eukaryotic genome, DNA is wrapped around four core histone proteins, which then join to form nucleosomes. These nucleosomes further fold together into highly condensed chromatin, which renders the organism's genetic material far less accessible to the factors required for gene transcription, DNA replication, recombination and repair. Subsequently, eukaryotic organisms have developed intricate mechanisms to overcome this repressive barrier imposed by the chromatin through histone modification, a type of post-translational modification which typically involves covalently attaching certain groups to histone residues. Once added to the histone, these groups elicit either a loose and open histone conformation, euchromatin, or a tight and closed histone conformation, heterochromatin. Euchromatin marks active transcription and gene expression, as the light packing of histones in this way allows entry for proteins involved in the transcription process. As such, the tightly packed heterochromatin marks the absence of current gene expression.
Histone-binding protein RBBP4 is a protein that in humans is encoded by the RBBP4 gene.
While the cellular and molecular mechanisms of learning and memory have long been a central focus of neuroscience, it is only in recent years that attention has turned to the epigenetic mechanisms behind the dynamic changes in gene transcription responsible for memory formation and maintenance. Epigenetic gene regulation often involves the physical marking of DNA or associated proteins to cause or allow long-lasting changes in gene activity. Epigenetic mechanisms such as DNA methylation and histone modifications have been shown to play an important role in learning and memory.
H3K27ac is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates acetylation of the lysine residue at N-terminal position 27 of the histone H3 protein.
H4K16ac is an epigenetic modification to the DNA packaging protein Histone H4. It is a mark that indicates the acetylation at the 16th lysine residue of the histone H4 protein.
H4K5ac is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the acetylation at the 5th lysine residue of the histone H4 protein. H4K5 is the closest lysine residue to the N-terminal tail of histone H4. It is enriched at the transcription start site (TSS) and along gene bodies. Acetylation of histone H4K5 and H4K12ac is enriched at centromeres.
H4K8ac, representing an epigenetic modification to the DNA packaging protein histone H4, is a mark indicating the acetylation at the 8th lysine residue of the histone H4 protein. It has been implicated in the prevalence of malaria.
H4K12ac is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the acetylation at the 12th lysine residue of the histone H4 protein. H4K12ac is involved in learning and memory. It is possible that restoring this modification could reduce age-related decline in memory.
H4K91ac is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the acetylation at the 91st lysine residue of the histone H4 protein. No known diseases are attributed to this mark but it might be implicated in melanoma.
H3K23ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 23rd lysine residue of the histone H3 protein.
H3K36ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 36th lysine residue of the histone H3 protein.
H3K56ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 56th lysine residue of the histone H3 protein.