Histone Acetyltransferases and Associated Proteins

Background

Histone acetyltransferases (HATs) are a group of enzymes that catalyze the addition of acetyl groups to specific lysine residues on histone proteins. This post-translational modification, known as histone acetylation, plays a crucial role in the regulation of gene expression and chromatin structure.

Non-histone protein acetylation can also be induced by a large majority of histone acetyltransferases (HATs). Thus, HATs have recently been renamed as lysine acetyltransferases (KATs). This family of enzymes has been divided into two main groups. Type A is the larger group and includes several sub-families. The members of type A HATs are mostly localized in the nucleus and classified into families according to their sequence homology. The Gcn5-related N-acetyltransferases (GNAT) family, includes both KAT2A and KAT2B. The p300/CBP (CREB-binding protein) family consists of KAT3A and 3B.

The MYST (MOZ, Ybf2/Sas3, Sas2, and TIP60) family represents the largest HAT family, which includes KAT5, KAT6A, KAT6B, KAT7, and KAT8. Type B HATs are abundant in the cytoplasm such as KAT1 and KAT4. The members of both CBP/P300 and GNAT families contain a bromodomain (BD) that mainly binds to the acetylated lysine rich region of histone proteins. Moreover, the members of CBP/P300 and MYST family members possess a cysteine rich, zinc-binding domain which facilitates binding to acetyl group. Some MYST family HATs contain in addition an N-terminal chromodomain, which binds to methylated lysine residues. HATs can also acetylate non-histone proteins that could influence their promotor activities and specificities, such as β-catenin, Myc proto-oncogene protein (C-MYC), tumor suppressor protein p53, and the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB).

Fig.1 Different HAT/KAT subtypes and their domains. (Elmallah MIY, et al., 2019)

HATs typically consist of a catalytic domain responsible for acetyl group transfer and additional domains that contribute to their specific functions. The catalytic domain contains a conserved motif called the acetyl-CoA binding site, which binds to acetyl-CoA, the acetyl donor, and transfers the acetyl group to the target lysine residue on histones. The other domains present in HATs are responsible for protein-protein interactions, DNA binding, and recruitment to specific gene loci.

The biological processes in which HATs are involved are diverse and essential. Histone acetylation by HATs neutralizes the positive charge on lysine residues, leading to an open chromatin structure that allows access to transcription factors and other regulatory proteins. This facilitates gene transcription and regulates various cellular processes such as cell differentiation, development, DNA repair, and cell signaling. Furthermore, HATs can acetylate non-histone proteins, including transcription factors and coactivators, expanding their regulatory roles beyond chromatin remodeling. The acetylation of these non-histone proteins can influence protein-protein interactions, protein stability, and subcellular localization, thereby impacting gene expression and cellular functions.

Representative Members of Histone Acetyltransferases and Associated Proteins

Members	Classification and function
CLOCK	CLOCK is a HAT. CLOCK is a transcriptional coactivator that interacts with other proteins to regulate gene expression and circadian rhythms. It plays a crucial role in the circadian clock and the control of various physiological processes.
CBP and EP300	CBP (CREB-binding protein) and EP300 (p300) belong to the same family of HATs. CBP and EP300 are multifunctional transcriptional coactivators. They interact with numerous transcription factors and nuclear receptors and promote gene transcription by adding acetyl groups to histones. They are involved in cell differentiation, development, and cell cycle regulation. EP300 participates in cell differentiation, embryonic development, and tumor suppression.
CREBBP	CREBBP (CREB-binding protein) is a member of the CBP family and a HAT. CREBBP interacts with various transcription factors and nuclear receptors to enhance gene transcription. It is involved in cell differentiation, development, and the functioning of the nervous system. Mutations or deletions in the CREBBP gene are associated with neurodevelopmental disorders such as Rubinstein-Taybi syndrome.
KAT2A and KAT2B	KAT2A (GCN5) and KAT2B (PCAF) are members of the GNAT family of HATs. KAT2A and KAT2B participate in gene transcription regulation, particularly genes involved in cell cycle control, cell differentiation, and DNA repair. They play important roles in cellular differentiation, embryonic development, and tumor suppression.
KAT5, KAT6A, KAT6B and KAT7	KAT5, KAT6A (MOZ), KAT6B (MORF), and KAT7 are members of the MYST family of HATs. They are all involved in gene transcription regulation and participate in DNA repair, cell cycle control, apoptosis, and cell differentiation. They interact with transcription factors and other coactivators to regulate gene expression.
NCOA1, NCOA2, and NCOA3 (Nuclear receptor coactivators)	NCOA1 (SRC-1), NCOA2 (GRIP1/TIF2), and NCOA3 (SRC-3/AIB1) are coactivators of nuclear receptors and interact with HATs. NCOAs interact with nuclear receptors and cooperate with HATs to regulate gene transcription. They play roles in various biological processes, including cell differentiation, embryonic development, metabolic regulation, and reproductive system development.
TAF1	TAF1 (Transcription factor TAF1) belongs to the family of transcription factors. TAF1 is a component of the transcription initiation factor complex TFIID. It plays a crucial role in transcriptional regulation by promoting gene transcription initiation. TAF1 interacts with other transcription factors and coactivators, including HATs, and contributes to histone acetylation and chromatin remodeling, thereby regulating gene expression.

These histone acetyltransferases and their related proteins play an important role in regulating gene transcription, cell cycle, cell differentiation, DNA repair, and other biological processes. They interact and form a complex regulatory network to ensure the precise regulation of gene expression and the normal operation of cell function.

Mechanism of Histone Acetylation by HATs

The mechanism of histone acetylation by HATs involves the transfer of an acetyl group from acetyl-CoA to specific lysine residues on histone proteins. Here's a step-by-step explanation of the process:

1. HAT binding: HATs recognize specific target sites on histones through their associated domains, allowing them to be recruited to specific gene loci or chromatin regions.
2. Acetyl-CoA binding: HATs contain a conserved acetyl-CoA binding site within their catalytic domain. Acetyl-CoA, which serves as the acetyl donor, binds to this site.
3. Acetyl transfer: Once acetyl-CoA is bound, the HAT transfers the acetyl group to the ε-amino group of a specific lysine residue on the histone tail. This transfer results in the formation of an acetyl-lysine bond and the release of CoA.
4. Neutralization of positive charge: The addition of an acetyl group neutralizes the positive charge on the lysine residue, disrupting the electrostatic interaction between the positively charged histone tail and the negatively charged DNA backbone. This alteration leads to a more relaxed chromatin structure.

Effects on Gene Expression

Histone acetylation, mediated by HATs, has significant effects on gene expression. Here are some key impacts:

Significant effects	Details
Chromatin remodeling	Histone acetylation alters the interaction between histones and DNA, resulting in a more relaxed chromatin structure. The open chromatin conformation allows transcription factors and other regulatory proteins to access DNA more readily, promoting gene transcription.
Transcriptional activation	Acetylated histones create a permissive environment for transcriptional machinery to assemble at gene promoters. Acetylation neutralizes the positive charge on histones, reducing their affinity for DNA and facilitating the binding of transcription factors and RNA polymerase II. This process enhances transcriptional activation and increases gene expression.
Recruitment of chromatin remodelers and coactivators	Histone acetylation serves as a binding platform for chromatin remodelers and transcriptional coactivators. Acetyl-lysine residues act as docking sites for these proteins, promoting their recruitment to specific gene loci. Chromatin remodelers can alter nucleosome positioning, further facilitating transcription factor access to DNA, while coactivators enhance transcriptional activation by interacting with the transcriptional machinery.
Epigenetic memory	Histone acetylation can establish stable epigenetic marks associated with active gene expression. Acetylated histones can recruit additional HATs, leading to a self-perpetuating cycle of acetylation. These modified histones can be recognized by specific reader proteins, which maintain the acetylated state during cell division and ensure the faithful transmission of gene expression patterns.

Overall, histone acetylation by HATs plays a critical role in modulating gene expression by promoting an open chromatin structure, facilitating transcription factor binding, and recruiting coactivators. These modifications contribute to the activation of gene expression programs involved in various cellular processes, such as development, differentiation, and response to environmental cues.

Biological Functions of HATs

HATs play crucial roles in various biological processes by modifying histone proteins and regulating chromatin structure. Here are some important biological functions of HATs:

Biological functions	Details
Transcriptional activation	HATs are key regulators of gene expression. By acetylating specific lysine residues on histones, HATs create a permissive chromatin environment that facilitates transcriptional activation. Acetylation neutralizes the positive charge on histones, leading to a more relaxed chromatin structure, increased accessibility of DNA to transcription factors, and enhanced recruitment of the transcriptional machinery. HAT-mediated transcriptional activation is essential for driving various cellular processes, including development, differentiation, and response to environmental cues.
Chromatin remodeling	HATs interact with ATP-dependent chromatin remodeling complexes to modulate chromatin structure. These complexes use energy from ATP hydrolysis to reposition or evict nucleosomes, altering the accessibility of DNA. HATs contribute to chromatin remodeling by acetylating histones and creating a favorable environment for chromatin remodelers to function. This interplay between HATs and chromatin remodelers allows for precise regulation of gene expression and dynamic control of chromatin states.
Epigenetic memory	HAT-mediated histone acetylation can establish stable epigenetic marks associated with active gene expression. Acetylated histones serve as docking sites for reader proteins that recognize and maintain the acetylated state during cell division and in subsequent generations of cells. This epigenetic memory ensures the faithful transmission of gene expression patterns and contributes to cellular identity and differentiation.
Development and differentiation	HATs are essential for embryonic development and cell differentiation processes. They regulate the expression of genes involved in lineage commitment, cell fate determination, and tissue-specific functions. HATs cooperate with transcription factors and other coactivators to establish and maintain the appropriate gene expression programs required for the proper development and differentiation of cells and tissues.
DNA repair and genome stability	HATs play roles in DNA repair processes, ensuring genome stability. They are involved in the recruitment and activation of factors required for DNA repair pathways, such as nucleotide excision repair (NER) and double-strand break repair. HAT-mediated histone acetylation helps create an open chromatin structure at sites of DNA damage, allowing efficient repair machinery assembly and access to damaged DNA.
Cellular response to stress and signaling	HATs participate in the cellular response to various stress signals and signaling pathways. They can be recruited to gene promoters in response to extracellular stimuli, hormones, or environmental cues, leading to changes in gene expression and cellular adaptations. HATs contribute to the activation of stress-responsive genes and the modulation of signaling pathways involved in cell survival, proliferation, and differentiation.

These biological functions highlight the diverse roles of HATs in regulating gene expression, chromatin structure, and cellular processes. The precise control of histone acetylation by HATs is essential for the maintenance of cellular homeostasis and proper functioning of various biological systems.

HATs in Development, Differentiation, and Disease Processes

HATs play critical roles in development, differentiation, and disease processes. Here's a closer look at their specific contributions:

Specific contributions		Details
Development and Differentiation	Lineage commitment	HATs are involved in the establishment of lineage commitment during development. During embryonic development, HATs regulate the expression of key transcription factors and developmental genes that drive the specification of distinct cell lineages. HATs contribute to the activation of lineage-specific gene expression programs required for proper tissue development and differentiation. For instance, the HAT p300/CBP (CREB-binding protein) interacts with the transcription factor GATA4 to activate cardiac-specific gene expression, promoting the commitment of cells to the cardiac lineage.
	Cell fate determination	HATs participate in cell fate determination by regulating the expression of genes that influence cell identity and function. Through histone acetylation, HATs create permissive chromatin environments that allow lineage-specific transcription factors to access and activate their target genes. This precise regulation of gene expression by HATs is crucial for cell fate decisions during development. For example, the HAT MOZ (also known as KAT6A) is essential for hematopoiesis. MOZ acetylates histones at the promoters of genes important for hematopoietic stem cell self-renewal and differentiation, thereby influencing cell fate decisions in the blood cell lineage.
	Tissue-specific gene expression	HATs play a role in establishing tissue-specific gene expression patterns. They contribute to the activation of tissue-specific genes and the maintenance of their expression in a cell type- and context-dependent manner. HATs interact with tissue-specific transcription factors and coactivators to establish and maintain the appropriate chromatin state required for tissue-specific gene expression. The HAT PCAF (p300/CBP-associated factor) interacts with the transcription factor MyoD to activate muscle-specific genes, playing a crucial role in muscle development and differentiation.
Disease Mechanisms	Cancer	Dysregulation of HATs has been implicated in various aspects of cancer development and progression. Alterations in HAT activity can lead to aberrant histone acetylation patterns, resulting in disrupted gene expression profiles. HATs can act as oncogenes or tumor suppressors depending on the context. For example, the overexpression of certain HATs has been associated with increased histone acetylation levels at oncogenes, promoting their activation and driving tumor growth. Conversely, mutations or reduced expression of HATs can result in global hypoacetylation, leading to transcriptional silencing of tumor suppressor genes. For instance, the HAT p300 is frequently mutated in certain cancers, such as colorectal cancer and leukemia. Mutations in p300 can disrupt its normal acetyltransferase function, leading to altered gene expression and promoting oncogenesis.
	Neurological disorders	HATs are involved in the regulation of gene expression in the nervous system and play a role in neurodevelopment, synaptic plasticity, and neuronal function. Dysregulation of HATs has been linked to neurological disorders such as Alzheimer's disease, Huntington's disease, and Parkinson's disease. Aberrant histone acetylation patterns mediated by HATs can impact the expression of genes involved in neuronal survival, synaptic plasticity, and neurotransmitter signaling, contributing to disease pathogenesis.
	Metabolic diseases	HATs have been implicated in the regulation of metabolic processes and the development of metabolic disorders. HATs can modulate the expression of genes involved in lipid metabolism, glucose homeostasis, and energy balance. Dysregulation of HAT activity has been associated with conditions like obesity, diabetes, and metabolic syndrome. Altered histone acetylation patterns mediated by HATs can disrupt metabolic gene expression profiles, leading to deranged metabolic pathways and disease phenotypes.

Understanding the roles of HATs in development, differentiation, and disease is crucial for unraveling the underlying molecular mechanisms and identifying potential therapeutic targets. Targeting HAT activity or specific HAT isoforms holds promise for modulating gene expression patterns and restoring proper cellular function in various developmental disorders and diseases.

Case Study

Case 1: Liang F, Li X, Shen X, Yang R, Chen C. Expression profiles and functional prediction of histone acetyltransferases of the MYST family in kidney renal clear cell carcinoma. BMC Cancer. 2023;23(1):586.

The MYST family of histone acetyltransferases (HATs) has been implicated in various human cancers. However, their clinical significance in kidney renal clear cell carcinoma (KIRC) has not been thoroughly studied. In KIRC tissues, the expression levels of MYST HATs, except KAT8, were significantly reduced compared to normal renal tissues. This reduction was associated with high tumor grade, advanced TNM stage, and an unfavorable prognosis in KIRC patients.

The expression levels of MYST HATs were closely correlated with each other. Gene set enrichment analysis revealed functional differences between KAT5 and KAT6A, KAT6B, and KAT7. Additionally, the expression levels of KAT6A, KAT6B, and KAT7 showed significant positive correlations with immune cell infiltrates such as B cells, CD4+ T cells, and CD8+ T cells in KIRC. Tumor-infiltrating lymphocytes were identified as potential independent predictors of overall survival and sentinel lymph node status in cancer patients.

Fig.1 The correlations between the MYST HAT expression and immune infiltration level in KIRC.

Case 2: Chen M, Liu Y, Liu Z, et al. Histone acetyltransferase Gcn5-mediated histone H3 acetylation facilitates cryptococcal morphogenesis and sexual reproduction. mSphere. 2023;8(6):e0029923.

The sexual life cycle of Cryptococcus neoformans involves the transition from yeast to hyphae, followed by hyphal extension, basidium differentiation, meiosis, and sporulation. While previous studies have focused on genetic factors and pathways in this process, the role of epigenetic modifications remains unclear. In a genetic screening assay, researchers discovered that Gcn5, a specific histone acetyltransferase, is involved in yeast-hyphae morphogenesis in C. neoformans. They demonstrated that Gcn5 is essential for the entire sexual cycle, including the yeast-hyphae transition, hyphal development, basidium differentiation, meiosis, and sporulation.

The study investigated the effect of Gcn5 on histone acetylation in C. neoformans. Disruption of the GCN5 gene resulted in a significant decrease in histone H3 acetylation at specific lysine sites, indicating the role of Gcn5 in mediating histone acetylation in a manner similar to its homolog in S. cerevisiae. Reintroducing the GCN5 gene restored filamentation initiation and hyphal development in the gcn5Δ mutant during unisexual mating. Gcn5 was also found to be crucial for filamentation during bisexual mating.

Fig.2 Gcn5 is responsible for histone H3 acetylation and is required for filamentation and cell-cell fusion in response to mating stimulation.

Related References

• Marmorstein R, Roth SY. Histone acetyltransferases: function, structure, and catalysis. Curr Opin Genet Dev. 2001;11(2):155-161.
• Liew LC, Singh MB, Bhalla PL. An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process. PLoS One. 2013;8(10):e77502.
• Elmallah MIY, Micheau O. Epigenetic regulation of TRAIL signaling: implication for cancer therapy. Cancers (Basel). 2019;11(6):850.