Exploring Chromatin Remodeling: New Progress in Gene Regulation, Disease Correlation and Detection Technology

Chromatin remodeling refers to the process of changing the chromatin structure by regulating factors such as transcription factors, histone modifying enzymes and ATP-dependent remodeling complexes. This process includes changing nucleosome density, nucleosome assembly mode, and even adjusting the structure of the whole chromatin region, which directly affects chromatin accessibility and gene expression.

What is Chromatin Remodeling

Chromatin remodeling is to dynamically adjust the spatial conformation of genome through the action of a series of enzymes and complexes, so that DNA can be more easily combined with transcription factors or other regulatory proteins. These enzymes include SWI/SNF complex, CHRAC, ISWI, etc. They provide energy through ATP hydrolysis and rearrange the DNA on histones, thus changing the structure of chromatin. For example, histone acetyltransferases such as p300 and CBP promote chromatin loosening by acetylating histone H3, thus enhancing gene expression.

Mechanism of chromatin remodeling

• Nucleosome sliding: nucleosome is the basic structural unit of chromatin, which is formed by DNA winding histone octamer. In the process of chromatin remodeling, some remodeling complexes can use the energy generated by ATP hydrolysis to make nucleosomes slide along DNA chains. In this way, the DNA sequence originally covered by nucleosome may be exposed, which is convenient for protein binding of transcription factors and so on, thus promoting gene transcription; Or the original exposed DNA sequence is covered by nucleosome again, which hinders the combination of transcription factors and inhibits gene expression.
• Nucleosome removal: Some chromatin remodeling complexes can completely remove nucleosomes from DNA, so that large fragments of DNA sequences can be fully exposed. This provides a broad binding space for transcription-related proteins such as transcription factors and RNA polymerase, which greatly promotes the transcription activation of genes. This method usually plays an important role in the critical stage of gene expression activation, or when a large number of protein binding and regulation are needed for specific DNA regions.

Nucleosome core particle involves the formationand propagation of DNA loops (Morgan et al., 2020)

• Histone variant substitution: there are many variants of histone, which are different from conventional histone in amino acid sequence and structure. In the process of chromatin remodeling, some complexes can replace conventional histones with histone variants. For example, H2A.Z is a common histone variant. After replacing H2A, it will make the nucleosome structure unstable, increase the accessibility of DNA, and thus affect the expression state of genes. Different histone variants play a unique regulatory role in different biological processes and cell environments, and change the functional characteristics of chromatin through substitution.

The network of interactions between the DNA, histones, and the chromatin remodelers that influence nucleosome repositioning (Morgan et al., 2020)

• Histone modification: The tail of histone can undergo many covalent modifications, such as methylation, acetylation and phosphorylation. These modifications can change the interaction between histone and DNA, as well as the interaction between histones, and then affect the structure and function of chromatin. For example, histone acetylation usually weakens the binding force between histone and DNA, makes chromatin structure loose and promotes gene transcription. Histone methylation may activate or inhibit gene expression.

The genome into chromatin involves wrapping the DNA around octamers of histone proteins to form nucleosomes (Morgan et al., 2020)

Biological significance of chromatin remodeling

Chromatin remodeling is of great biological significance in gene expression regulation. It affects the transcriptional activity of genes by changing the topological structure and openness of chromatin. Specifically, chromatin remodeling enzymes such as SWI/SNF complex promote chromatin opening through histone acetylation and other mechanisms, thus enhancing transcription factor binding and gene expression. In addition, chromatin remodeling also involves the dynamic regulation of nucleosome remodeling and nucleosome localization, which have important effects on epigenetic regulation and gene expression.

Sequence-targeted chromatin remodeling can explain memory of nucleosome positions after replication (Bowman et al., 2017)

Chromatin remodeling not only affects the transcription activity of genes, but also participates in the regulation of gene methylation and chromatin structure, thus indirectly affecting gene expression. For example, chromatin remodeling factors can specifically target nucleosome positions through sequences, ensure the high fidelity and flexibility of nucleosome positions, and support cell dynamic processes. In disease states, such as cancer and developmental disorders, abnormal chromatin remodeling may lead to changes in global transcription programs.

Classifications of Chromatin Remodeling Complex

Chromatin remodeling complex is the key to regulate gene expression, DNA replication and repair and other important biological processes, molecular machines. According to whether it depends on ATP hydrolysis, chromatin remodeling complexes can be divided into two categories: ATP-dependent chromatin remodeling complexes and ATP-independent chromatin remodeling complexes.

ATP-dependent chromatin remodeling complexes

ATP-dependent chromatin remodeling complex drives nucleosome movement, recombination or exchange by hydrolyzing ATP, thus changing chromatin structure and increasing the accessibility of DNA to transcription factors and other protein. This kind of complex plays an important role in gene expression regulation, DNA replication and repair. Its function is realized through the following mechanisms.

• Nucleosome movement: By sliding or moving histone octamer, DNA is exposed, thus increasing the binding efficiency of transcription factors.
• Nucleosome recombination: By destroying and reassembling nucleosomes, the structure of chromatin is changed, thus affecting gene expression.
• Histone Variant Exchange: By exchanging histone H2A with H2A.Z or other histone variants, the chromatin dynamics can be regulated.

Single molecule studies of ATP-dependent chromatin remodeling (Choy et al., 2012)

These mechanisms enable ATP-dependent chromatin remodeling complex to play a role in many biological processes such as gene expression regulation, DNA replication and repair. For example, in gene expression regulation, SWI/SNF complexes increase the binding efficiency of transcription factors by sliding or moving nucleosomes, thus regulating the expression of specific genes. In the process of DNA replication, Isw2 and INO80 complexes support the advancement of replication fork by promoting the relocation and recombination of nucleosomes.

Classification of ATP-dependent chromatin remodeling complexes (Tang et al., 2010)

ATP-independent chromatin remodeling complexes

ATP-independent chromatin remodeling complex does not depend on ATP hydrolysis, but realizes the change of chromatin structure through other mechanisms. This kind of complex usually has higher specificity and faster reaction speed. Its features include:

• High specificity: it usually acts on specific DNA sequences or transcription factor binding sites.
• Fast response: These complexes can respond to the changes of signals inside and outside the cell more quickly because they do not depend on ATP hydrolysis.
• Multifunctional: In addition to chromatin remodeling, it may also participate in DNA repair, gene expression regulation and other biological processes.

Main chromatin remodeling enzymes and their functions

• RSC complex: Increasing the accessibility of DNA to transcription factors and regulating gene expression by sliding nucleosome.
• ACF/CHRAC complex: Increasing the accessibility of DNA to transcription factors and regulating gene expression by sliding nucleosome.
• SWI2/SNF2 related complex: Regulating gene expression by sliding or moving nucleosome.

Regulatory mechanisms of the SWI/SNF complex in various DNA damage repair pathways (Jian et al., 2021)

ATP-dependent chromatin remodeling complex and ATP-independent chromatin remodeling complex have their own unique functions and mechanisms in chromatin structure regulation. ATP-dependent complexes drive nucleosome movement and recombination by hydrolyzing ATP, and are widely involved in gene expression regulation, DNA replication and repair. However, ATP-independent complexes change chromatin structure through other mechanisms, which has higher specificity and faster reaction speed. The diversity and complexity of these complexes make them play a vital role in cell biology.

How to Regulate Gene Expression Through Chromatin Remodeling

Chromatin remodeling is an important mechanism to affect gene expression by changing the structure of chromatin. Specifically, chromatin remodeling can be achieved in the following ways:

• Histone modification: Amino acid residues at the tail of histone can undergo many covalent modifications, such as acetylation, methylation and phosphorylation. Among them, histone acetylation will neutralize the positive charge at the tail of histone, weaken the interaction between histone and DNA, loosen the chromatin structure, and make protein, such as transcription factors, more easily combine with DNA, thus promoting gene transcription and activating gene expression.
• Effect of chromatin remodeling complex: Chromatin remodeling complex can use the energy generated by ATP hydrolysis to move, remove or relocate nucleosomes, expose DNA sequences that were tightly wrapped by nucleosomes, and provide binding sites for transcription-related proteins such as transcription factors and RNA polymerase, thus activating gene expression.
• Interaction between enhancer and promoter: Chromatin remodeling can shorten the space between Enhancer and Promoter, form a specific chromatin ring structure, enable transcription activating factors bound to Enhancer region to interact with transcription machines in Promoter region, recruit RNA polymerase, etc., promote the initiation of gene transcription, and then activate gene expression.

LncRNAs can regulate DNA and histone modifying proteins by recruiting chromatin remodeling complexes (Fan et al., 2022)

Chromatin remodeling plays an important role in the process of cell differentiation and development, and it has a close relationship with cell differentiation and development, which is embodied in the following aspects.

• Cell fate determination: Chromatin remodeling regulates the activity of transcription factors by changing chromatin structure and histone modification, thus determining the fate of cells. For example, in somatic cell reprogramming, chromatin remodeling complex helps cell fate change from somatic cells to pluripotent stem cells by precisely regulating nucleosome remodeling.

Chromatin remodeler and DNA transcription (Nussinov et al., 2023)

• Tissue-specific expression: Chromatin remodeling plays an important role in tissue-specific gene expression. For example, in the process of neuron differentiation, chromatin remodeling complex promotes the expression of neuron-specific genes by regulating the binding of core transcription factors such as Oct4.
• Dynamic changes during development: During embryonic development, chromatin remodeling promotes cell differentiation and organ formation by dynamically regulating gene expression. For example, in higher plants, chromatin remodeling affects the growth and development of plants by regulating the maintenance and directional differentiation of apical meristem.
• Epigenetic memory: Chromatin remodeling is also involved in the maintenance of epigenetic memory. For example, in memory CD8+ T cells, chromatin remodeling maintains the immune memory function of cells by dynamically regulating chromatin state.

Relationship Between Chromatin Remodeling and Diseases

The relationship between chromatin remodeling and diseases is a complex and multifaceted research field, involving cancer, hereditary diseases and the potential application of chromatin remodeling in disease treatment. The relationship between chromatin remodeling and diseases is discussed in detail from three aspects:

Chromatin remodeling and cancer

Chromatin remodeling plays a key role in the occurrence, development and treatment of cancer. Chromatin remodeling complex affects the occurrence and development of cancer by changing chromatin structure, regulating gene expression, DNA repair and cell cycle process.

• Gene expression regulation: Chromatin remodeling complexes such as SWI/SNF and BRG1 directly affect the transcription activity of genes by changing the openness and compressibility of chromatin. For example, BRG1 plays a positive regulatory role in the progression of colon cancer. In addition, the mutation or disorder of chromatin remodeling factor has been found in many cancers, such as the role of SMARCA1 in breast cancer.

Catalytic subunits of chromatin remodelers fall into four families (Laura et al., 2017)

• Mechanism of DNA repair: Chromatin remodeling factors such as SMARCAD1 play an important role in DNA damage repair, and their deletion is related to high-risk areas of breast cancer. In addition, the subunits of chromatin remodeling complex are mutated or disordered in many human cancers, which affects the cancer gene expression program. .
• Cell cycle regulation: Chromatin remodeling factors such as NuRD complex play an important role in cell cycle progression and DNA damage response. Ki-67 protein promotes the proliferation of tumor cells by interacting with chromatin remodeling factors.
• Cancer therapeutic target: Chromatin remodeling complex has become a therapeutic target because of its key role in cancer. For example, inhibitors targeting SWI/SNF complexes have been proposed to improve the efficiency of chemotherapy.

Chromatin remodeling in hereditary diseases

Chromatin remodeling not only plays a role in cancer, but also is closely related to a variety of hereditary diseases, which mainly leads to diseases by affecting gene expression and chromatin state.

• Neurodevelopmental disorders: Chromatin remodeling factors such as CHD4 and BRAF1 play an important role in neurodevelopmental disorders. CHD4 plays a key role in the formation of cardiac muscle fibers, and the mutation of BRAF1 is related to brain diseases.
• Congenital diseases: Mutations in chromatin remodeling factors may lead to congenital diseases. For example, mutations in the SH2B3 gene are associated with Laron syndrome.
• Regulation of X chromosome inactivation: Chromatin remodeling factors such as SMARCA2 and SMARCA4 play an important role in the regulation of X chromosome inactivation, and their abnormality may lead to genetic diseases such as Rett syndrome.

Application of chromatin remodeling in diseases diagnosis

The study of chromatin remodeling provides a new perspective and method for the diagnosis and treatment of diseases, which mainly leads to diseases by affecting gene expression and chromatin state.

• Diagnostic markers: The expression level or mutation state of chromatin remodeling factor can be used as a diagnostic marker of cancer. For example, H3Citcullinated H3 (H3Cit) is considered as a prognostic biomarker for advanced cancer.
• Therapeutic targets: Inhibitors or agonists targeting chromatin remodeling complex are being developed to treat cancer and other diseases. For example, inhibitors of SWI/SNF complex have been proposed to improve chemotherapy efficiency.
• Gene editing technology: CRISPR/Cas9 and other gene editing technologies can be used to study the function of chromatin remodeling factors and develop new treatment methods.

A schematic showing enhancer-promoter interactions constrictedby TAD boundaries (Kim et al., 2019)

Chromatin Remodeling Detection Technology

Chromatin remodeling detection technology is an important means to study chromatin structural changes and gene regulation mechanism. The following are some common detection technologies.

• Chromatin immunoprecipitation sequencing (ChIP-seq): Chromatin fragments bound to the target protein were immunoprecipitated by specific antibodies, and then these fragments were sequenced to determine the binding sites of protein to DNA in the whole genome, so as to infer the interaction between protein and chromatin during chromatin remodeling. It can be used to study the binding pattern of transcription factors, histone modifying enzymes and chromatin, and is widely used in analyzing the mechanism of chromatin remodeling in cell differentiation, development and disease occurrence.
• Methylation specific PCR (MSP): First, the genomic DNA is treated with bisulfite to convert unmethylated cytosine into uracil, while methylated cytosine remains unchanged. Then, specific primers for methylated and unmethylated sequences are designed for PCR amplification, and the amplified products are detected by electrophoresis or sequencing to judge the methylation status of specific gene regions. The change of methylation status is often related to chromatin remodeling. It is often used to detect the methylation status of tumor-related genes, and provide basis for early diagnosis and prognosis evaluation.
• Fluorescence in situ hybridization (FISH): The fluorescent labeled nucleic acid probe hybridizes with chromosome DNA in cells or tissues, and the position and intensity of fluorescent signal are observed by fluorescence microscope, which can directly display the position and copy number changes of specific DNA sequences on chromosomes, and can be used to detect chromatin remodeling-related events such as changes in chromatin structure and gene rearrangement. It is widely used in the diagnosis and typing of hematological diseases such as leukemia, and can detect abnormalities such as chromosome translocation and gene amplification.
• DNase-Seq: Using the characteristic that DNase I enzyme can preferentially cut open areas in chromatin, the cut DNA fragments are sequenced, and the open areas of chromatin, i.e. accessible areas of chromatin, are determined by analyzing the sequencing data. It is used to draw cell-specific chromatin accessibility maps and understand the differences of chromatin opening state in different cell types or cell States, which is helpful to analyze the role of gene regulatory elements in chromatin remodeling.

Conclusion

Chromatin remodeling is an important biological process in cells, which mainly involves the dynamic changes of chromatin structure. In this process, chromatin remodeling complex plays a key role, which provides energy through ATP hydrolysis, mediates physical changes such as nucleosome sliding, removal, relocation and the incorporation of histone variants, and is accompanied by covalent modification of histones, such as methylation, acetylation and phosphorylation. These changes can adjust the compactness and spatial conformation of chromatin.

Chromatin remodeling has a profound influence on gene expression regulation. When the chromatin structure becomes loose, DNA is more easily combined with transcription factors and RNA polymerase, thus promoting gene transcription. However, when the chromatin structure becomes compact, it will inhibit the expression of genes. In addition, chromatin remodeling is also involved in many important biological processes, such as cell differentiation, individual development, DNA damage repair and tumorigenesis, which plays an important role in maintaining normal cell function and the health of organisms.

References

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