{"title":"乙酰甲基赖氨酸:用于标记染色质的一种新的翻译后修饰","authors":"Hua Guo, Fangfang Zhou, Long Zhang","doi":"10.1002/mef2.74","DOIUrl":null,"url":null,"abstract":"<p>A recent study, conducted by Lu-Culligan et al., published in <i>Nature</i>, proposed <i>N<sup>ε</sup></i>-acetyl-<i>N<sup>ε</sup></i> -methyllysine (Kacme) that both methylation and acetylation occur on the same side chain of lysine as a cellular posttranslational modification (PTM) on histone H4.<span><sup>1</sup></span> Kacme can be recognized and bound by the chromatin protein bromodomain-containing 2 (BRD2), associating with active chromatin marks and enhanced transcriptional initiation. This discovery offers a novel avenue for investigation of chromatin biology (Figure 1).</p><p>Histones play a crucial role in regulating gene expression and chromatin structure through PTMs such as acetylation (Kac) and methylation (Kme), impacting transcriptional activity. Acetylation neutralizes histone's positive charge, weakening the DNA–histone interaction for easier binding with transcription factors. Unlike acetylation, methylation affects reader protein binding and leads to changes in chromatin structure, resulting in transcription suppression or activation.<span><sup>2</sup></span> Although it is commonly believed that acetylation and monomethylation are mutually exclusive modifications on a single residue, chemical principles permit a lysine residue to be stably acetylated and monomethylated to create a tertiary amide, Kacme.</p><p>To provide evidence for the existence of Kacme in cellular proteins, researchers synthesized Fmoc–Lys (Ac, Me)-OH as a building block to create a central Kacme residue peptide library and used them as an antigen to generate a specific antiserum against Kacme.<span><sup>1</sup></span> Kacme antisera demonstrated high specificity toward Kacme peptides but not otherwise identical Kac, Kme1, and propionyllysine (Kpr). By utilizing this antiserum, researchers analyzed intracellular Kacme modifications in fruit fly, mouse, and human cell lines and identified histone H4 Lys5 and Lys12 as Kacme-modified sites in human cells. To confirm Kacme modification through an antisera-independent approach, the authors isotopically labeled the synthetic H4K5acme peptide to obtain distinct ion diagnostic peaks before conducting intracellular proteomic analysis, which further supported the presence of Kacme in histones.</p><p>Chromatin immunoprecipitation sequencing (ChIP-seq) is an extremely powerful tool for studying interactions between multiple transcription factors and other chromatin-associated proteins and DNA.<span><sup>3</sup></span> By performing ChIP-seq with Kacme antisera in fruit flies and human cells, the authors found that Kacme was significantly enriched around gene promoters, especially in highly expressed genes, and its localization was strongly associated with active chromatin modifications. Subsequently, Lu-Culligan et al. conducted transient-transcriptome time-lapse sequencing to examine transcriptional activity, and start-time-lapse sequencing to investigate the kinetics of promoter–proximal pausing,<span><sup>1</sup></span> confirming the positive correlation between Kacme and both transcription and transcription initiation.</p><p>The lysine residue in the Kacme form undergoes monomethylation and subsequent acetylation, linking Kacme modifications to two enzymes: lysine methyltransferases (KMT) and acetyltransferases (KAT). Through analysis of previous ChIP-seq data, the authors identified that KAT p300 specifically acetylates Kme1 to generate Kacme, providing substantial evidence for this enzymatic process. Consistent results were observed in cell lines treated with A-485 (a p300 inhibitor).</p><p>Next, researchers focused on eliminating the Kacme modifications. By employing immunoblotting and proteomic techniques, the authors observed an increased Kacme signal in cells treated with trichostatin A, an inhibitor of histone deacetylase (HDAC)/zinc hydrolase. Simultaneously, they discovered that HDAC1 and HDAC3 could remove the acetyl group from H4K5ac but not H4K5acme in vitro. These findings support the idea that Kacme shares chemical and functional properties with Kac; however, its susceptibility to scavenging reactions varies significantly.<span><sup>1</sup></span></p><p>Bromodomain-containing proteins (BRDs) are conserved protein–protein interaction modules that selectively recognize and bind to acetylated lysine residues, particularly in histones, and play a crucial role in regulating gene expression.<span><sup>4</sup></span> BRD2 was selectively enriched in extracts using biotinylated Kacme peptides, along with BRD3 and GAS41, indicating that Kacme has the ability to identify and interact with chromatin proteins. By the crystal structural and isothermal titration calorimetry analysis, the authors demonstrated that Kacme residues occupy the same binding pocket on BRD2 that has been shown to bind Kac residues and identified asparagine (N156) as a critical residue for Kacme and BRD2 interaction.</p><p>In conclusion, a new modification, in which both methylation and acetylation occur at the same lysine residue, raises both opportunities and challenges in chromatin biology and related disease. For example, targeting the different sensitivities of Kacme and Kac to deacetylase may offer new treatment strategies for deacetylase-related diseases. Moreover, the chemical characteristics of Kacme resemble those of neutral Kac, suggesting its involvement in nonhistone proteins, which are crucial in various cellular processes or may be related to diseases, reinforcing the importance of this novel modification. One limitation of studying Kacme is its interaction with Kac, Kme, and other factors that may cause interference and affect the reliability of experimental results during the analysis. This paper introduces novel concepts and methods for studying protein modifications by proposing reasonable hypotheses, followed by chemical biological synthesis of modified peptides and subsequent verification through biological experiments. Although these new ideas come with complex methods and technologies, continuous progress in science and technology will overcome these challenges.</p><p>Hua Guo wrote the manuscript and prepared the figure. Fangfang Zhou and Long Zhang provided valuable discussion. All authors have read and approved the article.</p><p>The authors declare no conflict of interest.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"3 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.74","citationCount":"0","resultStr":"{\"title\":\"Acetyl-methyllysine: A new posttranslational modification used to mark chromatin\",\"authors\":\"Hua Guo, Fangfang Zhou, Long Zhang\",\"doi\":\"10.1002/mef2.74\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>A recent study, conducted by Lu-Culligan et al., published in <i>Nature</i>, proposed <i>N<sup>ε</sup></i>-acetyl-<i>N<sup>ε</sup></i> -methyllysine (Kacme) that both methylation and acetylation occur on the same side chain of lysine as a cellular posttranslational modification (PTM) on histone H4.<span><sup>1</sup></span> Kacme can be recognized and bound by the chromatin protein bromodomain-containing 2 (BRD2), associating with active chromatin marks and enhanced transcriptional initiation. This discovery offers a novel avenue for investigation of chromatin biology (Figure 1).</p><p>Histones play a crucial role in regulating gene expression and chromatin structure through PTMs such as acetylation (Kac) and methylation (Kme), impacting transcriptional activity. Acetylation neutralizes histone's positive charge, weakening the DNA–histone interaction for easier binding with transcription factors. Unlike acetylation, methylation affects reader protein binding and leads to changes in chromatin structure, resulting in transcription suppression or activation.<span><sup>2</sup></span> Although it is commonly believed that acetylation and monomethylation are mutually exclusive modifications on a single residue, chemical principles permit a lysine residue to be stably acetylated and monomethylated to create a tertiary amide, Kacme.</p><p>To provide evidence for the existence of Kacme in cellular proteins, researchers synthesized Fmoc–Lys (Ac, Me)-OH as a building block to create a central Kacme residue peptide library and used them as an antigen to generate a specific antiserum against Kacme.<span><sup>1</sup></span> Kacme antisera demonstrated high specificity toward Kacme peptides but not otherwise identical Kac, Kme1, and propionyllysine (Kpr). By utilizing this antiserum, researchers analyzed intracellular Kacme modifications in fruit fly, mouse, and human cell lines and identified histone H4 Lys5 and Lys12 as Kacme-modified sites in human cells. To confirm Kacme modification through an antisera-independent approach, the authors isotopically labeled the synthetic H4K5acme peptide to obtain distinct ion diagnostic peaks before conducting intracellular proteomic analysis, which further supported the presence of Kacme in histones.</p><p>Chromatin immunoprecipitation sequencing (ChIP-seq) is an extremely powerful tool for studying interactions between multiple transcription factors and other chromatin-associated proteins and DNA.<span><sup>3</sup></span> By performing ChIP-seq with Kacme antisera in fruit flies and human cells, the authors found that Kacme was significantly enriched around gene promoters, especially in highly expressed genes, and its localization was strongly associated with active chromatin modifications. Subsequently, Lu-Culligan et al. conducted transient-transcriptome time-lapse sequencing to examine transcriptional activity, and start-time-lapse sequencing to investigate the kinetics of promoter–proximal pausing,<span><sup>1</sup></span> confirming the positive correlation between Kacme and both transcription and transcription initiation.</p><p>The lysine residue in the Kacme form undergoes monomethylation and subsequent acetylation, linking Kacme modifications to two enzymes: lysine methyltransferases (KMT) and acetyltransferases (KAT). Through analysis of previous ChIP-seq data, the authors identified that KAT p300 specifically acetylates Kme1 to generate Kacme, providing substantial evidence for this enzymatic process. Consistent results were observed in cell lines treated with A-485 (a p300 inhibitor).</p><p>Next, researchers focused on eliminating the Kacme modifications. By employing immunoblotting and proteomic techniques, the authors observed an increased Kacme signal in cells treated with trichostatin A, an inhibitor of histone deacetylase (HDAC)/zinc hydrolase. Simultaneously, they discovered that HDAC1 and HDAC3 could remove the acetyl group from H4K5ac but not H4K5acme in vitro. These findings support the idea that Kacme shares chemical and functional properties with Kac; however, its susceptibility to scavenging reactions varies significantly.<span><sup>1</sup></span></p><p>Bromodomain-containing proteins (BRDs) are conserved protein–protein interaction modules that selectively recognize and bind to acetylated lysine residues, particularly in histones, and play a crucial role in regulating gene expression.<span><sup>4</sup></span> BRD2 was selectively enriched in extracts using biotinylated Kacme peptides, along with BRD3 and GAS41, indicating that Kacme has the ability to identify and interact with chromatin proteins. By the crystal structural and isothermal titration calorimetry analysis, the authors demonstrated that Kacme residues occupy the same binding pocket on BRD2 that has been shown to bind Kac residues and identified asparagine (N156) as a critical residue for Kacme and BRD2 interaction.</p><p>In conclusion, a new modification, in which both methylation and acetylation occur at the same lysine residue, raises both opportunities and challenges in chromatin biology and related disease. For example, targeting the different sensitivities of Kacme and Kac to deacetylase may offer new treatment strategies for deacetylase-related diseases. Moreover, the chemical characteristics of Kacme resemble those of neutral Kac, suggesting its involvement in nonhistone proteins, which are crucial in various cellular processes or may be related to diseases, reinforcing the importance of this novel modification. One limitation of studying Kacme is its interaction with Kac, Kme, and other factors that may cause interference and affect the reliability of experimental results during the analysis. This paper introduces novel concepts and methods for studying protein modifications by proposing reasonable hypotheses, followed by chemical biological synthesis of modified peptides and subsequent verification through biological experiments. Although these new ideas come with complex methods and technologies, continuous progress in science and technology will overcome these challenges.</p><p>Hua Guo wrote the manuscript and prepared the figure. Fangfang Zhou and Long Zhang provided valuable discussion. 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Acetyl-methyllysine: A new posttranslational modification used to mark chromatin
A recent study, conducted by Lu-Culligan et al., published in Nature, proposed Nε-acetyl-Nε -methyllysine (Kacme) that both methylation and acetylation occur on the same side chain of lysine as a cellular posttranslational modification (PTM) on histone H4.1 Kacme can be recognized and bound by the chromatin protein bromodomain-containing 2 (BRD2), associating with active chromatin marks and enhanced transcriptional initiation. This discovery offers a novel avenue for investigation of chromatin biology (Figure 1).
Histones play a crucial role in regulating gene expression and chromatin structure through PTMs such as acetylation (Kac) and methylation (Kme), impacting transcriptional activity. Acetylation neutralizes histone's positive charge, weakening the DNA–histone interaction for easier binding with transcription factors. Unlike acetylation, methylation affects reader protein binding and leads to changes in chromatin structure, resulting in transcription suppression or activation.2 Although it is commonly believed that acetylation and monomethylation are mutually exclusive modifications on a single residue, chemical principles permit a lysine residue to be stably acetylated and monomethylated to create a tertiary amide, Kacme.
To provide evidence for the existence of Kacme in cellular proteins, researchers synthesized Fmoc–Lys (Ac, Me)-OH as a building block to create a central Kacme residue peptide library and used them as an antigen to generate a specific antiserum against Kacme.1 Kacme antisera demonstrated high specificity toward Kacme peptides but not otherwise identical Kac, Kme1, and propionyllysine (Kpr). By utilizing this antiserum, researchers analyzed intracellular Kacme modifications in fruit fly, mouse, and human cell lines and identified histone H4 Lys5 and Lys12 as Kacme-modified sites in human cells. To confirm Kacme modification through an antisera-independent approach, the authors isotopically labeled the synthetic H4K5acme peptide to obtain distinct ion diagnostic peaks before conducting intracellular proteomic analysis, which further supported the presence of Kacme in histones.
Chromatin immunoprecipitation sequencing (ChIP-seq) is an extremely powerful tool for studying interactions between multiple transcription factors and other chromatin-associated proteins and DNA.3 By performing ChIP-seq with Kacme antisera in fruit flies and human cells, the authors found that Kacme was significantly enriched around gene promoters, especially in highly expressed genes, and its localization was strongly associated with active chromatin modifications. Subsequently, Lu-Culligan et al. conducted transient-transcriptome time-lapse sequencing to examine transcriptional activity, and start-time-lapse sequencing to investigate the kinetics of promoter–proximal pausing,1 confirming the positive correlation between Kacme and both transcription and transcription initiation.
The lysine residue in the Kacme form undergoes monomethylation and subsequent acetylation, linking Kacme modifications to two enzymes: lysine methyltransferases (KMT) and acetyltransferases (KAT). Through analysis of previous ChIP-seq data, the authors identified that KAT p300 specifically acetylates Kme1 to generate Kacme, providing substantial evidence for this enzymatic process. Consistent results were observed in cell lines treated with A-485 (a p300 inhibitor).
Next, researchers focused on eliminating the Kacme modifications. By employing immunoblotting and proteomic techniques, the authors observed an increased Kacme signal in cells treated with trichostatin A, an inhibitor of histone deacetylase (HDAC)/zinc hydrolase. Simultaneously, they discovered that HDAC1 and HDAC3 could remove the acetyl group from H4K5ac but not H4K5acme in vitro. These findings support the idea that Kacme shares chemical and functional properties with Kac; however, its susceptibility to scavenging reactions varies significantly.1
Bromodomain-containing proteins (BRDs) are conserved protein–protein interaction modules that selectively recognize and bind to acetylated lysine residues, particularly in histones, and play a crucial role in regulating gene expression.4 BRD2 was selectively enriched in extracts using biotinylated Kacme peptides, along with BRD3 and GAS41, indicating that Kacme has the ability to identify and interact with chromatin proteins. By the crystal structural and isothermal titration calorimetry analysis, the authors demonstrated that Kacme residues occupy the same binding pocket on BRD2 that has been shown to bind Kac residues and identified asparagine (N156) as a critical residue for Kacme and BRD2 interaction.
In conclusion, a new modification, in which both methylation and acetylation occur at the same lysine residue, raises both opportunities and challenges in chromatin biology and related disease. For example, targeting the different sensitivities of Kacme and Kac to deacetylase may offer new treatment strategies for deacetylase-related diseases. Moreover, the chemical characteristics of Kacme resemble those of neutral Kac, suggesting its involvement in nonhistone proteins, which are crucial in various cellular processes or may be related to diseases, reinforcing the importance of this novel modification. One limitation of studying Kacme is its interaction with Kac, Kme, and other factors that may cause interference and affect the reliability of experimental results during the analysis. This paper introduces novel concepts and methods for studying protein modifications by proposing reasonable hypotheses, followed by chemical biological synthesis of modified peptides and subsequent verification through biological experiments. Although these new ideas come with complex methods and technologies, continuous progress in science and technology will overcome these challenges.
Hua Guo wrote the manuscript and prepared the figure. Fangfang Zhou and Long Zhang provided valuable discussion. All authors have read and approved the article.