Acetyl-HIST1H4A (K16) Antibody

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Description

Definition and Target Specificity

Acetyl-HIST1H4A (K16) antibodies recognize the acetylated lysine 16 residue on the N-terminal tail of histone H4, a core component of nucleosomes. This modification is associated with chromatin decondensation and transcriptional activation . Key characteristics include:

  • Immunogen: Synthetic peptides corresponding to the acetyl-K16 region of human histone H4 .

  • Host Species: Rabbit (polyclonal) or human (monoclonal) .

  • Clonality: Both monoclonal (e.g., ab109463 from Abcam) and polyclonal (e.g., CAC15226 from Biomatik) variants exist .

  • Cross-Reactivity: Primarily validated for human samples, with some reactivity in mouse and rat .

Applications and Validation

These antibodies are widely used in epigenetic research, as demonstrated by their validation in multiple assays:

ApplicationDetailsSources
Western Blot (WB)Detects H4K16ac in HeLa cell lysates, with dilutions ranging from 1:500 to 1:2000 .
Immunofluorescence (IF)Localizes H4K16ac in nuclei of HeLa cells, often after trichostatin A (TSA) treatment to enhance acetylation .
ChIP/ChIP-seqIdentifies H4K16ac-enriched genomic regions, such as transcription start sites (TSS) .
Flow Cytometry (FC)Quantifies H4K16ac levels in cell populations, optimized at 1:50 dilution .
ELISAMeasures acetylation levels in peptide competition assays .

Chromatin Dynamics and Transcription

  • H4K16ac is enriched at TSS of actively transcribed genes, facilitating RNA polymerase II recruitment .

  • Depletion of H4K16ac correlates with heterochromatin formation and gene silencing .

DNA Repair and Replication

  • H4K16ac marks sites of DNA damage and recruits repair complexes like BRCA1 .

  • Newly synthesized histone H4 is diacetylated at K5 and K12, distinct from H4K16ac, which is linked to replication-coupled chromatin assembly .

Disease Associations

  • Dysregulated H4K16ac levels are observed in cancers, including transitional cell carcinoma, and are linked to oncogene activation .

Antibody Performance

ParameterDetails
Storage-20°C long-term; 2–8°C for short-term .
BufferContains 50% glycerol and 0.03% Proclin 300 preservative .
Positive ControlsHeLa cells, rat lung tissue, and TSA-treated lysates .

Validation Data

  • Western Blot: Clear detection of a ~11 kDa band corresponding to histone H4 .

  • ChIP-seq: Peaks at TSS and enhancer regions in human and Drosophila genomes .

Biological Significance

H4K16ac is a hallmark of open chromatin and serves as a docking site for bromodomain-containing proteins like MOF (males absent on the first), which regulate histone acetyltransferase activity . Its roles include:

  • Transcriptional Activation: Facilitating chromatin unwinding to enable transcription factor binding .

  • Epigenetic Memory: Maintaining active gene states during cellular differentiation .

  • Cellular Senescence: Reduced H4K16ac levels are linked to aging-related gene silencing .

Product Specs

Buffer
Preservative: 0.03% Proclin 300
Constituents: 50% Glycerol, 0.01M PBS, pH 7.4
Form
Liquid
Lead Time
Typically, we can ship products within 1-3 business days after receiving your order. Delivery time may vary depending on the purchasing method or location. For specific delivery time information, please contact your local distributor.
Synonyms
dJ160A22.1 antibody; dJ160A22.2 antibody; dJ221C16.1 antibody; dJ221C16.9 antibody; FO108 antibody; H4 antibody; H4.k antibody; H4/a antibody; H4/b antibody; H4/c antibody; H4/d antibody; H4/e antibody; H4/g antibody; H4/h antibody; H4/I antibody; H4/j antibody; H4/k antibody; H4/m antibody; H4/n antibody; H4/p antibody; H4_HUMAN antibody; H4F2 antibody; H4F2iii antibody; H4F2iv antibody; H4FA antibody; H4FB antibody; H4FC antibody; H4FD antibody; H4FE antibody; H4FG antibody; H4FH antibody; H4FI antibody; H4FJ antibody; H4FK antibody; H4FM antibody; H4FN antibody; H4M antibody; HIST1H4A antibody; HIST1H4B antibody; HIST1H4C antibody; HIST1H4D antibody; HIST1H4E antibody; HIST1H4F antibody; HIST1H4H antibody; HIST1H4I antibody; HIST1H4J antibody; HIST1H4K antibody; HIST1H4L antibody; HIST2H4 antibody; HIST2H4A antibody; Hist4h4 antibody; Histone 1 H4a antibody; Histone 1 H4b antibody; Histone 1 H4c antibody; Histone 1 H4d antibody; Histone 1 H4e antibody; Histone 1 H4f antibody; Histone 1 H4h antibody; Histone 1 H4i antibody; Histone 1 H4j antibody; Histone 1 H4k antibody; Histone 1 H4l antibody; Histone 2 H4a antibody; histone 4 H4 antibody; Histone H4 antibody; MGC24116 antibody
Target Names
HIST1H4A
Uniprot No.

Target Background

Function
Histone H4 is a core component of the nucleosome. Nucleosomes are responsible for wrapping and compacting DNA into chromatin, thereby restricting DNA accessibility to cellular machinery that utilizes DNA as a template. Consequently, histones play a crucial role in regulating transcription, DNA repair, DNA replication, and maintaining chromosomal stability. DNA accessibility is meticulously regulated through a complex set of post-translational modifications of histones, often referred to as the histone code, and nucleosome remodeling.
Gene References Into Functions
  1. Studies demonstrate that PP32 and SET/TAF-Ibeta proteins inhibit HAT1-mediated H4 acetylation. PMID: 28977641
  2. Research suggests that post-translational modifications of histones, specifically trimethylation of lysine 36 in H3 (H3K36me3) and acetylation of lysine 16 in H4 (H4K16ac), play significant roles in DNA damage repair. H3K36me3 stimulates H4K16ac upon DNA double-strand breaks, and this process requires the involvement of SETD2, LEDGF, and KAT5 (SETD2 = SET domain containing 2; LEDGF = lens epithelium-derived growth factor; KAT5 = lysine acetyltransferase 5). PMID: 28546430
  3. Data indicate that the Omomyc protein co-localizes with the proto-oncogene protein c-myc (c-Myc), protein arginine methyltransferase 5 (PRMT5), and histone H4 H4R3me2s-enriched chromatin domains. PMID: 26563484
  4. H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription. PMID: 25788266
  5. Systemic lupus erythematosus appears to be linked to an imbalance in histone acetyltransferases and histone deacetylase enzymes, favoring pathological H4 acetylation. PMID: 25611806
  6. Sumoylated human histone H4 prevents chromatin compaction by inhibiting long-range internucleosomal interactions. PMID: 25294883
  7. Acetylation at lysine 5 of histone H4 is associated with lytic gene promoters during reactivation of Kaposi's sarcoma-associated herpesvirus. PMID: 25283865
  8. An increase in histone H4 acetylation caused by hypoxia in human neuroblastoma cell lines corresponds to elevated levels of N-myc transcription factor in these cells. PMID: 24481548
  9. Data suggest that G1-phase histone assembly is restricted to CENP-A and H4. PMID: 23363600
  10. This research focused on the distribution of a specific histone modification, namely H4K12ac, in human sperm and characterized its specific enrichment sites in promoters throughout the human genome. PMID: 22894908
  11. SRP68/72 heterodimers act as major nuclear proteins whose binding of histone H4 tail is inhibited by H4R3 methylation. PMID: 23048028
  12. TNF-alpha inhibition of AQP5 expression in human salivary gland acinar cells is attributed to an epigenetic mechanism involving the suppression of acetylation of histone H4. PMID: 21973049
  13. Findings suggest that global histone H3 and H4 modification patterns serve as potential markers for tumor recurrence and disease-free survival in non-small cell lung cancer. PMID: 22360506
  14. HAT1 differentially impacts nucleosome assembly of H3.1-H4 and H3.3-H4. PMID: 22228774
  15. Phosphorylation of histone H4 Ser 47 catalyzed by the PAK2 kinase promotes nucleosome assembly of H3.3-H4 and inhibits nucleosome assembly of H3.1-H4 by enhancing the binding affinity of HIRA to H3.3-H4 and reducing the association of CAF-1 with H3.1-H4. PMID: 21724829
  16. The imatinib-induced hemoglobinization and erythroid differentiation in K562 cells are associated with global histone H4 modifications. PMID: 20949922
  17. Research reveals the molecular mechanisms by which DNA sequences within specific gene bodies are sufficient to nucleate the monomethylation of histone H4 lysine 200, which subsequently reduces gene expression by half. PMID: 20512922
  18. Histone H4 expression is downregulated by zinc and upregulated by docosahexaenoate in a neuroblastoma cell line. PMID: 19747413
  19. Low levels of histone acetylation are associated with the development and progression of gastric carcinomas, potentially through alterations in gene expression. PMID: 12385581
  20. Overexpression of MTA1 protein and acetylation levels of histone H4 protein are closely linked. PMID: 15095300
  21. Peptidylarginine deiminase 4 regulates histone Arg methylation by converting methyl-Arg to citrulline and releasing methylamine. Data suggest that PAD4 mediates gene expression by regulating Arg methylation and citrullination in histones. PMID: 15345777
  22. The lack of biotinylation of K12 in histone H4 represents an early signaling event in response to double-strand breaks. PMID: 16177192
  23. The incorporation of acetylated histone H4-K16 into nucleosomal arrays inhibits the formation of compact 30-nanometer-like fibers and hinders the ability of chromatin to form cross-fiber interactions. PMID: 16469925
  24. Apoptosis is associated with global DNA hypomethylation and histone deacetylation events in leukemia cells. PMID: 16531610
  25. BTG2 contributes to retinoic acid activity by promoting differentiation through gene-specific modifications of histone H4 arginine methylation and acetylation levels. PMID: 16782888
  26. There is a relationship between histone H4 modification, epigenetic regulation of BDNF gene expression, and long-term memory for the extinction of conditioned fear. PMID: 17522015
  27. The H4 tail and its acetylation have novel roles in mediating the recruitment of multiple regulatory factors that can alter chromatin states for transcription regulation. PMID: 17548343
  28. Brd2 bromodomain 2 exists as a monomer in solution and dynamically interacts with H4-AcK12. Additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. PMID: 17848202
  29. Spermatids Hypac-H4 impairment in mixed atrophy was not further deteriorated by AZFc region deletion. PMID: 18001726
  30. The interaction between SET8 and PCNA couples H4-K20 methylation with DNA replication. PMID: 18319261
  31. H4K20 monomethylation and PR-SET7 are essential for L3MBTL1 function. PMID: 18408754
  32. High expression of acetylated H4 is more prevalent in aggressive cutaneous T-cell lymphoma compared to indolent forms. PMID: 18671804
  33. Findings indicate a significant role of histone H4 modifications in bronchial carcinogenesis. PMID: 18974389
  34. Results suggest that during S-phase, acetylation of histone H4 K16 causes early replicating chromatin domains to acquire the H4K16ac-K20me2 epigenetic label, which persists on the chromatin throughout mitosis and is deacetylated in the early G1-phase of the subsequent cell cycle. PMID: 19348949
  35. Acetylated H4 is overexpressed in diffuse large B-cell lymphoma and peripheral T-cell lymphoma relative to normal lymphoid tissue. PMID: 19438744
  36. The release of histone H4 through holocrine secretion from the sebaceous gland may play a crucial role in innate immunity. PMID: 19536143
  37. Histone modifications, including PRC2-mediated repressive histone marker H3K27me3 and active histone marker acH4, may be involved in CD11b transcription during HL-60 leukemia cell reprogramming to terminal differentiation. PMID: 19578722
  38. The role of Cdk7 in regulating elongation is further supported by enhanced histone H4 acetylation and diminished histone H4 trimethylation on lysine 36, two hallmarks of elongation, within genes when the kinase was inhibited. PMID: 19667075
  39. Data reveal dynamic fluctuations in histone H4 acetylation levels during mitosis, as well as acetylation changes in response to structurally distinct histone deacetylase inhibitors. PMID: 19805290
  40. Research directly implicates BBAP in the monoubiquitylation and additional posttranslational modification of histone H4 and an associated DNA damage response. PMID: 19818714

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Database Links

HGNC: 4781

OMIM: 142750

KEGG: hsa:121504

STRING: 9606.ENSP00000367034

UniGene: Hs.143080

Involvement In Disease
Chromosomal aberrations involving HISTONE H4 is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;6)(q27;p21), with BCL6.
Protein Families
Histone H4 family
Subcellular Location
Nucleus. Chromosome.

Q&A

What is the Acetyl-HIST1H4A (K16) antibody and what specific modification does it detect?

The Acetyl-HIST1H4A (K16) antibody is a specialized immunoglobulin that specifically recognizes histone H4 proteins acetylated at the lysine 16 position. This post-translational modification occurs on the N-terminal tail of histone H4 and plays critical roles in chromatin structure and gene regulation. The antibody is designed to bind specifically to the acetylated lysine at position 16 of histone H4, without cross-reactivity to unmodified H4 or H4 acetylated at other lysine residues. This high specificity makes it valuable for investigating the precise epigenetic state of chromatin related to H4K16 acetylation . The modification site is consistently identified as "K16" across different commercial antibodies, and the target protein is encoded by multiple histone H4 genes including H4-16 (HIST1H4A) with UniProt accession number P62805 .

How do polyclonal and monoclonal Acetyl-HIST1H4A (K16) antibodies differ in research applications?

Polyclonal and monoclonal Acetyl-HIST1H4A (K16) antibodies differ significantly in their production, specificity, and optimal research applications. Polyclonal antibodies are derived from multiple B-cell lineages in the host animal (typically rabbit) immunized with a synthetic peptide corresponding to human histone H4 acetylated at K16. These antibodies recognize multiple epitopes on the target and offer high sensitivity but potentially lower specificity due to their heterogeneous nature . They are particularly useful for applications where signal amplification is important, such as immunohistochemistry or when the target protein is present in low abundance.

Monoclonal antibodies, in contrast, are produced from a single B-cell clone, resulting in antibodies that recognize a single epitope. The monoclonal Acetyl-HIST1H4A (K16) antibodies demonstrate higher specificity and consistency between batches, making them especially valuable for quantitative applications and experiments requiring precise epitope recognition . They are preferred for applications like ChIP-seq where high specificity is critical to distinguish the acetylation at K16 from other nearby modifications on the histone H4 tail. Both types have been validated for applications including Western blot, ELISA, and immunofluorescence, but researchers should select the appropriate antibody type based on their specific experimental requirements and the level of specificity needed .

What is the biological significance of H4K16 acetylation in chromatin regulation?

H4K16 acetylation serves as a critical epigenetic mark with profound implications for chromatin structure and genomic functions. This modification plays a central role in chromatin decompaction by neutralizing the positive charge of lysine, thereby weakening histone-DNA and nucleosome-nucleosome interactions. When H4K16 is acetylated, it disrupts higher-order chromatin structure and increases DNA accessibility to various DNA-binding proteins, including transcription factors and the transcriptional machinery .

Research has revealed that H4K16ac is distinctly enriched around transcription start sites (TSSs), suggesting its important role in gene activation and transcriptional regulation . This modification works in concert with other histone modifications as part of the "histone code" that collectively determines chromatin states. Unlike some other histone H4 acetylation marks, H4K16ac shows characteristic distribution patterns that undergo dynamic changes during the cell cycle, making it an important regulator of cell cycle-dependent gene expression .

From an evolutionary perspective, H4K16 acetylation is highly conserved, underscoring its fundamental importance in eukaryotic genome regulation. Perturbations in H4K16 acetylation patterns have been associated with various diseases, including cancer, where global loss of H4K16ac is observed as a common hallmark of malignancy. Understanding the precise distribution and dynamics of this modification is therefore essential for comprehensive epigenome studies and potential therapeutic interventions targeting chromatin-modifying enzymes .

What are the validated applications for Acetyl-HIST1H4A (K16) antibodies and their optimal dilutions?

Acetyl-HIST1H4A (K16) antibodies have been validated across multiple experimental applications that enable researchers to investigate histone modifications in diverse contexts. Based on the combined data from multiple suppliers, the following applications have been validated with recommended dilution ranges:

ApplicationPolyclonal Antibody DilutionMonoclonal Antibody DilutionKey Considerations
Western Blot (WB)1:100-1:5001:300-1:5000Detects ~11-15 kDa band of acetylated histone H4
ELISA1 μg/mlNot specifiedHigh sensitivity for quantitative detection
Chromatin Immunoprecipitation (ChIP)Not specifiedAs recommendedCritical for genome-wide mapping of H4K16ac
Immunofluorescence (IF)1:50-1:2001:50-1:200Reveals nuclear localization patterns
Flow Cytometry (FCM)Not specified1:20-1:100Quantifies H4K16ac in individual cells
Immunocytochemistry (ICC)1:50-1:200Not specifiedCellular distribution analysis

These recommended dilutions serve as starting points, but researchers should perform optimization experiments for their specific samples and experimental conditions . The antibody's performance may vary depending on the sample type (cell lines, tissues), fixation method, and detection system employed. For critical quantitative applications like ChIP-seq, validation using appropriate controls (including peptide competition assays and knockout/knockdown samples) is strongly recommended to ensure specificity and reproducibility .

How should Acetyl-HIST1H4A (K16) antibodies be validated prior to use in chromatin immunoprecipitation experiments?

Proper validation of Acetyl-HIST1H4A (K16) antibodies before use in chromatin immunoprecipitation (ChIP) experiments is essential to ensure experimental success and data reliability. A comprehensive validation approach should include multiple complementary methods:

First, perform peptide competition assays using synthetic peptides containing acetylated K16 and unmodified control peptides. Pre-incubation of the antibody with the specific acetylated peptide should block antibody binding in Western blot or ELISA, while unmodified peptides should have no effect. This confirms specificity for the acetylated form .

Second, conduct cross-reactivity tests against other acetylated lysine residues on histone H4 (K5, K8, K12) using synthetic peptides or recombinant proteins harboring specific modifications. This is particularly important because the histone H4 tail contains multiple acetylation sites that can be simultaneously modified, and distinguishing between them requires high antibody specificity .

Third, validate by Western blot analysis comparing samples treated with histone deacetylase inhibitors (which increase acetylation levels) against control samples. The antibody should show increased signal intensity in treated samples, confirming its ability to detect dynamic changes in H4K16 acetylation .

Fourth, perform immunofluorescence microscopy to verify the expected nuclear localization pattern of H4K16ac. The staining should show characteristic nuclear distribution consistent with published patterns for this modification .

Finally, preliminary ChIP-qPCR should be conducted targeting genomic regions known to be enriched for H4K16ac (such as transcriptionally active promoters) and regions expected to lack this modification. This step confirms the antibody's performance in the ChIP workflow before proceeding to genome-wide applications like ChIP-seq . Implementation of these validation steps will significantly enhance the reliability and reproducibility of ChIP experiments using Acetyl-HIST1H4A (K16) antibodies.

What are the proper storage and handling conditions to maintain antibody activity?

Proper storage and handling of Acetyl-HIST1H4A (K16) antibodies are critical for maintaining their activity and ensuring consistent experimental results. These antibodies are typically provided in liquid form, containing preservatives and stabilizers such as glycerol, and require specific conditions to preserve their functionality.

The optimal storage temperature for long-term preservation is -20°C, which helps prevent protein degradation and maintains antibody activity. Many commercial Acetyl-HIST1H4A (K16) antibodies are supplied in a buffer containing 50% glycerol, which prevents freezing at -20°C and allows for aliquoting without repeated freeze-thaw cycles . Upon receipt of a new antibody, it is recommended to prepare small working aliquots (10-20 μL) to minimize the number of freeze-thaw cycles, as repeated freezing and thawing can substantially reduce antibody activity and specificity.

The typical buffer composition for these antibodies includes 0.01 M PBS (pH 7.4) with small amounts of preservatives like 0.03% Proclin-300 or similar agents. Some manufacturers formulate their antibodies with 1% BSA to enhance stability . When removing the antibody from storage for use, allow it to equilibrate to room temperature before opening the tube to prevent condensation, which can introduce contaminants and affect protein stability.

Working dilutions of the antibody should be prepared immediately before use and kept at 4°C only for the duration of the experiment. For applications requiring longer incubation times, such as overnight primary antibody incubation in immunostaining protocols, diluted antibodies should be supplemented with BSA (0.5-1%) and sodium azide (0.02-0.05%) to prevent microbial growth and maintain stability during the incubation period. Following these storage and handling recommendations will help ensure optimal antibody performance and reproducible experimental results .

How can Acetyl-HIST1H4A (K16) antibodies be used to investigate changes in chromatin structure during the cell cycle?

Acetyl-HIST1H4A (K16) antibodies provide powerful tools for investigating the dynamic changes in chromatin structure that occur throughout the cell cycle. Research has demonstrated that H4K16 acetylation undergoes significant redistribution during different cell cycle phases, making it an excellent marker for studying chromatin reorganization during replication, mitosis, and cell division.

To effectively track these changes, researchers can implement a multi-faceted approach combining immunofluorescence microscopy with cell synchronization techniques. By synchronizing cells at specific phases using methods such as double thymidine block (G1/S boundary), nocodazole treatment (M phase), or serum starvation followed by release (G0 to G1 transition), investigators can systematically analyze H4K16ac patterns at defined timepoints. Immunofluorescence analysis using Acetyl-HIST1H4A (K16) antibodies enables visualization of the spatial distribution of this modification within the nucleus during different cell cycle stages . Co-staining with cell cycle markers such as cyclin B1 (G2/M), PCNA (S phase), or phospho-histone H3 (mitosis) can provide precise cell cycle context.

For quantitative assessment, flow cytometry combining DNA content staining (propidium iodide or DAPI) with immunodetection of H4K16ac allows correlation between acetylation levels and cell cycle position at the single-cell level . This approach is particularly valuable for heterogeneous cell populations. At the molecular level, ChIP-seq analysis in synchronized cell populations reveals genome-wide redistribution of H4K16ac during cell cycle progression, particularly around replication origins and transcription start sites .

Importantly, H4K16ac has been shown to have distinct patterns from other histone H4 acetylation marks. While newly synthesized histone H4 is diacetylated at K5 and K12, H4K16ac shows a different distribution pattern that relates to transcriptional activity rather than replication status. Using antibodies that can distinguish between these different acetylation patterns enables researchers to differentiate newly assembled chromatin from transcriptionally active regions . This integrated approach provides comprehensive insights into the role of H4K16 acetylation in cell cycle-dependent chromatin dynamics and gene regulation.

What are the optimal protocols for using Acetyl-HIST1H4A (K16) antibodies in ChIP-seq experiments?

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) with Acetyl-HIST1H4A (K16) antibodies requires careful optimization to generate high-quality genome-wide maps of this important epigenetic modification. The following protocol incorporates best practices from epigenetic research to ensure robust and reproducible results.

Sample Preparation and Chromatin Extraction:
Begin with 1-5×10^6 cells per ChIP reaction, and crosslink with 1% formaldehyde for 10 minutes at room temperature. Quench with 125 mM glycine for 5 minutes. Cell lysis should be performed in buffer containing protease inhibitors and, critically, histone deacetylase inhibitors (such as sodium butyrate at 5-10 mM) to preserve acetylation status. Chromatin should be sheared to 200-500 bp fragments using sonication or enzymatic digestion, with fragmentation efficiency verified by agarose gel electrophoresis .

Immunoprecipitation Optimization:
For Acetyl-HIST1H4A (K16) antibodies, the optimal amount typically ranges from 2-5 μg per ChIP reaction, though this should be determined empirically for each antibody lot. Include appropriate controls: (1) input chromatin (typically 5-10% of the amount used for ChIP), (2) immunoprecipitation with non-specific IgG, and (3) a positive control using antibodies against histone marks known to be abundant (such as H3K4me3). Pre-clear chromatin with protein A/G beads before adding the antibody to reduce background. Antibody-chromatin binding should proceed overnight at 4°C with gentle rotation .

Washing, Elution and Library Preparation:
Following immunoprecipitation, implement a stringent washing regimen with increasing salt concentrations to minimize non-specific binding. Reversal of crosslinks should be performed at 65°C for 4-6 hours, followed by RNase A and Proteinase K treatment. Purified DNA can then be quantified using fluorometric methods (Qubit) or qPCR targeting known H4K16ac-enriched regions before proceeding to library preparation. For ChIP-seq libraries, a minimum of 5-10 ng of immunoprecipitated DNA is recommended, though amplification protocols for lower input amounts exist .

Sequencing and Data Analysis:
Sequence to a depth of at least 20-30 million uniquely mapped reads per sample for robust genome-wide coverage. During data analysis, H4K16ac signals show characteristic enrichment around transcription start sites, and this pattern can serve as a quality control metric. When analyzing the distribution of H4K16ac, comparison with other histone modifications, particularly other acetylation marks on H4 (K5, K8, K12), provides valuable context for understanding the specific roles of H4K16ac in gene regulation . This comprehensive approach ensures high-quality ChIP-seq data for investigating the genomic distribution of this critically important histone modification.

How can researchers distinguish between H4K16 acetylation and other histone H4 acetylation marks?

Distinguishing between H4K16 acetylation and other histone H4 acetylation marks (K5, K8, K12) presents a significant challenge in epigenetic research due to their proximity on the histone H4 tail and potential co-occurrence. Researchers can employ several complementary strategies to achieve this differentiation with high confidence.

The foundation of accurate differentiation lies in antibody specificity. High-quality Acetyl-HIST1H4A (K16) antibodies should be validated using peptide arrays or ELISA with synthetic peptides containing single acetylation marks at different positions (K5ac, K8ac, K12ac, K16ac) and various combinations of these modifications. This validation ensures that the antibody specifically recognizes K16ac regardless of the acetylation status of neighboring lysines . Some antibodies have been characterized to have unique binding properties - for example, certain H4K5ac antibodies only react when K8 is unacetylated, allowing distinction between different acetylation patterns .

Mass spectrometry provides an antibody-independent approach for distinguishing between different acetylation marks. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of histone extracts can precisely identify and quantify the relative abundance of different acetylation marks and their combinations. This method is particularly valuable for detecting co-occurrence of multiple modifications on the same histone tail .

Sequential ChIP (re-ChIP) experiments, where chromatin is immunoprecipitated with one acetylation-specific antibody followed by a second immunoprecipitation with another antibody, can reveal regions where different acetylation marks co-exist. This approach is particularly useful for understanding the combinatorial patterns of histone modifications across the genome .

Correlation analysis of ChIP-seq data using antibodies against different H4 acetylation marks can reveal distinct genomic distribution patterns. Research has shown that while H4K5ac and K12ac are associated with newly synthesized histones during replication, H4K16ac and H4K8ac show enrichment around transcription start sites, indicating different functional roles . By implementing these complementary approaches, researchers can reliably distinguish H4K16 acetylation from other H4 acetylation marks and better understand their specific roles in chromatin regulation.

How does H4K16 acetylation change in cancer progression and how can researchers accurately quantify these changes?

H4K16 acetylation undergoes significant alterations during cancer progression, making it both a valuable biomarker and a target for understanding oncogenic mechanisms. Global loss of H4K16 acetylation has been identified as a common hallmark across multiple cancer types, often occurring early in the tumorigenic process. This epigenetic change contributes to genomic instability and altered gene expression patterns that drive cancer development and progression.

To accurately quantify changes in H4K16 acetylation across cancer models and clinical samples, researchers can employ multiple complementary approaches. Immunohistochemistry using Acetyl-HIST1H4A (K16) antibodies on tissue microarrays enables evaluation of H4K16ac levels in patient samples, allowing correlation with clinical parameters and outcomes . The recommended dilution for immunohistochemistry applications ranges from 1:200-1:400, with optimal conditions depending on tissue type and fixation method .

For more quantitative assessment, Western blot analysis with densitometry provides relative quantification of H4K16ac levels normalized to total H4 or other loading controls. This approach can compare acetylation levels between normal and cancer cells or among different cancer stages . Flow cytometry using Acetyl-HIST1H4A (K16) antibodies (dilutions of 1:20-1:100) allows single-cell quantification of H4K16ac levels and can identify subpopulations with distinct acetylation profiles within heterogeneous tumor samples .

At the genomic level, ChIP-seq analysis reveals changes in the genome-wide distribution of H4K16ac, identifying specific genes and regulatory elements where this modification is altered during cancer progression . Integration of these H4K16ac profiles with transcriptomic data can elucidate the functional consequences of these epigenetic alterations on gene expression programs driving malignancy.

For mechanistic studies, researchers should investigate the enzymes regulating H4K16 acetylation—primarily the MYST family acetyltransferase hMOF (KAT8) and class III histone deacetylases (sirtuins, particularly SIRT1)—as their dysregulation often underlies the global loss of H4K16ac in cancer. By comprehensively profiling H4K16 acetylation changes using these approaches, researchers can gain valuable insights into epigenetic reprogramming during cancer progression and identify potential targets for epigenetic therapy.

What are the methodological considerations for studying H4K16ac in different tissue types?

Studying H4K16 acetylation across different tissue types presents unique methodological challenges that require careful consideration to ensure accurate and reproducible results. Tissue-specific optimization is essential for meaningful comparative analyses of this important epigenetic mark.

For fixed tissue samples, the fixation method significantly impacts antibody accessibility and epitope preservation. For Acetyl-HIST1H4A (K16) detection in FFPE (formalin-fixed paraffin-embedded) tissues, antigen retrieval is crucial. Heat-induced epitope retrieval using citrate buffer (pH 6.0) or Tris-EDTA buffer (pH 9.0) is typically effective, but the optimal protocol may vary by tissue type. The duration of fixation should be standardized across samples being compared, as overfixation can mask epitopes and reduce signal intensity .

When extracting histones from different tissues for biochemical analyses, tissue-specific compositions require adapted extraction protocols. Tissues with high lipid content (brain, adipose) may require additional delipidation steps, while fibrous tissues (muscle, skin) might need extended homogenization or digestion. Regardless of tissue type, histone deacetylase inhibitors (like sodium butyrate) must be included in all buffers to prevent active deacetylation during extraction .

For ChIP applications, chromatin accessibility varies significantly between tissue types, necessitating optimization of crosslinking conditions and sonication parameters. Dense tissues often require longer sonication times or different fragmentation approaches. The antibody concentration may also need adjustment—tissues with lower cell density might require higher antibody-to-chromatin ratios to achieve efficient immunoprecipitation .

When performing immunofluorescence on tissue sections, autofluorescence presents a major challenge, particularly in tissues containing lipofuscin, elastin, or collagen. Preprocessing with Sudan Black B or spectral unmixing during image acquisition can minimize these tissue-specific background issues. Signal amplification systems (TSA, polymer-based detection) may be necessary for tissues with lower H4K16ac abundance .

Finally, appropriate tissue-specific controls are essential for accurate interpretation. For comparative studies, matched normal and diseased tissues should be processed identically. Including tissues known to have high (testis, brain) or low (certain muscle cells) H4K16ac levels as reference points provides valuable context for interpreting relative acetylation levels across different tissue types .

What are the most common problems when using Acetyl-HIST1H4A (K16) antibodies and how can they be resolved?

Researchers working with Acetyl-HIST1H4A (K16) antibodies frequently encounter several technical challenges that can compromise experimental outcomes. Understanding these common problems and their solutions is essential for generating reliable data.

High Background Signal:
High background is often observed in immunofluorescence and Western blot applications. This typically results from insufficient blocking, excessive antibody concentration, or cross-reactivity. To resolve this issue, increase the blocking time using 5% BSA or 5% non-fat dry milk in TBS-T (depending on the application) and optimize the primary antibody dilution through a titration series. For Western blots, increase the number and duration of washing steps using TBS-T with 0.1-0.3% Tween-20. In ChIP experiments, adding 100-500 μg/ml competing sheared salmon sperm DNA to the antibody incubation step can reduce non-specific binding to DNA .

Weak or Absent Signal:
Insufficient signal strength may result from low H4K16ac abundance, epitope masking during fixation, or antibody degradation. To address this, incorporate histone deacetylase inhibitors (5-10 mM sodium butyrate) in all buffers during sample preparation to preserve acetylation levels. For immunohistochemistry and immunofluorescence, optimize antigen retrieval methods—test both citrate buffer (pH 6.0) and Tris-EDTA (pH 9.0) at different temperatures and durations. If working with an older antibody, verify its activity using positive control samples known to have high H4K16ac levels .

Inconsistent ChIP Results:
Variability in ChIP experiments often stems from insufficient chromatin fragmentation or inconsistent immunoprecipitation. Optimize sonication conditions for each cell or tissue type to consistently achieve 200-500 bp fragments. Use glycine to completely quench the formaldehyde crosslinking reaction. For reproducible ChIP results, standardize the ratio of antibody to chromatin across experiments and include spike-in controls of exogenous chromatin for normalization .

Cross-Reactivity with Other Acetylation Sites:
Some antibodies may exhibit cross-reactivity with other acetylated lysines on histone H4. Verify antibody specificity using peptide competition assays with synthetic peptides containing individual acetylation marks (K5ac, K8ac, K12ac, K16ac). For critical applications, consider using monoclonal antibodies, which generally offer higher specificity than polyclonal antibodies . By systematically addressing these common problems, researchers can significantly improve the reliability and reproducibility of experiments using Acetyl-HIST1H4A (K16) antibodies.

How can researchers integrate H4K16ac data with other epigenetic marks for comprehensive chromatin state analysis?

Integrative analysis of H4K16ac with other epigenetic marks provides a comprehensive view of chromatin states and regulatory networks. This multi-layered approach reveals the functional interplay between different modifications and offers deeper insights into epigenetic regulation mechanisms.

For effective integration, researchers should first generate aligned datasets by performing parallel ChIP-seq experiments for H4K16ac alongside other relevant histone modifications (H3K4me3, H3K27ac, H3K9me3, H3K27me3) and chromatin accessibility assays (ATAC-seq or DNase-seq) using the same biological samples. Standardized experimental protocols, including identical fixation conditions, sonication parameters, and sequencing depth are essential for quantitative comparisons across different marks .

Computational integration requires specialized bioinformatic approaches. Correlation analysis between H4K16ac and other modifications across genomic regions identifies co-occurring marks that may function together. ChromHMM or similar hidden Markov model-based algorithms can integrate binary presence/absence data from multiple histone modifications to define and annotate distinct chromatin states across the genome. These states can then be correlated with gene expression data to infer their functional significance .

Visualization tools such as heatmaps and aggregation plots centered on transcription start sites, enhancers, or other genomic features allow comparison of multiple modification patterns and their relationships. Genome browsers with overlaid tracks enable locus-specific examination of the spatial relationships between H4K16ac and other epigenetic features.

For mechanistic studies, sequential ChIP (re-ChIP) experiments can determine whether H4K16ac co-exists with other modifications on the same nucleosomes. This approach is particularly valuable for understanding the combinatorial histone code at specific regulatory elements. Mass spectrometry analysis of histone peptides can identify and quantify combinations of modifications that occur on the same histone tail, providing insights into modification crosstalk that cannot be obtained from ChIP-based methods .

Integration with transcription factor binding data from ChIP-seq experiments helps identify the regulatory proteins associated with different H4K16ac patterns. This can reveal potential recruitment mechanisms for histone acetyltransferases and deacetylases that regulate H4K16 acetylation levels. By implementing these integrative approaches, researchers can place H4K16ac within the broader context of the epigenetic landscape and better understand its specific contributions to gene regulation and chromatin organization.

What are the latest technological advances in detecting and quantifying site-specific histone modifications like H4K16ac?

Recent technological advances have significantly enhanced our ability to detect and quantify site-specific histone modifications like H4K16ac with unprecedented sensitivity, specificity, and resolution. These innovations are transforming epigenetic research by enabling more comprehensive and precise analyses of chromatin states.

Single-molecule techniques represent a major breakthrough in studying histone modifications at the individual nucleosome level. Single-molecule Förster resonance energy transfer (smFRET) can detect H4K16ac on individual nucleosomes and reveal how this modification affects nucleosome dynamics and DNA accessibility in real-time. This approach overcomes the population averaging limitations of traditional bulk methods and can detect rare or transient modification states .

Mass spectrometry technologies have evolved substantially for histone modification analysis. Targeted approaches like parallel reaction monitoring (PRM) and multiple reaction monitoring (MRM) offer quantitative measurements of specific histone modifications with high sensitivity and reproducibility. These methods can accurately quantify the stoichiometry of H4K16ac relative to other modifications and detect combinatorial patterns on the same histone tail. Top-down proteomics approaches that analyze intact histone proteins preserve information about co-occurring modifications that might be lost in traditional bottom-up approaches .

Antibody-independent technologies are emerging to overcome the limitations of antibody-based detection methods. CUT&RUN (Cleavage Under Targets and Release Using Nuclease) and CUT&Tag (Cleavage Under Targets and Tagmentation) provide higher signal-to-noise ratios than conventional ChIP-seq, requiring fewer cells and less sequencing depth. These methods are particularly valuable for precious clinical samples or rare cell populations .

Single-cell epigenomics represents another frontier in H4K16ac analysis. Single-cell ChIP-seq and CUT&Tag protocols can map H4K16ac distribution in individual cells, revealing cell-to-cell heterogeneity that would be masked in bulk analyses. These approaches are particularly powerful when integrated with single-cell transcriptomics to connect epigenetic variations to gene expression differences at the individual cell level .

Spatial epigenomics techniques, including imaging mass cytometry and multiplexed immunofluorescence, allow visualization of H4K16ac and other histone modifications within the nuclear spatial context. These methods can reveal the three-dimensional organization of chromatin domains enriched for specific modifications and their relationships to nuclear landmarks like the nuclear lamina or nucleolus. By adopting these cutting-edge technologies, researchers can gain unprecedented insights into the dynamics, regulation, and functional consequences of H4K16 acetylation in diverse biological contexts.

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