Target: Acetylated lysine 5 (K5) on human HIST1H2BB, a core histone H2B isoform involved in nucleosome assembly .
Host Species: Rabbit .
Clonality: Polyclonal .
Immunogen: Synthetic acetylated peptide corresponding to residues surrounding K5 of human HIST1H2BB .
Purification: Affinity chromatography using antigen-specific peptides .
Chromatin Immunoprecipitation (ChIP): Identifies HIST1H2BB acetylation at gene promoters (e.g., β-globin) in HeLa cells treated with sodium butyrate .
Immunofluorescence (IF)/Immunocytochemistry (ICC): Localizes acetylated HIST1H2BB in HeLa cell nuclei at dilutions up to 1:200 .
Western Blot (WB): Detects a ~14–15 kDa band in HeLa lysates, confirming specificity for acetyl-K5 .
ELISA: Quantifies acetylation levels using peptide-based assays .
ChIP-qPCR: Demonstrated enrichment of acetyl-HIST1H2BB at the β-globin promoter in sodium butyrate-treated cells .
Cross-Reactivity: Recognizes endogenous acetyl-K5 in human, mouse, and rat samples .
Dilution Range:
Acetylation at HIST1H2BB-K5 correlates with open chromatin states, facilitating transcriptional activation . This antibody has been used to:
Acetyl-HIST1H2BB (K5) Antibody is a primary antibody specifically designed to recognize the acetylation of lysine 5 (K5) on Histone H2B type 1-B (HIST1H2BB). This histone variant is part of the core nucleosome structure and its acetylation status is associated with transcriptional regulation and chromatin accessibility. The antibody targets the peptide sequence surrounding the acetylated lysine 5 residue of Human Histone H2B type 1-B . Detection of this specific post-translational modification provides researchers with information about chromatin states and epigenetic regulation in cellular processes.
Acetyl-HIST1H2BB (K5) Antibody serves multiple applications in epigenetic research:
ELISA (Enzyme-Linked Immunosorbent Assay): For quantitative detection of acetylated H2B
ICC (Immunocytochemistry): To visualize cellular localization patterns
IF (Immunofluorescence): For higher resolution imaging of acetylation distribution
ChIP (Chromatin Immunoprecipitation): To identify genomic regions associated with acetylated H2B
This range of applications makes the antibody versatile for investigating how histone acetylation correlates with gene expression, cell cycle progression, DNA repair, and various nuclear processes.
Acetyl-HIST1H2BB (K5) represents one of several acetylation sites on histone H2B. While Acetyl-HIST1H2BB (K5) targets lysine 5, other antibodies such as those targeting Acetyl-K20 recognize different acetylation positions that may have distinct biological functions . The specificity for K5 makes this antibody valuable for studying targeted epigenetic mechanisms. Research indicates that different acetylation marks on histone H2B may be associated with distinct chromatin states and functional outcomes. For instance, histone H2B variants have undergone substantial divergence during evolution, suggesting specialized functions within different cellular contexts and organisms .
To investigate chromatin state transitions using Acetyl-HIST1H2BB (K5) Antibody, researchers should implement a multi-faceted experimental approach:
Time-course ChIP-seq analysis: Perform chromatin immunoprecipitation followed by sequencing at different time points during differentiation to track dynamic changes in H2B K5 acetylation across the genome.
Integration with transcriptomic data: Correlate acetylation patterns with RNA-seq data to establish relationships between H2B K5 acetylation and gene expression changes.
Co-immunoprecipitation studies: Identify protein complexes associated with acetylated H2B to elucidate the molecular machinery involved in establishing and reading this mark.
Perturbation experiments: Use HDAC inhibitors or HAT activators to modulate acetylation levels and assess the impact on differentiation outcomes.
The high specificity of the antibody for the acetylated K5 position allows for precise mapping of this modification, which can be compared with other histone marks to construct comprehensive epigenetic landscapes during cellular differentiation .
For optimal ChIP experiments using Acetyl-HIST1H2BB (K5) Antibody, the following methodological considerations should be implemented:
Crosslinking and sonication optimization:
Use 1% formaldehyde for 10-15 minutes at room temperature
Sonicate to generate fragments of 200-500 bp for highest resolution
Verify fragmentation efficiency by gel electrophoresis
Antibody concentration and incubation:
Titrate antibody for optimal signal-to-noise ratio (typically 2-5 μg per ChIP reaction)
Incubate chromatin-antibody mixture overnight at 4°C with rotation
Include appropriate controls (IgG control, input samples)
Washing and elution conditions:
Use increasingly stringent wash buffers to reduce background
Perform reverse crosslinking at 65°C for 4-6 hours
Include RNase and Proteinase K treatments
Validation steps:
Confirm enrichment at known acetylated regions by qPCR
Use positive control loci where H2B K5 acetylation has been previously documented
Since the antibody is antigen-affinity purified, it provides high specificity for the target modification, making it well-suited for ChIP applications when these optimal conditions are maintained .
Differentiating between various histone acetylation marks in multiplex imaging requires careful experimental design and controls:
Spectral separation strategy:
Select secondary antibodies with minimal spectral overlap
Utilize primary antibodies from different host species (e.g., rabbit for Acetyl-HIST1H2BB (K5) and mouse for other marks)
Implement linear unmixing algorithms during image analysis
Sequential staining protocol:
Apply antibodies in sequence with blocking steps between rounds
Consider signal amplification methods for low-abundance marks
Use tyramide signal amplification (TSA) for enhanced sensitivity
Validation and controls:
Perform single-staining controls to confirm antibody specificity
Include samples treated with HDAC inhibitors as positive controls
Use peptide competition assays to validate signal specificity
Advanced imaging approaches:
Consider super-resolution microscopy techniques (STORM, STED) for improved spatial resolution
Use proximity ligation assays (PLA) to detect co-occurrence of different marks
These approaches allow researchers to distinguish Acetyl-HIST1H2BB (K5) from other histone modifications, providing insights into the spatial organization and co-occurrence of different epigenetic marks within the nucleus .
To maintain optimal activity of Acetyl-HIST1H2BB (K5) Antibody, researchers should follow these storage and handling guidelines:
Long-term storage:
Store at -20°C in small aliquots to prevent repeated freeze-thaw cycles
Add glycerol (typically 50%) as a cryoprotectant if not already present in the formulation
Keep protected from light, especially if conjugated to fluorescent dyes
Short-term storage and working solutions:
For frequent use, store small aliquots at 4°C for up to one month
Avoid repeated freeze-thaw cycles as they can lead to protein denaturation and loss of activity
Return to -20°C promptly after use
Handling precautions:
Thaw on ice when removing from -20°C storage
Centrifuge briefly after thawing to collect contents at the bottom of the tube
Use sterile technique when handling to prevent contamination
Buffer considerations:
Maintain antibody in manufacturer's buffer when possible
If buffer exchange is necessary, use methods that minimize protein loss (e.g., centrifugal filter units)
Consider adding stabilizers like BSA (0.5-1%) if not already present
Following these procedures will help ensure consistent antibody performance across experiments and maximize the usable lifespan of the antibody .
Optimizing Western blot protocols for Acetyl-HIST1H2BB (K5) detection requires attention to several critical parameters:
Parameter | Recommended Condition | Rationale |
---|---|---|
Sample preparation | Include HDAC inhibitors (e.g., TSA, sodium butyrate) | Preserves acetylation marks during extraction |
Protein amount | 10-20 μg of nuclear extract | Ensures adequate signal without oversaturation |
SDS-PAGE conditions | 15-18% gels | Provides better resolution for small histone proteins |
Transfer parameters | 100V for 1 hour or 30V overnight at 4°C | Efficient transfer of small proteins |
Blocking solution | 5% BSA in TBST (not milk) | Milk contains bioactive proteins that may interfere with acetylation detection |
Primary antibody dilution | 1:5000-1:20000 | Optimal range for specific detection with minimal background |
Incubation time | Overnight at 4°C | Enhances specific binding |
Detection method | Enhanced chemiluminescence (ECL) | Provides sensitivity needed for acetylation mark detection |
Additional considerations include implementing a loading control with a total H2B antibody to normalize for variations in protein loading, and validating results with positive controls such as cells treated with HDAC inhibitors to increase global acetylation levels .
When faced with inconsistent results in immunofluorescence experiments using Acetyl-HIST1H2BB (K5) Antibody, implement these troubleshooting strategies:
Fixation optimization:
Try different fixatives (4% paraformaldehyde, methanol, or combination)
Adjust fixation time (10-20 minutes) to balance epitope preservation and cell permeabilization
Consider epitope retrieval methods if formaldehyde fixation interferes with antibody binding
Permeabilization assessment:
Test different permeabilization agents (0.1-0.5% Triton X-100, 0.05% SDS, or methanol)
Optimize permeabilization time to ensure nuclear access without destroying epitopes
Use appropriate blocking agents (BSA, normal serum) to reduce nonspecific binding
Antibody parameters:
Titrate antibody concentration (1:50-1:200 range recommended)
Extend primary antibody incubation time (overnight at 4°C versus 1-2 hours at room temperature)
Test different antibody diluents to improve signal-to-noise ratio
Technical considerations:
Include positive controls (cell lines known to express acetylated H2B)
Use freshly prepared buffers and reagents
Ensure consistent handling of all samples being compared
Image acquisition settings:
Standardize exposure settings across experiments
Use appropriate filter sets to minimize autofluorescence
Implement background subtraction consistently
By systematically addressing these variables, researchers can identify and resolve factors contributing to inconsistent immunofluorescence results .
Quantitative analysis of ChIP-seq data generated with Acetyl-HIST1H2BB (K5) Antibody involves several key analytical steps:
Quality control and preprocessing:
Assess sequencing quality with FastQC
Trim adapters and low-quality bases
Align reads to reference genome using Bowtie2 or BWA
Remove PCR duplicates and filter for uniquely mapped reads
Peak calling and annotation:
Use MACS2 with input control for peak identification (recommended parameters: --nomodel --extsize 147)
Annotate peaks relative to genomic features using HOMER or ChIPseeker
Generate normalized coverage tracks (bigWig format) for visualization
Differential binding analysis:
Apply DESeq2 or DiffBind to identify regions with significant changes in acetylation
Normalize for sequencing depth and local biases
Calculate fold changes and statistical significance
Integration with other data types:
Correlate H2B K5 acetylation patterns with:
Transcriptomic data (RNA-seq)
Other histone modifications
Transcription factor binding sites
Chromatin accessibility (ATAC-seq, DNase-seq)
Functional interpretation:
Perform gene ontology and pathway enrichment analysis of genes associated with acetylated regions
Analyze motif enrichment within peak regions using MEME or HOMER
Visualize data using genome browsers (IGV, UCSC)
This analytical framework provides a comprehensive assessment of H2B K5 acetylation patterns across the genome, facilitating insights into its functional roles in chromatin organization and gene regulation .
When comparing acetylation at different lysine residues on HIST1H2BB, researchers should consider these key factors:
Biological context and function:
K5 and K20 acetylation may have distinct roles in chromatin regulation
K5 is located in the N-terminal tail, while K20 is positioned differently in the histone structure
These positions may influence interaction with different chromatin remodeling complexes
Experimental design considerations:
Use antibodies with validated specificity for each modification
Perform sequential ChIP experiments to determine co-occurrence of marks
Include appropriate controls to account for antibody efficiency differences
Data normalization approaches:
Normalize signal to total H2B levels
Account for differences in antibody efficiency using spike-in controls
Consider relative abundance of each mark when interpreting results
Genomic distribution patterns:
Analyze the distribution of each modification across genomic features
K5 and K20 acetylation may show differential enrichment at:
Promoters versus gene bodies
Euchromatic versus heterochromatic regions
Specific types of regulatory elements
Evolutionary conservation analysis:
Compare conservation of acetylation sites across species
Analyze conservation of proteins recognizing each modification
Consider the functional implications of evolutionary constraints
Understanding these distinctions helps researchers interpret the specific roles of different acetylation marks on HIST1H2BB and their potential cooperation or antagonism in regulating chromatin structure and function .
When facing conflicting data between different techniques measuring Acetyl-HIST1H2BB (K5), researchers should implement this systematic interpretation framework:
Technical limitations assessment:
ChIP-seq provides genome-wide resolution but averages signals across cell populations
Immunofluorescence offers single-cell resolution but limited genomic information
Western blot provides bulk quantification without spatial or genomic context
Each technique may have different sensitivity thresholds and dynamic ranges
Sample preparation differences:
Crosslinking conditions vary between techniques and may affect epitope accessibility
Cell fixation for microscopy can alter chromatin structure
Nuclear extraction protocols for Western blot may lead to selective enrichment
Antibody behavior in different contexts:
The same antibody may perform differently under various experimental conditions
Buffer compositions, incubation times, and temperatures can affect binding properties
Epitope accessibility may vary between techniques
Reconciliation strategies:
Use orthogonal approaches (e.g., mass spectrometry) for validation
Implement controlled spike-in standards across techniques
Design experiments to address specific discrepancies
Consider biological heterogeneity as a source of apparent contradiction
Biological interpretation framework:
Cell-to-cell variation may explain differences between population-based and single-cell techniques
Dynamic nature of histone modifications may result in temporal discrepancies
Histone variants and neighboring modifications can influence antibody recognition
By systematically evaluating these factors, researchers can develop more nuanced interpretations of seemingly conflicting data and identify the true biological patterns of histone acetylation .
Studying evolutionary conservation of histone modifications across species using Acetyl-HIST1H2BB (K5) Antibody requires a comprehensive comparative approach:
Cross-species reactivity testing:
Validate antibody reactivity in target species through Western blot
Optimize immunoprecipitation conditions for each species
Consider using multiple antibodies targeting the same modification for validation
Comparative genomics approach:
Perform ChIP-seq across multiple species using standardized protocols
Map orthologous regions using whole-genome alignments
Analyze conservation of acetylation patterns at:
Orthologous genes
Conserved regulatory elements
Species-specific genomic regions
Evolutionary analysis framework:
Quantify conservation versus divergence of acetylation patterns
Correlate changes in acetylation with sequence evolution
Identify lineage-specific changes in acetylation profiles
Functional validation:
Test conserved acetylated regions for functional conservation using reporter assays
Investigate the conservation of writer/eraser/reader proteins for K5 acetylation
Analyze phenotypic consequences of disrupting conserved acetylation patterns
This approach provides insights into how histone modifications have evolved and which aspects are fundamentally conserved across evolutionary timescales. Research has revealed significant evolutionary divergence in histone H2B family members across plant lineages, suggesting that similar divergence patterns may exist in other taxonomic groups .
Working with tissue samples rather than cell cultures requires specific methodological adaptations:
Parameter | Cell Culture Approach | Tissue Sample Adaptation | Rationale |
---|---|---|---|
Sample preparation | Standard lysis protocols | Tissue-specific homogenization | Different tissue densities require optimized disruption |
Crosslinking | Standard formaldehyde protocols | Modified fixation with tissue penetration enhancers | Ensures uniform fixation throughout heterogeneous tissue |
Chromatin shearing | Sonication of cell suspensions | Optimized sonication times for tissue density | Different tissues require adjusted energy input |
IP conditions | Standard protocols | Increased antibody amounts (2-3x) | Compensates for higher background in complex tissues |
Washing stringency | Standard wash buffers | Additional washes with increased detergent | Removes tissue-specific background |
Blocking reagents | Standard BSA/milk | Tissue-matched normal serum | Reduces tissue-specific background binding |
Antigen retrieval | Rarely needed | Often essential (citrate or EDTA buffer) | Unmasks epitopes in fixed tissue sections |
Counterstaining | Optional nuclear stain | Cell type-specific markers | Identifies specific cell populations in heterogeneous tissues |
Additionally, researchers should consider tissue-specific autofluorescence when performing immunofluorescence and implement appropriate quenching methods or spectral unmixing techniques. For lung tissue specifically, additional optimization might be needed due to its complex architecture and high elastin content, which can contribute to background signal .
Integrating Acetyl-HIST1H2BB (K5) data with other epigenetic marks requires sophisticated computational and experimental approaches:
Multimodal data generation:
Perform parallel ChIP-seq for multiple histone modifications
Include DNA methylation data (WGBS or RRBS)
Add chromatin accessibility information (ATAC-seq or DNase-seq)
Incorporate chromosome conformation data (Hi-C or ChIA-PET)
Computational integration methods:
Apply hidden Markov models (ChromHMM or EpiCSeg) to identify recurrent combinatorial patterns
Use non-negative matrix factorization for dimension reduction
Implement deep learning approaches (e.g., convolutional neural networks) for pattern recognition
Apply multivariate statistical methods to identify correlations between marks
Biological interpretation framework:
Annotate chromatin states with functional genomic elements
Correlate states with gene expression patterns
Analyze dynamics of state transitions during biological processes
Identify cell type-specific chromatin signatures
Validation strategies:
Perform perturbation experiments targeting specific marks
Use CRISPR-based epigenome editing to test causality
Implement single-cell approaches to address heterogeneity
Design reporter assays to test functional predictions
This integrative approach reveals how Acetyl-HIST1H2BB (K5) functions within the broader epigenetic landscape, providing insights into the combinatorial logic of chromatin regulation. Research on plant histone H2B variants has shown that different variants can have distinct genomic distributions, with some preferentially associating with euchromatic or heterochromatic regions, suggesting complex patterns of functional specialization .
Adapting Acetyl-HIST1H2BB (K5) Antibody for CUT&RUN or CUT&Tag requires specific optimization strategies:
Antibody validation for enzyme-tethered techniques:
Test antibody function in bulk ChIP before moving to CUT&RUN/CUT&Tag
Validate antibody binding in unfixed cells (required for CUT&RUN/CUT&Tag)
Optimize antibody concentration through titration experiments (typically 0.5-1 μg per reaction)
Protocol adaptations:
Use longer primary antibody incubation times (overnight at 4°C)
Optimize wash conditions to maintain antibody-antigen interaction
Adjust pA-MNase or pA-Tn5 concentration based on preliminary results
Consider adding a rabbit anti-mouse secondary antibody if using mouse primary antibodies
Quality control measures:
Include positive control targets (known H2B K5 acetylation sites)
Implement IgG negative controls
Compare fragment size distribution with expected patterns
Assess signal-to-noise ratio through peak calling metrics
Data analysis considerations:
Account for different background patterns compared to traditional ChIP
Adjust peak calling parameters for sharper peaks typical of CUT&RUN/CUT&Tag
Implement spike-in normalization for quantitative comparisons
These advanced techniques offer significant advantages including reduced background, lower input requirements, and improved resolution, making them valuable for studying histone modifications in limited samples or single-cell applications.
Successful conjugation of Acetyl-HIST1H2BB (K5) Antibody for advanced microscopy requires attention to these critical factors:
Antibody preparation:
Use carrier-free antibody formulations without BSA or sodium azide
Implement buffer exchange to remove incompatible components
Concentrate antibody to optimal concentration (typically >1 mg/ml)
Verify antibody quality by SDS-PAGE before conjugation
Conjugation chemistry selection:
For fluorescent dyes: NHS ester chemistry targeting primary amines
For quantum dots: Use specialized coupling kits with optimized protocols
For gold nanoparticles: Consider thiol-based coupling strategies
For enzyme conjugates (HRP, AP): Use activated aldehyde chemistry
Optimization parameters:
Dye-to-protein ratio (typically 2-4 fluorophores per antibody)
Reaction time and temperature (4°C overnight versus room temperature for 1-2 hours)
pH optimization (typically pH 8.0-8.5 for NHS ester reactions)
Purification method (size exclusion versus affinity-based)
Quality control assessment:
Measure degree of labeling (DOL) spectrophotometrically
Test conjugate functionality through standard applications (IF, flow cytometry)
Assess stability over time under various storage conditions
Compare performance to unconjugated antibody plus secondary detection
Storage considerations:
Add cryoprotectants like trehalose or glycerol for frozen storage
Aliquot to minimize freeze-thaw cycles
Protect fluorescent conjugates from light
Consider lyophilization for long-term stability
For biotin conjugation specifically, researchers should use a buffer exchange to remove BSA and sodium azide, followed by adding cryoprotectants like glycerol or trehalose that won't interfere with conjugation chemistry while providing good protection from degradation during storage .
Single-cell epigenomics offers promising approaches for studying cell-specific HIST1H2BB K5 acetylation patterns:
Emerging methodological approaches:
Single-cell CUT&Tag for high-resolution profiling
scChIC-seq (single-cell chromatin immunocleavage sequencing)
Imaging-based approaches combining IF with in situ sequencing
Mass cytometry (CyTOF) with metal-conjugated antibodies
Technical challenges and solutions:
Antibody specificity becomes more critical at single-cell level
Signal amplification strategies may be necessary
Data sparsity requires specialized computational approaches
Cell fixation methods must balance epitope preservation with cell integrity
Analytical frameworks:
Pseudotime trajectory analysis to reveal dynamic acetylation changes
Integration with scRNA-seq to correlate acetylation with transcription
Supervised and unsupervised clustering to identify cell populations
Transfer learning approaches to overcome data sparsity
Biological applications:
Heterogeneity of acetylation patterns in seemingly homogeneous populations
Cell state transitions during development or disease progression
Identification of rare cell populations with unique acetylation signatures
Stochastic versus deterministic aspects of epigenetic regulation
These approaches will provide unprecedented insights into the dynamic nature of histone acetylation and its role in defining cellular identity and function. The study of plant histone variants has already revealed cell-type specific expression patterns, suggesting similar specificity may exist for acetylation marks in animal systems .
Emerging applications of Acetyl-HIST1H2BB (K5) Antibody in disease research span multiple fields:
Cancer biology applications:
Characterizing acetylation changes during oncogenic transformation
Identifying epigenetic biomarkers for cancer subtypes
Studying resistance mechanisms to epigenetic therapies
Monitoring responses to HDAC inhibitors in clinical samples
Neurodegenerative disease research:
Analyzing histone acetylation alterations in Alzheimer's and Parkinson's
Investigating the impact of metabolic changes on brain epigenetics
Studying the role of histone acetylation in neuronal plasticity and memory
Developing epigenetic biomarkers for early disease detection
Immunological disorders:
Characterizing acetylation dynamics during immune cell activation
Studying epigenetic dysregulation in autoimmune conditions
Investigating trained immunity through histone modification analysis
Developing targeted epigenetic interventions for immune modulation
Developmental disorders:
Profiling acetylation patterns in congenital disorders
Investigating the impact of environmental exposures on developmental epigenetics
Studying transgenerational inheritance of epigenetic modifications
Developing early intervention strategies based on epigenetic profiles
These applications highlight the growing importance of histone acetylation analysis in understanding disease mechanisms and developing novel diagnostic and therapeutic approaches.
Implementing these consensus best practices ensures validation and reproducibility when working with Acetyl-HIST1H2BB (K5) Antibody:
Antibody validation requirements:
Perform peptide competition assays to confirm specificity
Use knockout or knockdown controls when possible
Test cross-reactivity with related histone modifications
Validate lot-to-lot consistency for key experiments
Experimental design considerations:
Include biological replicates (minimum n=3)
Implement technical replicates for critical measurements
Use appropriate positive and negative controls
Standardize protocols and record detailed methodology
Data reporting standards:
Document complete antibody information (supplier, catalog number, lot, dilution)
Report all optimization procedures and controls
Present both representative images and quantitative analyses
Make raw data available when possible
Quality control metrics:
Signal-to-noise ratio assessment
Reproducibility between technical and biological replicates
Consistency across different detection methods
Statistical analysis of variability
Adherence to these practices enhances research quality and facilitates comparison across studies, advancing our understanding of histone acetylation biology and its implications in various biological processes.
Future technological advances will transform how Acetyl-HIST1H2BB (K5) Antibody is used in epigenetic research:
Next-generation antibody technologies:
Recombinant antibodies with improved consistency
Nanobodies providing enhanced access to compact chromatin
Engineered antibody fragments with superior tissue penetration
Aptamer-based alternatives with programmable binding properties
Advanced imaging innovations:
Super-resolution microscopy beyond current diffraction limits
Live-cell temporal tracking of acetylation dynamics
Multiplexed imaging of numerous modifications simultaneously
Integration of spatial transcriptomics with histone modification mapping
Sequencing technology advancements:
Direct detection of histone modifications in native chromatin
Single-molecule long-read approaches capturing modification co-occurrence
Improved sensitivity requiring fewer cells or even single cells
Real-time monitoring of dynamic modification changes
Computational and AI developments:
Machine learning algorithms predicting modification patterns
AI-assisted image analysis for quantification and pattern recognition
Integrated multi-omics data analysis platforms
Systems biology approaches modeling epigenetic network dynamics