ATXN7L1 Antibody

What is the molecular basis of ATXN7L1 and why is it significant in research?

ATXN7L1 (Ataxin-7-like protein 1) is a protein coded by a gene located on chromosome 7q22.2. Its significance stems from its role as a component of the histone acetyl transferase (HAT) and deubiquitinase SAGA complex, which is integral to transcription regulation. Research has confirmed that ATXN7L1 is a bona fide component of the human SAGA complex, suggesting it has a similar functional role to the related protein ATXN7 in transcription regulation via USP22 dependent deubiquitination of histones .

The protein has particular significance in hematological malignancy research, as it has been identified as potentially downregulated due to hypermethylation in acute myeloid leukemia (AML) patients, suggesting a possible tumor suppressor function . This makes ATXN7L1 a valuable research target for understanding epigenetic regulation in cancer development and progression.

What are the key considerations when selecting an ATXN7L1 antibody for experimental applications?

When selecting an ATXN7L1 antibody for research applications, several critical factors must be considered to ensure experimental success:

• Clonality: Determine whether a monoclonal or polyclonal antibody is more suitable for your application. Monoclonal antibodies like the mouse monoclonal (clone 1H2) from Aviva Systems Biology offer high specificity to a single epitope , while polyclonal antibodies such as those from Boster Bio and Novus Biologicals provide broader epitope recognition .

• Host Species: Consider potential cross-reactivity issues - rabbit-host antibodies (Boster, Novus) versus mouse-host antibodies (Aviva) may be preferable depending on your experimental system .

• Immunogen Region: Evaluate whether the antibody was raised against a specific region relevant to your research. For example, Boster's antibody targets the 441-490 sequence region , while Novus Biologicals' antibody targets the middle region .

• Validated Applications: Ensure the antibody has been validated for your specific application. Available ATXN7L1 antibodies have been validated for:

  • Western Blot (Novus, Aviva)

  • Immunohistochemistry (Boster)

  • Immunofluorescence (Boster)

  • ELISA (Boster, Aviva)

• Species Reactivity: Confirm reactivity with your experimental model system. Current antibodies show reactivity primarily with human and mouse samples .

How do the characteristics of different ATXN7L1 antibodies affect experimental design?

The specific characteristics of ATXN7L1 antibodies significantly influence experimental design considerations:

When designing experiments:

• For protein localization in tissues or cells, Boster's antibody has validated IHC and IF applications with established protocols

• For precise protein quantification in Western blots, the Novus or Aviva antibodies may be preferable

• For detecting different isoforms or fragments, consider the target epitope location relative to potential splice variants or proteolytic processing sites

How can ATXN7L1 antibodies be optimized for studying epigenetic modifications in leukemia models?

Optimizing ATXN7L1 antibodies for epigenetic studies in leukemia models requires a multifaceted approach:

• Combined Chromatin Immunoprecipitation (ChIP) Strategy:
  Since ATXN7L1 is part of the SAGA complex involved in histone modification, design a sequential ChIP approach using the ATXN7L1 antibody followed by antibodies against relevant histone marks (H3K9ac, H2Bub1) to identify genomic regions where ATXN7L1 contributes to specific modifications.

• Methylation-Expression Correlation:
  Research has identified ATXN7L1 as hypermethylated in AML patients . Design experiments that combine:

  • Bisulfite sequencing of the ATXN7L1 promoter

  • ATXN7L1 protein detection using validated antibodies

  • Expression analysis by RT-qPCR

  This approach would establish relationships between methylation status and protein expression in different leukemic cell lines or patient samples.

• Optimized Co-Immunoprecipitation Protocol:
  To study ATXN7L1's role in SAGA complex:

  • Use crosslinking optimized for nuclear proteins (1-2% formaldehyde, 10 minutes)

  • Include nuclear extraction buffers with appropriate salt concentrations (250-300mM NaCl)

  • Pull down with ATXN7L1 antibody and probe for other SAGA components (GCN5, USP22)

  This approach has been validated in HeLa cells using GCN5 antibodies for co-IP followed by mass spectrometry, which successfully identified ATXN7L1 as a component of SAGA .

• Cell Line Selection for Maximum Signal:
  Based on expression data, select appropriate cell lines where ATXN7L1 is normally expressed (like CD34+ cells) and compare with AML lines to optimize antibody concentrations for detecting biologically relevant differences .

What methodological approaches can address specificity concerns when using ATXN7L1 antibodies in complex protein complexes?

When studying ATXN7L1 within complex protein assemblies like the SAGA complex, addressing specificity is crucial:

• Validation Through Multiple Antibody Approach:

  • Employ antibodies targeting different epitopes of ATXN7L1, such as the N-terminal region (Aviva, 1-146aa) and middle region (Novus)

  • Compare immunoprecipitation results to establish consensus interacting partners

  • Confirm specificity using siRNA/shRNA knockdown of ATXN7L1 followed by antibody detection

• Confirmation by Reciprocal Co-Immunoprecipitation:

  • Primary IP with ATXN7L1 antibody, probe for SAGA components

  • Secondary IP with antibodies against known SAGA components (GCN5), probe for ATXN7L1

  • This approach has been successfully employed in research demonstrating ATXN7L1 as part of the SAGA complex

• Peptide Competition Assay Protocol:

  • Pre-incubate the ATXN7L1 antibody with increasing concentrations of the immunogenic peptide

  • Compare signal intensity between competed and non-competed antibody

  • Boster's antibody offers the advantage of available blocking peptide derived from the immunogen (aa 441-490)

• Sequential Immunodepletion Methodology:

  • Perform initial immunoprecipitation with ATXN7L1 antibody

  • Subject unbound fraction to secondary IP with antibodies against related proteins (ATXN7, ATXN7L4)

  • Analyze both fractions to determine specific versus overlapping functions

• Mass Spectrometry Validation Workflow:

  • Compare protein interactomes identified by IP-MS using different ATXN7L1 antibodies

  • Cross-reference with published SAGA complex components

  • This approach successfully identified ATXN7L1 as a component of SAGA in previous research

How can ATXN7L1 antibodies be applied in studying the relationship between epigenetic dysregulation and leukemogenesis?

ATXN7L1 antibodies can be strategically employed to investigate epigenetic mechanisms in leukemia development:

• Chromatin Landscape Mapping Protocol:

  • Perform ChIP-seq using ATXN7L1 antibodies in normal CD34+ cells versus AML samples

  • Integrate with histone modification maps (H3K4me3, H3K27ac, H3K9me3)

  • This approach can reveal how ATXN7L1 localization changes correlate with altered chromatin states in leukemia

• Sequential Epigenetic Profiling Methodology:

  • Map ATXN7L1 binding sites in relation to hypermethylated regions in AML

  • Research has identified ATXN7L1 as one of four genes hypermethylated in their promoters in the 7q22 region, showing 5-20% higher methylation in AML compared to healthy controls

  • Integrate DNA methylation data with ATXN7L1 ChIP data to establish relationships between ATXN7L1 displacement and DNA hypermethylation

• Functional Reconstitution Experiments:

  • Restore ATXN7L1 expression in AML cells with 7q deletion/ATXN7L1 hypermethylation

  • Use antibodies to confirm restored protein levels

  • Assess changes in histone modification patterns and transcriptional programs

  • This builds on research suggesting ATXN7L1 silencing may affect the leukemic phenotype

• Therapeutic Response Monitoring:

  • Apply ATXN7L1 antibodies to track protein re-expression after treatment with demethylating agents (5-azacytidine, decitabine)

  • Correlate with changes in SAGA complex activity and global histone modification patterns

  • This approach addresses the hypothesis that ATXN7L1 downregulation upon hypermethylation contributes to leukemogenesis

What are the critical steps for optimizing immunohistochemistry protocols with ATXN7L1 antibodies?

Optimizing immunohistochemistry with ATXN7L1 antibodies requires attention to several critical parameters:

• Antigen Retrieval Optimization:

  • Test multiple methods, particularly heat-induced epitope retrieval (HIER)

  • For formalin-fixed tissue, citrate buffer (pH 6.0) and EDTA buffer (pH 9.0) should be compared

  • Optimization is especially important as ATXN7L1 is a nuclear protein involved in chromatin-associated complexes

• Antibody Dilution Titration:

  • Begin with manufacturer-recommended dilutions (e.g., 1:100-1:300 for Boster's antibody)

  • Test serial dilutions to identify optimal signal-to-noise ratio

  • Include positive control tissue (human testis has been validated with Boster's antibody)

• Signal Amplification Selection:

  • Standard DAB detection systems work well for initial testing

  • For low-expression scenarios, consider tyramide signal amplification (TSA)

  • When optimizing, compare results between polymer-based and avidin-biotin complex (ABC) detection systems

• Blocking Protocol Optimization:

  • Test whether additional blocking is needed beyond standard protocols

  • Consider 5% BSA or 10% normal serum from the same species as the secondary antibody

  • For tissues with high background, include an avidin-biotin blocking step

• Incubation Parameters:

  • Compare overnight incubation at 4°C versus 1-2 hours at room temperature

  • For each condition, assess specificity using the blocking peptide control

  • Validated conditions from published IHC results with ATXN7L1 antibody on human testis can serve as a starting point

The inclusion of appropriate controls is essential:

• Positive control (tissue with known ATXN7L1 expression)

• Negative control (omitting primary antibody)

• Peptide competition control (particularly useful as Boster offers blocking peptide)

How should Western blot protocols be modified to address challenges in detecting ATXN7L1?

Western blot detection of ATXN7L1 presents several unique challenges that require protocol modifications:

• Molecular Weight Discrepancy Resolution:
  A significant consideration is the discrepancy between observed (72 kDa) and calculated (91.5 kDa) molecular weights for ATXN7L1 . This may be due to:

  • Post-translational modifications

  • Alternative splicing

  • Proteolytic processing

  Protocol recommendations:

  • Use gradient gels (4-15% or 4-20%) to capture all potential isoforms

  • Include molecular weight markers spanning 50-100 kDa

  • When analyzing results, document all observed bands for comprehensive interpretation

• Protein Extraction Optimization:
  As a nuclear protein involved in chromatin regulation, ATXN7L1 requires effective nuclear extraction:

  • Include detergent-based lysis (0.5-1% NP-40 or Triton X-100)

  • Supplement with DNase treatment

  • Consider sonication (3-5 pulses of 10 seconds) to ensure dissociation from chromatin

  • Maintain phosphatase and protease inhibitors throughout extraction

• Antibody Selection Strategy:

  • For detection of full-length protein, the Aviva antibody targeting amino acids 1-146 is suitable

  • For detection of specific regions, consider the Novus antibody targeting the middle region

  • When studying potential truncations, consider using multiple antibodies targeting different regions

• Transfer and Detection Optimization:

  • For proteins >70 kDa, extend transfer time or use semidry transfer with PVDF membranes

  • Extend blocking time to minimize background (2 hours at room temperature)

  • Consider overnight primary antibody incubation at 4°C

  • For Novus and Aviva antibodies validated for Western blot, follow manufacturer-recommended dilutions

• Loading Control Selection:

  • Use nuclear protein loading controls (Lamin B1, Histone H3)

  • Avoid cytoplasmic controls like GAPDH or β-actin

  • Consider using total protein normalization methods (Ponceau S, REVERT)

What are the methodological considerations for multiplex immunofluorescence studies involving ATXN7L1?

Multiplex immunofluorescence studies involving ATXN7L1 require careful technical considerations:

• Antibody Compatibility Assessment:

  • For co-localization with other SAGA components, consider antibody host species compatibility

  • Boster's rabbit polyclonal can be paired with mouse antibodies against other targets

  • Aviva's mouse monoclonal can be paired with rabbit antibodies against other targets

  Create a compatibility matrix:

  Target Protein	Recommended Host	Fluorophore Recommendation
  ATXN7L1	Rabbit (Boster)	Alexa Fluor 488 or 568
  GCN5 (SAGA component)	Mouse	Alexa Fluor 647
  USP22 (SAGA component)	Mouse	Alexa Fluor 555

• Sequential Staining Protocol Development:
  For complex multiplex panels:

  • Begin with validated ATXN7L1 antibody conditions (dilution 1:50-200 for IF as recommended for Boster's antibody)

  • Implement tyramide signal amplification (TSA) for sequential detection

  • Include microwave treatment (95°C, 10 minutes in citrate buffer) between antibody rounds to strip previous antibodies

• Cross-Reactivity Elimination Strategy:

  • Perform single-color controls for each antibody

  • Include absorption controls with relevant blocking peptides

  • Validate specificity through siRNA knockdown of ATXN7L1 followed by staining

• Subcellular Localization Enhancement:
  Since ATXN7L1 functions within the SAGA complex in the nucleus:

  • Include nuclear counterstain (DAPI)

  • Consider super-resolution microscopy (SIM, STED) for co-localization studies

  • Implement image analysis workflows that quantify nuclear vs. cytoplasmic signal

• Spectral Overlap Mitigation:

  • Design panels accounting for emission/excitation spectra

  • Implement linear unmixing algorithms for closely spaced fluorophores

  • Consider spectral imaging systems for complex multiplex panels

• Controls and Validation:

  • Include single antibody controls

  • Implement fluorescence minus one (FMO) controls

  • Cross-validate findings with proximity ligation assay (PLA) for protein-protein interactions

How can researchers reconcile contradictory ATXN7L1 expression patterns across different experimental systems?

Reconciling contradictory ATXN7L1 expression patterns requires a systematic analytical approach:

• Isoform-Specific Analysis Protocol:
  ATXN7L1 has multiple aliases including ATXN7L4 , which may reflect different isoforms or related family members:

  • Design primers/probes targeting unique regions of each potential isoform

  • Use antibodies recognizing different epitopes (N-terminal vs. middle region)

  • Compare expression patterns using both protein (Western blot) and transcript (RT-qPCR) analysis

  • Create a cross-reference table documenting which detection method identifies which isoform

• Tissue-Specific Expression Assessment:
  Research indicates ATXN7L1 is expressed in CD34+ cells and granulocytes but downregulated in certain AML contexts :

  • Implement tissue microarray analysis using validated antibodies

  • Compare expression across hematopoietic lineages at different differentiation stages

  • Correlate protein detection with mRNA expression data from public databases

• Epigenetic Regulation Analysis Framework:
  Given the documented hypermethylation of ATXN7L1 in AML :

  • Correlate ATXN7L1 protein levels with promoter methylation status

  • Assess expression changes after treatment with epigenetic modifiers

  • Compare methylation patterns across different cell types that show variable expression

• Post-Translational Modification Assessment:
  The discrepancy between observed (72 kDa) and calculated (91.5 kDa) molecular weights suggests potential processing:

  • Implement phosphatase/deglycosylase treatments before Western blot

  • Use domain-specific antibodies to detect potential proteolytic fragments

  • Consider mass spectrometry to identify modifications and processing events

• Experimental Conditions Standardization:

  • Document culture conditions, fixation protocols, and antibody lots

  • Implement standard operating procedures for sample processing

  • Use common reference standards across experiments

What analytical approaches can differentiate between ATXN7L1's role in normal cellular processes versus pathological states?

Differentiating ATXN7L1's normal versus pathological functions requires sophisticated analytical approaches:

• Temporal Expression Profiling Methodology:

  • Track ATXN7L1 expression during normal hematopoietic differentiation

  • Compare with expression patterns during leukemic transformation

  • Implement time-course experiments with synchronized cell populations

  • This approach builds on findings that ATXN7L1 is expressed in normal CD34+ cells but downregulated in certain AML contexts

• Functional Domain Mapping Strategy:

  • Create truncation/deletion constructs of ATXN7L1

  • Assess which domains are required for:

    • SAGA complex integration

    • Chromatin association

    • Transcriptional regulation

  • Compare domain requirements between normal and malignant cells

  • This extends research showing ATXN7L1 as a component of the SAGA complex

• Interactome Comparative Analysis:

  • Perform immunoprecipitation with ATXN7L1 antibodies in normal versus malignant cells

  • Identify differential protein interactions by mass spectrometry

  • Create protein interaction networks to visualize altered complexes

  • Quantify changes in associations with key SAGA components

• Chromatin Occupancy Differential Analysis:

  • Perform ChIP-seq using ATXN7L1 antibodies in normal CD34+ cells versus AML samples

  • Identify genomic regions with differential binding

  • Correlate with changes in histone modifications and gene expression

  • This approach addresses ATXN7L1's role in histone modification via the SAGA complex

• Loss-of-Function/Gain-of-Function Experimental Design:

  • Implement CRISPR-based ATXN7L1 knockout in normal CD34+ cells

  • Assess impact on differentiation, proliferation, and transcriptome

  • Conversely, restore ATXN7L1 expression in 7q-deleted or hypermethylated AML cells

  • This addresses ongoing research into how ATXN7L1 silencing affects leukemic phenotype

How should researchers interpret the relationship between ATXN7L1 molecular weight discrepancies and functional implications?

The observed discrepancy between calculated (91.5 kDa) and detected (72 kDa) molecular weights of ATXN7L1 requires careful interpretation:

• Alternative Splicing Analysis Protocol:

  • Design RT-PCR assays targeting all potential exon junctions

  • Sequence identified splice variants and predict resulting protein sizes

  • Create expression constructs of major variants for functional testing

  • Compare variant expression across tissue types and disease states

• Post-Translational Modification Mapping Strategy:

  • Implement immunoprecipitation with ATXN7L1 antibodies followed by:

    • Phosphorylation analysis (phospho-specific antibodies, phosphatase treatment)

    • Ubiquitination analysis (particularly relevant given ATXN7L1's association with deubiquitinase complex)

    • Sumoylation assessment

  • Use mass spectrometry to identify and map modifications

  • Create modification-specific mutants to assess functional impact

• Proteolytic Processing Assessment Framework:

  • Test whether ATXN7L1 undergoes specific cleavage during activation

  • Implement protease inhibitor panels to identify responsible proteases

  • Use N-terminal and C-terminal tagged constructs to track fragment localization

  • Compare processing patterns between normal and malignant cells

• Functional Correlation Analysis:

  • Isolate different molecular weight forms of ATXN7L1

  • Assess:

    • SAGA complex incorporation efficiency

    • Chromatin binding capacity

    • Protein-protein interaction profiles

  • Determine if size differences correlate with functional differences

  • This approach extends research on ATXN7L1's role in the SAGA complex

• Structural Prediction and Validation:

  • Use bioinformatic tools to predict compact structural domains

  • Assess whether structural features could explain aberrant migration

  • Design truncation constructs to test migration patterns

  • Implement circular dichroism or limited proteolysis to assess domain folding

What are the methodological considerations for ChIP-seq experiments targeting ATXN7L1 in chromatin regulation studies?

Optimizing ChIP-seq for ATXN7L1 requires specialized approaches given its role in chromatin modification:

• Crosslinking Optimization Protocol:

  • Compare formaldehyde concentrations (1-2%) and times (10-20 minutes)

  • Consider dual crosslinking with DSG (disuccinimidyl glutarate) followed by formaldehyde

  • Optimize sonication conditions for chromatin shearing (200-500bp fragments)

  • These parameters are crucial for capturing transient interactions of ATXN7L1 within the SAGA complex

• Antibody Selection and Validation Strategy:

  • Test multiple ATXN7L1 antibodies targeting different epitopes

  • Validate ChIP efficiency by qPCR at known SAGA-regulated genes

  • Include ChIP for other SAGA components (GCN5, USP22) as positive controls

  • This multi-antibody approach helps address potential epitope masking in the chromatin context

• Sequential ChIP Methodology:

  • Implement sequential ChIP (Re-ChIP) protocol:

    • Primary IP with ATXN7L1 antibody

    • Secondary IP with antibodies against histone marks (H3K9ac, H2Bub1)

  • This approach identifies genomic regions where ATXN7L1 and specific histone modifications co-occur

• Bioinformatic Analysis Framework:

  • Compare ATXN7L1 binding with:

    • Transcription start sites

    • Enhancer regions

    • Other SAGA component binding sites

  • Implement motif analysis to identify potential DNA sequence preferences

  • Correlate binding sites with gene expression changes in ATXN7L1-deficient cells

• Reference Dataset Integration:

  • Incorporate publicly available datasets for:

    • Histone modifications (H3K4me3, H3K27ac, H2Bub1)

    • Transcription factors associated with SAGA complex

    • DNase hypersensitivity

  • This integration provides context for ATXN7L1 function in chromatin regulation

How can mass spectrometry be optimized to study ATXN7L1 interactions and modifications?

Mass spectrometry approaches for ATXN7L1 require specialized protocols:

• Sample Preparation Optimization for Low-Abundance Proteins:

  • Implement ATXN7L1 immunoprecipitation from nuclear extracts

  • Use on-bead digestion to minimize sample loss

  • Consider label-free quantification for comparative studies

  • These approaches have been successful in identifying ATXN7L1 as part of the SAGA complex

• Post-Translational Modification Mapping Protocol:

  • Enrich for phosphopeptides using TiO2 or IMAC

  • Implement parallel reaction monitoring (PRM) for targeted PTM detection

  • Use electron transfer dissociation (ETD) fragmentation for labile modifications

  • This approach addresses the molecular weight discrepancy between calculated and observed ATXN7L1

• Crosslinking Mass Spectrometry Methodology:

  • Apply protein-protein crosslinkers (BS3, DSS) to stabilize SAGA complex

  • Implement specialized search algorithms for crosslinked peptides

  • Create distance restraint models of ATXN7L1 within the SAGA complex

  • This extends research confirming ATXN7L1 as a component of SAGA

• Interaction Proteomics Workflow:

  • Compare ATXN7L1 interactome between:

    • Normal hematopoietic cells versus AML

    • ATXN7L1 wild-type versus mutants

    • Different cellular compartments

  • Implement SILAC or TMT labeling for quantitative comparisons

  • Construct interaction networks based on quantitative data

• Targeted Mass Spectrometry Strategy:

  • Develop multiple reaction monitoring (MRM) assays for:

    • ATXN7L1 isoforms

    • Key phosphorylation sites

    • Ubiquitination

  • Create heavy-labeled internal standards for absolute quantification

  • Monitor changes during hematopoietic differentiation and leukemic transformation

What role might ATXN7L1 play in the integration of epigenetic signals in hematological disorders beyond AML?

Current evidence suggests broader implications for ATXN7L1 in hematological regulation:

• Comparative Hematological Disorder Analysis Framework:

  • Extend methylation analysis from AML to other myeloid disorders (MDS, CMML)

  • Compare ATXN7L1 expression patterns across lymphoid malignancies

  • Evaluate correlation with specific cytogenetic abnormalities beyond 7q deletions

  • This builds upon research identifying ATXN7L1 hypermethylation in AML patients

• Lineage-Specific Function Assessment:

  • Implement ATXN7L1 knockdown/knockout in various hematopoietic lineages

  • Assess impact on:

    • Myeloid versus lymphoid differentiation

    • Erythroid development

    • Megakaryocyte formation

  • This approach extends findings of ATXN7L1 expression in normal CD34+ cells

• Therapeutic Response Prediction Strategy:

  • Correlate ATXN7L1 expression/methylation with response to:

    • Conventional chemotherapy

    • Hypomethylating agents

    • Histone deacetylase inhibitors

  • Develop predictive models incorporating ATXN7L1 status

  • This approach leverages ATXN7L1's role in the SAGA complex and potential epigenetic dysregulation

• SAGA Complex Dysfunction Comparative Analysis:

  • Compare ATXN7L1-associated SAGA dysfunction across hematological malignancies

  • Assess whether different components are affected in different disorders

  • Evaluate whether SAGA targeting could be a broad therapeutic strategy

  • This extends research confirming ATXN7L1 as part of the SAGA complex

• Single-Cell Heterogeneity Assessment:

  • Implement single-cell approaches to analyze ATXN7L1 expression

  • Identify potential rare subpopulations with altered ATXN7L1 function

  • Correlate with differentiation state and leukemia stem cell markers

  • This addresses potential heterogeneity in ATXN7L1's role in disease development

How can functional genomics approaches be optimized to elucidate ATXN7L1's role in transcriptional regulation?

Advanced functional genomics approaches can reveal ATXN7L1's regulatory mechanisms:

• CRISPR-Based Functional Screening Protocol:

  • Design CRISPR libraries targeting:

    • ATXN7L1 binding sites identified by ChIP-seq

    • ATXN7L1 protein domains

    • Putative regulatory elements

  • Implement pooled screens with various cellular readouts

  • This approach systematically maps functional regions relevant to ATXN7L1 activity

• Transcriptome-Wide Binding Profile Analysis:

  • Implement CLIP-seq (Crosslinking Immunoprecipitation) to identify RNA interactions

  • Compare with ChIP-seq data to distinguish DNA versus RNA binding

  • Assess whether ATXN7L1 has RNA-mediated functions beyond its known role in the SAGA complex

• Enhancer Function Mapping Strategy:

  • Identify enhancers regulated by ATXN7L1 using:

    • STARR-seq (Self-Transcribing Active Regulatory Region Sequencing)

    • CRISPRa/CRISPRi at ATXN7L1 binding sites

  • Correlate enhancer activity with gene expression changes

  • This extends understanding of ATXN7L1's role in transcriptional regulation

• Chromatin Accessibility Dynamics Assessment:

  • Implement ATAC-seq in ATXN7L1 knockdown/knockout models

  • Map changes in accessibility upon ATXN7L1 depletion or overexpression

  • Correlate with histone modification changes

  • This approach leverages ATXN7L1's role in the histone-modifying SAGA complex

• Integrative Multi-Omics Analysis Framework:

  • Integrate datasets from:

    • ChIP-seq (ATXN7L1 binding)

    • RNA-seq (transcriptional output)

    • ATAC-seq (chromatin accessibility)

    • Hi-C (chromatin conformation)

  • Develop computational models of ATXN7L1's impact on 3D genome organization

  • This comprehensive approach provides a systems-level view of ATXN7L1 function