What is the minimum starting material required for your PIRCh-seq service?

We typically recommend starting with sufficient input (for example, millions of cells or equivalent tissue mass) so that chromatin-bound RNAs are captured with robust signal; lower‐input samples may still be processed but could yield reduced sensitivity or require additional pilot optimisation.

How do you ensure specificity for RNA bound to chromatin rather than nascent transcripts?

Our workflow incorporates glutaraldehyde cross-linking of live cells, sonication of chromatin to ~300–2000 bp fragments, and immunoprecipitation with antibodies specific to histone modifications; this design was shown in the foundational study to recover chromatin-associated RNAs with significantly fewer intronic reads compared to other approaches, implying effective discrimination from nascent transcripts.

Can I target multiple histone marks or conditions in a single experiment?

Yes — the sample design is flexible, allowing you to IP chromatin using different histone modifications (e.g., H3K4me3, H3K27ac, H3K27me3) and/or compare conditions (cell types, treatments, time-points). This enables direct comparison of RNA binding across epigenetic states and experimental interventions.

What types of RNA can be detected through PIRCh-seq?

While our platform is optimised for long non-coding RNAs (lncRNAs) and nuclear microRNAs (miRNAs) that associate with chromatin, the workflow can accommodate a broad range of chromatin-bound RNAs — including eRNAs, promoter-associated RNAs or other non-coding species — provided the material is amenable to library preparation and sequencing.

What form of deliverables will I receive and how are they useful?

Upon completion you will receive raw sequencing FASTQ files, aligned data, enrichment tables of RNAs bound to specified histone marks, proximity annotation of nearby coding genes (± 100 kb), functional enrichment (GO/KEGG), visualisations (heatmaps, clustering plots), and a summary interpretive report. These deliverables are designed for integration into manuscripts, conference presentations or downstream target validation workflows.

Does PIRCh-seq replace other RNA–chromatin or RNA–protein interaction assays like CLIP-seq, RIP-seq or R-loop-seq?

Not exactly — each of these methods addresses a distinct question: CLIP-seq and RIP-seq map RNA–protein interactions; R-loop-seq maps RNA:DNA hybrids. PIRCh-seq specifically identifies RNAs associated with chromatin under defined epigenetic (histone modification) states, making it ideal when your question centres on RNA–chromatin binding rather than RNA–protein or RNA–DNA hybrid interactions.

What kinds of quality control and replicates are recommended?

We recommend including an input control (no IP), an IgG or mock IP control, and biological replicates to ensure reproducibility. In the original PIRCh-seq publication, replicate correlations ranged from R = 0.90 to 0.988, demonstrating high reproducibility when protocols are rigorously followed.

How long does turnaround take and what factors may extend timeline?

Turnaround time depends on factors such as sample availability, number of histone‐mark conditions, depth of sequencing, and custom bioinformatics. Complex study designs or very limited material may require additional optimisation or pilot runs.

PIRCh-seq Service – Profiling Interacting RNAs on Chromatin by Deep Sequencing

As multi-omics becomes essential in epigenetic research, PIRCh-seq reveals how RNAs shape chromatin landscapes beyond standard RNA-seq, RIP, or CLIP-seq.

Unlock the hidden layer of regulation in your genome. With our PIRCh-seq service, you'll map how non-coding RNAs (especially lncRNAs) bind to chromatin marked by specific histone modifications. At CD Genomics, we deliver an end-to-end solution for profiling interacting RNAs on chromatin, enabling you to explore RNA–chromatin interactions, identify lncRNA–chromatin binding events, and perform high-resolution chromatin sequencing beyond standard RIP-seq or CLIP-seq workflows.

What we provide:

Discovery of RNAs that bind to chromatin bearing active or repressive histone marks
Insights into epigenetic regulation driven by lncRNAs and nuclear miRNAs
A robust workflow designed for academic labs, research institutes, biotech teams and pharma R&D (research-use only)

Submit Your Request Now

PIRCh-seq workflow: histone-mark IP, RNA purification, deep sequencing, and bioinformatics outputs (CD Genomics)

Identify RNAs bound to active/repressive chromatin (H3K4me3/H3K27ac/H3K27me3)"
Reduce nascent-RNA noise for cleaner biology"
Publication-ready figures and annotations"

What Is PIRCh-seq?

PIRCh-seq mechanism diagram showing RNAs binding to histone-marked chromatin (H3K4me3, H3K27ac, H3K27me3) regulating transcription.

Understanding how RNA interacts with chromatin is essential for decoding epigenetic regulation. PIRCh-seq—short for Profiling Interacting RNAs on Chromatin followed by deep sequencing—is an innovative sequencing technology that systematically identifies RNAs bound to chromatin regions carrying specific histone modifications.

Unlike conventional RNA immunoprecipitation (RIP-seq) or crosslinking immunoprecipitation (CLIP-seq) methods, which focus on RNA–protein binding, PIRCh-seq directly captures RNA–chromatin associations under defined epigenetic states. By combining histone mark–specific immunoprecipitation with next-generation sequencing, researchers can map how long non-coding RNAs (lncRNAs) and other regulatory RNAs influence gene expression, chromatin structure, and transcriptional activity.

This approach offers a more precise view of RNA's epigenetic roles. PIRCh-seq distinguishes RNAs associated with active, repressive, or bivalent chromatin domains and reveals lncRNA-mediated regulatory mechanism behind chromatin remodeling and transcriptional control.

In essence:

PIRCh-seq bridges RNA biology and epigenomics.
It provides a histone modification-specific landscape of RNA–chromatin interactions.
It supports a wide range of research in gene regulation, epigenetic modification, and non-coding RNA function.

For complementary assays, see our RNA–Chromatin Interaction service and Non-coding RNA Sequencing.

PIRCh-seq Workflow

Workflow Overview

Our PIRCh-seq service offers a streamlined, three-phase workflow designed to identify RNAs that bind to chromatin under specific epigenetic states. Each phase is engineered for precision, reproducibility and compatibility with downstream bioinformatics. The core steps are:

Cross-linking & Chromatin Preparation

Live cells are treated—typically using glutaraldehyde—to stabilize RNA–chromatin interactions, avoiding loss of transient binding events.
Cells are quenched (e.g., with glycine) to stop cross-linking and protect RNA integrity.
Chromatin is extracted and fragmented to ~300–2,000 bp (commonly ~300–500 bp) by sonication to balance resolution and yield.

Histone-Mark-Specific Immunoprecipitation (IP)

Fragmented chromatin is incubated with antibodies specific to histone modifications (e.g., H3K4me3, H3K27ac, H3K27me3) or RNA binding proteins (optional), enabling selective pull-down of RNA–chromatin complexes in defined epigenetic contexts.
After IP, residual DNA and proteins are removed; the enriched fraction contains RNA molecules bound to the selected chromatin state.

If you're focusing on RNA–protein interactions, explore RIP-seq or CLIP-seq.

Library Construction, Sequencing & Data Analysis

Extracted RNAs are used to build sequencing libraries (long RNAs such as lncRNAs, or small RNAs like miRNAs) compatible with high-throughput platforms.
Deep sequencing generates reads that are mapped and analysed to yield genome-wide maps of RNA–chromatin association, enrichment scores, functional classification and annotation of proximal coding genes.
Bioinformatic outputs include read-quality control, intron/exon ratio checking (to assess nascent transcription contamination), enrichment fold-changes over input, histone‐mark co-association patterns, and proximity analyses of ±100 kb around RNAs for gene association.

Why This Workflow Matters

Epigenetic specificity = higher biological relevance:

By using histone mark-specific antibodies, you connect RNA binding not just to chromatin presence but to its functional state (active promoter, enhancer, repressed region) — a key advantage over generic RNA–chromatin methods.

Lower nascent RNA contamination:

The method's cross-linking and fragmentation strategy results in fewer intronic reads, meaning the RNAs captured are more likely to be mature and functionally bound, rather than newly transcribed.

Versatility for non-coding RNA types:

Whether your target is a long non-coding RNA involved in chromatin regulation or a nuclear miRNA binding to enhancer regions, the workflow supports both biotypes in one integrated pipeline.

Sample & Data Requirements

Sample input: Generally requires ~10 million cells as a minimum starting point for sufficient signal in histone-rich chromatin contexts.
Replicates: Biological replicates are strongly recommended to ensure reproducibility; original studies reported high correlation coefficients (R = 0.900–0.988) across replicates.
Controls: Include an input (no IP) and an IgG or mock IP control to assess background binding.
Data deliverables: FASTQ files, alignment statistics, enrichment lists, proximity annotation, visualisations (heatmaps, cluster plots), and a summary report.

Technology Comparison & Service Portfolio

Technology	Target Type	Core Principle	Typical Resolution / Coverage	Key Advantages	Suitable Applications	When to Choose
PIRCh-seq (Profiling Interacting RNAs on Chromatin)	Chromatin-bound RNAs (e.g., lncRNAs, nuclear miRNAs)	Immunoprecipitation of chromatin using histone-mark-specific antibodies, then deep-seq of bound RNA.	Genome-wide; ability to distinguish RNAs bound to specific histone modifications; low nascent transcript contamination.	Histone-modification specificity → functional context for RNA binding Reduced intronic reads → mature RNA associations Designed for non-coding RNA & chromatin interplay	Epigenetic regulation studies, lncRNA-chromatin binding discovery, enhancer-RNA interactions	When you need to identify RNAs bound to specific histone marks (active, repressive, bivalent).
RIP-seq (RNA Immunoprecipitation Sequencing)	RNAs bound to specific RNA-binding proteins (RBPs)	IP of an RBP followed by RNA sequencing.	Transcriptome-wide; moderate resolution	Straightforward setup Good for dynamic RNA-RBP interactions	Mapping RNA-protein interaction networks, RBP target discovery	When you study RNAs associated with specific RNA-binding proteins (RBPs).
CLIP-seq (Cross-linking Immunoprecipitation Sequencing)	RNAs bound to RBPs (direct binding sites)	UV cross-linking of RBP-RNA complexes, IP, library prep & deep-seq.	High resolution (even single-nucleotide binding sites)	Very precise binding site mapping Minimal background noise	Detailed mechanistic studies of RBP-RNA binding, miRNA/AGO profiling	When you need precise RBP–RNA binding site mapping.
R-loop-seq (or DRIP-seq)	RNA-DNA hybrids (R-loops)	Antibody (S9.6) capture of RNA-DNA hybrids followed by sequencing	Genome-wide mapping of R-loops	Direct capture of RNA-DNA hybrids Insight into transcription or genomic instability	Studies of R-loop biology, transcription-replication conflict, DNA damage research	When you study RNA:DNA hybrids or transcriptional instability
Other multi-omic integrated services (e.g., combining ATAC-seq, ChIP-seq, Hi-C, RNA-seq)	Chromatin accessibility, DNA-protein binding, chromatin interactions, transcriptome	Integrative sequencing workflows	Multi-layer resolution depending on assay	Broad epigenomic context Enables building regulatory networks	Systems-level chromatin regulation studies, chromatin architecture + RNA interactions	When you want a systems-level view of chromatin accessibility and RNA regulation.

Note: Among these options, PIRCh-seq is especially recommended when your research question focuses on which RNAs bind to chromatin in a specific epigenetic state (e.g., active vs repressive histone marks). It fills a niche that other methods (RIP-seq, CLIP-seq) don't address directly because those focus on RNA-protein rather than RNA-chromatin.

Key Advantages of Our PIRCh-seq Service

When selecting a sequencing service for RNA-chromatin interaction profiling, the right technology must deliver precision, biological relevance, and actionable insights. Our PIRCh-seq (Profiling Interacting RNAs on Chromatin by deep sequencing) platform is uniquely positioned to deliver those outcomes. Below are the major advantages you'll gain when partnering with us.

1. Histone-Modification Specificity

Instead of capturing all RNA loosely associated with chromatin, PIRCh-seq uses antibodies against specific histone marks (e.g., H3K4me3, H3K27ac, H3K27me3) to pull down RNA–chromatin complexes in defined epigenetic contexts.
This specificity means you can link a given lncRNA or miRNA not just to "chromatin" in general, but to chromatin in the active promoter, enhancer, or repressive state, providing deeper mechanistic insight.
As demonstrated in Fang et al. (2019), that chromatin-associated RNAs are enriched in certain histone states and classified into functional groups accordingly.

2. Low Nascent Transcript Contamination

Many global RNA-chromatin assays capture co-transcriptional ("nascent") transcripts tethered to chromatin, confounding functional interpretation. In the original PIRCh-seq paper, the authors showed significantly lower intronic read ratios (indicating fewer nascent RNAs).
This means your data from our service are more likely to reflect mature RNA–chromatin interactions rather than mere transcription by-products — ensuring reliable interpretation of RNA–chromatin interactions.

3. Non-coding RNA Focus (lncRNAs & Nuclear miRNAs)

The pipeline is optimized for capturing long non-coding RNAs (lncRNAs) and nuclear microRNAs (miRNAs) bound to chromatin, which are often missed or under-represented in standard RNA-seq.
Because non-coding RNAs are increasingly implicated in epigenetic regulation, our service gives you access to that cutting-edge layer of regulation — ideal for research institutions and biotech programmes exploring beyond protein-coding genes.

4. High Reproducibility & Data Quality

The published data from PIRCh-seq include biological replicates with correlation coefficients of R = 0.900-0.988, demonstrating the method's robustness across cell types and conditions.
By leveraging our end-to-end service (from sample prep, IP optimisation, library construction, to bioinformatics), you benefit from a reliable, publication-ready workflow, reducing risk and accelerating your research timelines.

5. Versatile Multi-Condition and Multi-Mark Support

Whether you're comparing cell types, differentiation states, drug treatments, or genetic perturbations, our platform supports multi-condition experimental designs.
You can target multiple histone marks (active, repressive, bivalent), combine with RNA-binding protein (RBP) IPs, or integrate with your existing assays (e.g., RNA-seq, R-loop-seq, CLIP-seq) for a multi-omics viewpoint.
This flexibility empowers CROs, pharma R&D, and academic labs to tailor experiments to their hypotheses with a single contract service.

6. Actionable Data & Clear Deliverables

Post-sequencing, you receive:

Enrichment tables of RNAs bound to specific histone marks
Proximity annotation of coding genes (± 100 kb) near bound RNAs
Functional annotation (GO/KEGG) of adjacent genes
Visualisation outputs (heatmaps, cluster plots, network graphs)
A summary report highlighting key insights

These deliverables are designed for integration into manuscripts, grant applications, or drug-target pipelines — not merely raw data.

How Researchers & R&D Teams Are Applying PIRCh-seq

Our PIRCh-seq service offers a versatile platform for exploring RNA-chromatin interactions in epigenetic contexts. Below are key applications tailored to academic labs, biotech teams, CROs, and pharma R&D groups.

1. Mapping lncRNA–Chromatin Interaction Networks

Understanding where long non-coding RNAs bind on chromatin can reveal mechanisms of transcriptional regulation, enhancer-promoter looping, and epigenetic memory. For example, a foundational study using PIRCh-seq classified hundreds of chromatin-associated non-coding RNAs by their binding to specific histone marks (H3K4me3, H3K27ac, H3K27me3) and found that these binding patterns reflect functional categories of non-coding RNAs (Fang et al., 2019 DOI: 10.1186/s13059-019-1880-3)

Through our service, you can:

Identify novel lncRNA candidates strongly associated with active or repressive chromatin regions.
Prioritize functional non-coding RNAs for downstream validation or CRISPR screening.
Link specific RNAs to chromatin states, enabling mechanistic hypotheses.

2. Histone-Modification-Specific RNA Binding Profiling

The binding of RNA to chromatin is not uniform; RNAs preferentially associate with particular epigenetic states. The PIRCh-seq method directly interrogates RNA bound to histone-marked nucleosomes, allowing you to investigate questions like:

Which RNAs target promoter-associated marks (H3K4me3) versus enhancer-associated (H3K27ac) or repressive marks (H3K27me3)?
How does RNA-chromatin binding change upon differentiation, drug treatment, or genetic perturbation?

Again, the original dataset applied PIRCh-seq across multiple histone mark IPs and demonstrated that RNAs can be classified into groups by their chromatin–RNA enrichment profiles.

In practice, this means you can:

Perform comparative studies across marks or conditions (e.g., control vs treated, cell type A vs B).
Combine your PIRCh-seq results with ChIP-seq, ATAC-seq or Hi-C data for integrated epigenomic insight.

3. Discovery of Nuclear miRNAs and Enhancer-Associated RNAs

While many assays focus on cytoplasmic RNA, PIRCh-seq supports profiling of nuclear RNAs (including miRNAs) bound to chromatin. Since some miRNAs bind enhancers or regulatory regions marked by acetylation or methylation, our platform allows you to:

Detect nuclear miRNAs associated with active regulatory regions (e.g., H3K27ac).
Map enhancer-bound small RNAs and annotate their nearby target genes (±100 kb).
Explore novel regulatory RNA classes beyond lncRNAs.

4. Integration with Multi-Omics for Epigenetic Research

For R&D strategies aiming to integrate transcriptomic, epigenomic and chromatin-interaction datasets, PIRCh-seq offers a "bridge" layer: non-coding RNA bound to chromatin. You can:

Overlay PIRCh-seq data with your existing RNA-seq, R-loop-seq, or CLIP-seq datasets to link RNA function to chromatin binding.
Combine with ChIP-seq/ATAC-seq/Hi-C to examine how RNA binding correlates with chromatin accessibility, looping or gene expression.
Leverage our deliverables (RNA enrichment lists, gene proximity annotation, functional GO/KEGG) to feed into downstream target‐validation workflows or therapeutic target pipelines.

Learn how integrated R-loop-seq or ATAC-seq, ChIP-seq, Hi-C data can complement PIRCh-seq insights.

Demo Results

Here's a concise overview of typical results you can expect from our PIRCh-seq service:

Genome-wide enrichment tables showing RNAs (lncRNAs, miRNAs) significantly bound to chromatin marked by specific histone modifications.
Heatmaps illustrating relative enrichment of transcripts across different histone marks (e.g., H3K4me3 vs H3K27me3) and cell-types.
Classification plots grouping chromatin-associated non-coding RNAs into functional clusters based on their binding patterns.
Allele-specific interaction graphs revealing differential inheritance or variant-driven RNA–chromatin binding events.
Deliverables include annotated proximal coding gene lists (±100 kb), GO/KEGG enrichment summaries, and interactive visuals ready for publication or internal reports.

example data from PIRCh-seq showing histone-mark-specific RNA enrichment, clustering, and chromatin state classification (CD Genomics).

Ready to map RNA–chromatin interactions with PIRCh-seq?

Discuss your project with our experts today.

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FAQs

- What is the minimum starting material required for your PIRCh-seq service?
  - We typically recommend starting with sufficient input (for example, millions of cells or equivalent tissue mass) so that chromatin-bound RNAs are captured with robust signal; lower‐input samples may still be processed but could yield reduced sensitivity or require additional pilot optimisation.
- How do you ensure specificity for RNA bound to chromatin rather than nascent transcripts?
  - Our workflow incorporates glutaraldehyde cross-linking of live cells, sonication of chromatin to ~300–2000 bp fragments, and immunoprecipitation with antibodies specific to histone modifications; this design was shown in the foundational study to recover chromatin-associated RNAs with significantly fewer intronic reads compared to other approaches, implying effective discrimination from nascent transcripts.
- Can I target multiple histone marks or conditions in a single experiment?
  - Yes — the sample design is flexible, allowing you to IP chromatin using different histone modifications (e.g., H3K4me3, H3K27ac, H3K27me3) and/or compare conditions (cell types, treatments, time-points). This enables direct comparison of RNA binding across epigenetic states and experimental interventions.
- What types of RNA can be detected through PIRCh-seq?
  - While our platform is optimised for long non-coding RNAs (lncRNAs) and nuclear microRNAs (miRNAs) that associate with chromatin, the workflow can accommodate a broad range of chromatin-bound RNAs — including eRNAs, promoter-associated RNAs or other non-coding species — provided the material is amenable to library preparation and sequencing.
- What form of deliverables will I receive and how are they useful?
  - Upon completion you will receive raw sequencing FASTQ files, aligned data, enrichment tables of RNAs bound to specified histone marks, proximity annotation of nearby coding genes (± 100 kb), functional enrichment (GO/KEGG), visualisations (heatmaps, clustering plots), and a summary interpretive report. These deliverables are designed for integration into manuscripts, conference presentations or downstream target validation workflows.
- Does PIRCh-seq replace other RNA–chromatin or RNA–protein interaction assays like CLIP-seq, RIP-seq or R-loop-seq?
  - Not exactly — each of these methods addresses a distinct question: CLIP-seq and RIP-seq map RNA–protein interactions; R-loop-seq maps RNA:DNA hybrids. PIRCh-seq specifically identifies RNAs associated with chromatin under defined epigenetic (histone modification) states, making it ideal when your question centres on RNA–chromatin binding rather than RNA–protein or RNA–DNA hybrid interactions.
- What kinds of quality control and replicates are recommended?
  - We recommend including an input control (no IP), an IgG or mock IP control, and biological replicates to ensure reproducibility. In the original PIRCh-seq publication, replicate correlations ranged from R = 0.90 to 0.988, demonstrating high reproducibility when protocols are rigorously followed.
- How long does turnaround take and what factors may extend timeline?
  - Turnaround time depends on factors such as sample availability, number of histone‐mark conditions, depth of sequencing, and custom bioinformatics. Complex study designs or very limited material may require additional optimisation or pilot runs.

References:

Fang, J., Ma, Q., Chu, C. et al. PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications. Genome Biol 20, 292 (2019).
Li, L., Luo, H., Lim, DH. et al. Global profiling of RNA–chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis. Nat. Plants 7, 1364–1378 (2021).
Khyzha, N., Henikoff, S. & Ahmad, K. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation. Nat Methods 19, 1383–1392 (2022).