Pol II ChIP-seq Service

RNA polymerase II (Pol II) ChIP-seq enables genome-wide profiling of transcriptional activity by mapping the occupancy of Pol II across promoter, gene body, and regulatory regions. Unlike enhancer- or histone-focused ChIP-seq, Pol II ChIP-seq directly reflects active transcription states and offers unique insights into transcription initiation, pausing, elongation, and co-transcriptional regulation.

CD BioSciences's Pol II ChIP-seq service provides precise characterization of RNA Pol II binding and pausing profiles using optimized protocols compatible with both total and phosphorylated forms of Pol II (e.g., Ser5P and Ser2P), supporting transcriptional research across normal and disease systems.

Introduction to Pol II ChIP-seq

RNA polymerase II is the central enzyme responsible for transcribing protein-coding genes. During transcription, Pol II occupancy changes dynamically from:

1. Initiation (accumulating near transcription start sites, TSS)
2. Promoter-proximal pausing
3. Elongation (progression into the gene body)
4. Termination

ChIP-seq using antibodies against Pol II or its phosphorylated forms (e.g., Pol II Ser5P for paused Pol II, Pol II Ser2P for elongating Pol II) allows high-resolution mapping of these stages. Compared with RNA-seq, which reflects steady-state mRNA levels, Pol II ChIP-seq captures real-time transcriptional engagement—particularly useful for identifying transcriptionally poised or paused genes, enhancer RNAs, or changes in polymerase dynamics under perturbation.

Fig.1 Experimental design and overview of ChIP targets. (Mchaourab, Z. F., et al., 2018)

Applications of Pol II ChIP-seq

1. Defining active transcription units and gene body activity
2. Detecting promoter-proximal Pol II pausing and its release
3. Comparing transcriptional engagement between conditions or cell types
4. Studying immediate transcriptional responses to signaling or drugs
5. Investigating transcription factor cooperation with Pol II
6. Profiling super-enhancer–driven transcriptional programs
7. Integrating with RNA-seq, ATAC-seq, and nascent RNA (GRO-seq, PRO-seq)

Our Services

To capture the dynamic transcriptional landscape with high fidelity, CD BioSciences has developed a robust ChIP-seq workflow optimized specifically for RNA Polymerase II profiling. From chromatin preparation to bioinformatic interpretation, each step is designed to preserve transcription-associated signals and resolve Pol II distribution across the genome.

Sample Processing & Chromatin Preparation

1. Accepts cells and tissues (fresh or frozen)
2. Crosslinking with formaldehyde, chromatin fragmentation via sonication
3. Compatibility with input amounts ≥1 million cells or equivalent tissue

Immunoprecipitation

1. High-specificity antibodies for Pol II (total), Pol II Ser5P (initiation), Pol II Ser2P (elongation)
2. Negative controls: IgG or isotype-matched antibody
3. Optimization for low-background signal and broad coverage

Library Construction & Sequencing

1. Indexed NGS library preparation with QC
2. Illumina paired-end sequencing (30–50M reads/sample recommended)
3. High sensitivity for both sharp TSS peaks and broad gene body signals

Bioinformatics Analysis

1. Read alignment and peak calling (e.g., using MACS2, SICER)
2. TSS enrichment analysis and gene body coverage plots
3. Metagene plots of Pol II distribution (TSS, TES, gene body)
4. Optional pausing index calculation, elongation ratio, and promoter–gene correlation
5. Data visualization: IGV tracks, heatmaps, and genome-wide signal maps

Supported Sample Types

1. Cultured Cells
2. Primary Cells (immune)
3. Fresh-Frozen Tissues

1. Time-Course or Drug-Treated Samples
2. Cell Differentiation or Induction Models
3. Other Types (Please Inquire)

Our Advantages

1. Stage-Specific Pol II Resolution: Profiles total Pol II and phosphorylated states (Ser2P, Ser5P) for dynamic transcription analysis.
2. Real-Time Transcriptional Insight: Captures promoter pausing, elongation, and termination patterns genome-wide.
3. Integration-Friendly Output: Seamlessly integrates with RNA-seq, GRO/PRO-seq, or chromatin accessibility data.
4. High Resolution and Coverage: Ensures quality signal across TSS, gene bodies, and TES regions.
5. Pausing Index and Metrics: Calculates transcriptional pausing index and elongation rates per gene.
6. Visual and Analytical Reporting: Delivers metagene plots, genome browser tracks, and functional interpretations.

Pol II ChIP-seq offers a real-time view of transcriptional activity, enabling precise detection of gene regulation beyond mRNA abundance. It is particularly valuable in contexts where transcriptional pausing, enhancer–promoter communication, or immediate-early gene activation are key—such as immune activation, developmental transitions, or cancer transcriptional addiction. CD BioSciences combines validated Pol II antibodies, optimized workflows, and expert analysis to help you dissect transcriptional control with clarity and confidence. Contact us to initiate your Pol II transcriptional profiling project.

Reference

1. Mchaourab, Z. F., et al. (2018). ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells. Scientific data, 5, 180030.