Why Compartment-Specific RNA Matters
- RNA function depends on where it lives in the cell
- circRNA, lncRNA, and miRNA interactions are location-dependent
- Mislocalization drives disease, especially cancer
- Total RNA hides important regulatory events
- Mechanistic studies require clean fractions
Separate nuclear and cytoplasmic RNA in a single workflow—
Get clearer, more relevant data from every sample.
Our C&N RNA Kit separates RNA from cytoplasmic (C) and nuclear (N) fractions, giving you compartment-specific insights. This allows you to:
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Understand RNA localization
Different RNA species have distinct functions depending on whether they reside in the cytoplasm or nucleus.
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Detect regulatory RNAs accurately
Nuclear-enriched RNAs, such as long non-coding RNAs (lncRNAs), can be studied without interference from abundant cytoplasmic RNAs.
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Improve experiment sensitivity
By isolating RNAs from specific compartments, downstream analyses like qPCR, RNA-seq, or Northern blotting yield more meaningful results.
TRIzol vs. C&N
Why Researchers Choose the C&N RNA Kit Instead of TRIzol
Traditional total RNA extraction methods such as TRIzol efficiently recover RNA but are not designed to preserve compartment-specific information.
| TRIzol | C&N Kit |
|---|---|
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Not designed for clean cytoplasmic vs nuclear separation
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Purpose-built to separate cytoplasmic and nuclear RNA cleanly
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Fractions can cross-contaminate
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Minimal cross-contamination and consistent
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Results depend heavily on user technique
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Reproducible fractions regardless of skill level
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Long, multi-step protocol
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Simple column-based workflow
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Requires phase separation
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No phase separation
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Difficult to scale
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Faster, cleaner, easier
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Phenol based
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No phenol, no toxic organic solvents
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Good for total RNA But RNA integrity can vary
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Designed to preserve RNA compartment integrity & Delivers high-purity RNA from both fractions
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Hard to preserve nuclear structure during isolation
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Clear distinction between:
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Applications
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lncRNA
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Cancer Biology
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circRNA
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RNA-Protein Interactions
Frequently Asked Questions
Cytoplasmic and nuclear RNA isolation separates RNA molecules from the cytoplasm and nucleus before purification, allowing researchers to study RNA localization and compartment-specific functions.
RNA localization influences gene regulation, RNA processing, translation, and cellular signaling. Understanding where RNA resides can reveal biological mechanisms that are hidden in total RNA samples.
Yes. The kit is commonly used for circRNA localization studies because many circular RNAs show distinct nuclear or cytoplasmic enrichment patterns.
Yes. Both cytoplasmic and nuclear RNA fractions are suitable for downstream applications including RNA-seq, RT-qPCR, Northern blotting, and transcriptomic analyses.
TRIzol is designed for total RNA extraction and does not provide clean separation of nuclear and cytoplasmic fractions. The C&N RNA Kit is specifically optimized for compartment-specific RNA isolation with minimal cross-contamination.
No. The C&N RNA Kit uses a column-based workflow and does not require phenol, chloroform, or phase separation.
The kit can be used to analyze: • circRNAs • lncRNAs • mRNAs • miRNAs • pre-mRNAs • nuclear-retained transcripts • regulatory non-coding RNAs
Yes. Many cancer-associated RNAs display altered cellular localization. Separating nuclear and cytoplasmic fractions can help identify disease-related regulatory mechanisms.
Researchers typically assess fraction purity using compartment-specific markers such as GAPDH (cytoplasmic) and MALAT1, U6, or pre-mRNA markers (nuclear).
Yes. By reducing background RNA from unrelated cellular compartments, compartment-specific RNA isolation can improve biological signal detection and interpretation.
Publications & External References
| Title | Precursor RN ecursor RNA Properties Driving Cr ties Driving Cryptic 3’ Splice Site Selection yptic 3’ Splice Site Selection in SF3B1 Mutant Malignancies |
| Citation | Thesis 2026. |
| Authors | Austin A. Herbert |
| Title | m6A methylation of circKPNA2 promotes colorectal carcinogenesis by activating the RIN1-Ras pathway |
| Citation | Epigenetics 2026. |
| Authors | Jinhai Tian, Zongying Jiang, Qi Huang, Jia Wang & Yaqin He |
| Title | Correlation between circ_0092576 and Arterial Stenosis Severity and Inflammatory Status in Patients with Coronary Heart Disease and Its Clinical Value |
| Citation | Folia Biologica 2026. |
| Authors | Wenqin Dai, Lingli Wang, Yuan Li, Li Liu, Peng Chen |
| Title | Circ_0008777 promotes head and neck squamous cell carcinoma progression by elevating c-Myc expression levels via interacting with PC4 and miR-185–3p |
| Citation | Translational Oncology 2026. |
| Authors | Weixing Liu, Zhiyuan Wang, Pei Li, Yue Liu, Jia Chen, Zhi Shi, Hui Liu, Jin Ye |
| Title | CAF-derived extracellular vesicle-associated LINC02420 links stromal communication to HIF1A-dependent glycolytic regulation in head and neck cancer |
| Citation | Cancer Letters 2026. |
| Authors | Yun Li, Zhimou Cai, Ruihua Fang, Wenqing Chen, Kai Sun, Yi Shuai, Yuanyuan Li, Wenbin Guo, Xiaomao Fan, Lin Chen, Wenbin Lei |
| Title | Shikonin suppresses diffuse large B-cell lymphoma progression by inducing ferritinophagy and ferroptosis via lncRNA ADPGK-AS1 downregulation |
| Citation | Journal of Enzyme Inhibition and Medicinal Chemistry 2026. |
| Authors | Can Chen, Xiaofei Chen, Xilian Huang, Yaping Xie, Pengfei Shi, Shenxian Qian & Zhenzhen Chen |
| Title | Pathogen-responsive circSAFB2 promotes coelomocyte proliferation via JAK-STAT in sea cucumber |
| Citation | Water Biology and Security 2026. |
| Authors | Ming Guo, Wenjun Tao, Wanyu Wang, Chenghua Li |
| Title | LncRNA-MSTRG.16919.1 regulates the proliferation of BHV-1 in MDBK cells through TAK1/TAB1/TAB2/TAB3 complexes |
| Citation | Research Square 2026. |
| Authors | Fan Zhang, Caina Song, Jinzhu Ma, Liquan Yu, Chen Peng, Wenxue Wu, Baifen Song |
| Title | Bufalin targets E2F2 to transcriptionally inhibit LINC01410 and suppress Wnt/β-catenin signaling in esophageal squamous cell carcinoma |
| Citation | NPJ 2026. |
| Authors | Xiaohong Kang, Yufei Ma, Hongke Zhao, Haoling Zhang, Mridul Roy, Mingjuan Liao, Ying Wei, Xingqiao Li, Yueyang Zhou, Huange Xue, Xiaoxia Yan, Wangzheqi Zhang, Yadong Guo, Fei Cao & Tingmin Chang |
| Title | LncRNA IRENA promotes peripheral T-cell lymphoma progression through scaffolding ARHGEF1 and FMNL1 to modulate RHOA GTPase/MAPK signaling |
| Citation | Oncogene 2026. |
| Authors | Cong Wang, Ming-Ci Cai, Shu Cheng, Song Hu, Yao-Hui Huang, Liang-Juan Zhao, Yao Qin, Yu-Ran Qiu, Hong-Jing Dou, Ye-hui Tan, Su-Jun Gao, Jie Xiong & Wei-Li Zhao |