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PhaseCapture

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DNA/RNA extraction kit for phase-separated nuclear compartments

670.00 € 670.0 EUR 320.00 €

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A technology developed by Thierry Forne and Cosette Rebouissou (Institut de Génétique Moléculaire de Montpellier - CNRS UMR 5535, France)

The PhaseCapture kit isolates membrane-less compartments present in the cell nuclei while perfectly preserving their nucleic acid contents. It is used to recover and analyze the DNA/RNA associated with all nuclear bodies and large ribonucleoprotein (RNP) complexes formed by phase separation in the cell nucleus.    

High specificity

Nuclear bodies get specifically isolated​ thanks to high-salt treatments before extracting their associated DNA/RNA contents. No risk of biases due to random, aspecific interactions as it can be the case with chemical crosslinking procedures.

 Wide coverage

Relies on phase properties, rather than specific protein targets, to get an exhaustive sampling of all genomic sequences associated with nuclei sub-compartments.  

Simple protocol

No need to go through the generation of transgenic cell lines or other fastidious protocols. PhaseCapture offers the first ready-to-use kit for efficient purification of nuclear bodies for genetic analyses.

Applications


Extracted contents: DNA & RNA

Kit specificity: all membrane-less compartments formed by liquid-liquid phase separation in the cell nucleus, including histone locus bodies (HLBs), PML bodies, Cajal bodies, nuclear speckles & paraspeckles, nucleoles* & transcriptional condensates.

*including perinucleolar heterochromatin

Starting material: isolated nuclei from human & murine cells/tissues

Validated samples: 

  • mouse ESCs & ESC-derived neurons
  • human fibroblasts (IMR-90), lymphocytes, neurons and iPS-derived motoneurons

Compatible assays: 

  • DNA isolation for PCR, qPCR or sequencing*

*validated sequencing method: Illumina HiSeq 2000 (NGS sequencing)

  • RNA isolation for RT-qPCR or RNA-seq 


How does it work?

The HRS-Seq method relies on a specific high-salt treatment of cell nuclei that makes all nuclear bodies formed by liquid-liquid phase separation insoluble while perfectly preserving their nucleic acid contents.


All DNA/RNA associated with nuclear bodies from the same sample (insoluble fraction) are then separated from the rest of the genome (soluble fractions) using simple enzymatic digestion and washing steps. They can be further analyzed using PCR, qPCR, RT-qPCR or sequencing. 

Figure modified from Lecouvreur N. et al, Methods in Molecular Biology, 2025, 2962, pp.141-151. 


Use cases

  • Exploring the role of nuclear bodies & phase separation in epigenetics (Baudement et al, 2018)
  • Assessing nuclear body changes in response to external stresses at the genomic & transcriptomic level (i.e. heterochromatin changes, RNA composition, splicing profile)
  • Identifying gene contents of nuclear bodies & obtain a global profiling of associated sequences



Filtration kit

The filtration kit contains everything you need to process your nuclei samples (6 samples per run are extracted in parallel ). It is reusable and only needs to be purchased once for infinite extraction assays. 

Kit contents: 
Steel air valves x6
O-ring x6
Plugs x6
Pump x1
Tubing

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Small kit

The small extraction kit contains the  buffers and filtration units required to extract DNA/RNA from isolated nuclei (up to 24 samples*).   

  • Kit contents:
    Permeabilization buffer
    Extraction buffer
    Enzyme buffer
    10X PK buffer
    Filtration units x24

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Large kit

The large extraction kit contains the  buffers and filtration units required to extract DNA/RNA from isolated nuclei (up to 90 samples*).

  • Kit contents:
    Permeabilization buffer
    Extraction buffer
    Enzyme buffer
    10X PK buffer
    Filtration units x90

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*For sequencing applications, we recommend pooling the DNA/RNA contents extracted from 6 separate filtration units to get enough material.


Chromosomal mapping of genomic regions associated with nuclear bodies


(A) High-salt recovered sequences (HRSs) identified by sequencing performed in mouse ESCs have been mapped (brown bars) to mouse chromosomes. The mean densities of HRSs on each chromosome (HRS/Mb) are indicated on the figure. (B) The distance between consecutive HRSs (d) was determined. The graph shows the genome-wide distribution (1-kb bins) of non-null values for d corresponding to HRS (blue) and random (brown) StyI fragments. The median values of d for each distribution are indicated on the figure. The difference between the two distributions is highly significant, featuring a P-value lower than 10−100 (Wilcoxon rank-sum test). (C) The mean inter-chromosomal contact scores of 100-kb bins enriched in HRSs (red dots) were calculated from Hi-C data available for the same cell type (ESC) and compared to the mean contact scores obtained from 100 random sets of the same number of 100-kb bins (box plots). The box plot on the right represents the mean contact score and randomizations obtained when HRSs and random StyI fragments are taken only in the A compartment, while the box plot on the left represents the mean contact score and randomizations obtained from the whole genome. Bars, minimum and maximum values obtained in the 100 randomizations. The number of 100-kb bins (n) used for each randomizations is indicated on the figure. The P-value indicates the significance of the difference between the mean contact scores obtained for HRSs versus randomizations.
Credits: Baudement MO et al, Genome Res. 2018. doi: 10.1101/gr.237073.118


High-salt recovered sequences are associated with active epigenetic marks


(A) Browser snapshot showing the HRS density at the Sox2 gene locus on mouse Chromosome 3 as determined by HRS-seq experiments performed in ESCs. Tracks displaying DNase I–sensitive sites, RNA PolII peaks as well as ChIP-seq data for the indicated epigenetic marks (ENCODE E14 ESC data) were plotted using the WashU EpiGenome Browser. (B) Heat map depicting the Pearson correlation coefficients obtained between ESC HRSs and sequences (10-kb bins) enriched in distinct epigenetic marks as indicated on the figure. (Black/red) High positive correlation coefficient; (white/blue) low null/negative correlation coefficient.
Credits: Baudement MO et al, Genome Res. 2018. doi: 10.1101/gr.237073.118

les design...

et leurs applications

Protocol coming soon

Lecouvreur N, Rebouissou C, Lesne A, Forné T. Simultaneous Profiling of Transcripts and Genomic Regions Associated with Nuclear Bodies Using the RNA-DNA High-Salt Recovered Sequence (RD-HRS) Method. Methods Mol Biol. 2025;2962:141-151. doi: 10.1007/978-1-0716-4726-4_10. PMID: 40699427.

Baudement MO, Cournac A, Court F, Seveno M, Parrinello H, Reynes C, Sabatier R, Bouschet T, Yi Z, Sallis S, Tancelin M, Rebouissou C, Cathala G, Lesne A, Mozziconacci J, Journot L, Forné T. High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies. Genome Res. 2018 Nov;28(11):1733-1746. doi: 10.1101/gr.237073.118. Epub 2018 Oct 4. PMID: 30287550; PMCID: PMC6211644.

Lesne A, Baudement MO, Rebouissou C, Forné T. Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression. Genes (Basel). 2019 Dec 17;10(12):1049. doi: 10.3390/genes10121049. PMID: 31861077; PMCID: PMC6947181.

Rebouissou C, Baudement MO, Forné T. The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies. Methods Mol Biol. 2022;2532:187-197. doi: 10.1007/978-1-0716-2497-5_9. PMID: 35867250.