A Detailed Protocol for Subcellular RNA Sequencing (subRNA‐seq)

Andreas Mayer1, L. Stirling Churchman2

1 Max Planck Institute for Molecular Genetics, Berlin, 2 Department of Genetics, Harvard Medical School, Boston
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 4.29
DOI:  10.1002/cpmb.44
Online Posting Date:  October, 2017
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In eukaryotic cells, RNAs at various maturation and processing levels are distributed across cellular compartments. The standard approach to determine transcript abundance and identity in vivo is RNA sequencing (RNA‐seq). RNA‐seq relies on RNA isolation from whole‐cell lysates and thus mainly captures fully processed, stable, and more abundant cytoplasmic RNAs over nascent, unstable, and nuclear RNAs. Here, we provide a step‐by‐step protocol for subcellular RNA‐seq (subRNA‐seq). subRNA‐seq allows the quantitative measurement of RNA polymerase II–generated RNAs from the chromatin, nucleoplasm, and cytoplasm of mammalian cells. This approach relies on cell fractionation prior to RNA isolation and sequencing library preparation. High‐throughput sequencing of the subcellular RNAs can then be used to reveal the identity, abundance, and subcellular distribution of transcripts, thus providing insights into RNA processing and maturation. Deep sequencing of the chromatin‐associated RNAs further offers the opportunity to study nascent RNAs. Subcellular RNA‐seq libraries are obtained within 5 days. © 2017 by John Wiley & Sons, Inc.

Keywords: Cell fractionation; subcellular RNA‐seq; nascent RNA; RNA polymerase II (Pol II); transcription; next‐generation sequencing; RNA processing

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Table of Contents

  • Introduction
  • Basic Protocol 1: Cell Fractionation and RNA Isolation
  • Basic Protocol 2: Sequencing Library Preparation
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Cell Fractionation and RNA Isolation

  • Cultured mammalian cells: 1× 107 cells per experiment
  • Phosphate‐buffered saline (PBS; Life Technologies, cat. no. 10010‐023)
  • Cytoplasmic lysis buffer (see recipe)
  • Sucrose buffer (see recipe)
  • Nuclei wash buffer (see recipe)
  • Glycerol buffer (see recipe)
  • Nuclei lysis buffer (see recipe)
  • TRI reagent (MRC, cat. no. TR 118)
  • Chloroform (Sigma, cat. no. 288306)
  • RLT buffer (Qiagen, cat. no. 79216)
  • 100% (v/v) ethanol (VWR, cat. no. V1016)
  • RNeasy Mini Kit (Qiagen, cat. no.74104)
  • RNase‐Free DNase Set (Qiagen, cat. no. 79254)
  • RNase/DNase‐free H 2O (Life Technologies, cat. no. 10977‐015)
  • Antibodies (optional; for monitoring the experiment by western blotting):
    • Pol II Ser‐2P antibody (3E8; Active Motif, cat. no. 61083)
    • Histone 2B antibody (FL‐126; Santa Cruz Biotechnology, cat. no. sc‐10808)
    • U1 snRNP70 antibody(C‐18; Santa Cruz Biotechnology, cat. no. sc‐9571)
    • GAPDH antibody (6C5; Life Technologies, cat. no. AM4300)
  • Cell scrapers
  • Refrigerated centrifuge
  • Additional reagents and equipment for basic cell culture techniques including counting cells (Phelan & May, ) and for western blotting (immunoblotting; unit 10.8, Ni., Xu, and Gallagher, )

Basic Protocol 2: Sequencing Library Preparation

  • RNA ( protocol 1)
  • Ribo‐Zero rRNA Removal Kit (Epicentre, cat. no. MRZH116)
  • 80% (v/v) ethanol (VWR, cat. no. V1016)
  • RNase/DNase‐free H 2O (Life Technologies, cat. no. 10977‐015)
  • 50% PEG8000 (supplied with the truncated T4 RNA Ligase 2; NEB, cat. no. M0242S)
  • Dimethylsulfoxide (DMSO; Sigma, cat. no. D8418)
  • T4 RNA Ligase buffer, 10× (supplied with the truncated T4 RNA Ligase 2; NEB, cat. no. M0242S)
  • EDTA (0.5 M; Life Technologies, cat. no. AM9260G)
  • Alkaline fragmentation solution (see recipe)
  • RNA precipitation solution (see recipe)
  • RNA control ladder (0.1 to 2 kb; Life Technologies, cat. no. 15623‐100)
  • oGAB11 control (Table 4.29.1)
  • 2× TBU denaturing loading buffer (Life Technologies, cat. no. LC6876)
  • TBE‐urea gels, 15% (w/v) (Life Technologies, cat. no. EC68852BOX)
  • Gel staining solution (see recipe)
  • GlycoBlue (15 mg/ml; Life Technologies, cat. no. AM9515)
  • Sodium acetate, RNase‐free (3 M, pH 5.5; Life Technologies, cat. no. AM9740)
  • Isopropanol (Sigma, cat. no. 278475)
  • T4 PNK buffer, 10× (supplied with T4 Polynucleotide Kinase, NEB, cat. no. M0201S)
  • SUPERase.In (20 U/µl; Life Technologies, cat. no. AM2696)
  • T4 Polynucleotide Kinase (10,000 U/ml; NEB, cat. no. M0201S)
  • DNA linker‐1 (Table 4.29.1)
  • T4 RNA Ligase 2, truncated (NEB, cat. no. M0242S)
  • 5× First‐Strand Buffer (part of SuperScript III First‐Strand Synthesis System; Life Technologies, cat. no. 18080‐051)
  • dNTP mix (10 mM each dNTP; Life Technologies, cat. no. 18427‐013)
  • DTT (0.1 M; part of the SuperScript III First‐Strand Synthesis System, Life Technologies, cat. no. 18080‐051)
  • SUPERase.IN/DTT mix (see recipe)
  • 200 U/µl SuperScript III First‐Strand Synthesis System (Life Technologies, cat. no. 18080‐051)
  • 1 N NaOH
  • 1 N HCl
  • DNA control ladder (10 bp; Life Technologies, cat. no. 10821‐015)
  • TBE‐urea gels, 10% (w/v) (Life Technologies, cat. no. EC68752BOX)
  • TBE buffer, 10× (Life Technologies, cat. no. 15581‐044)
  • Gel staining solution (see recipe)
  • 5 M NaCl
  • 10 mM Tris⋅Cl, pH 8.0 ( appendix 22)
  • CircLigase reaction buffer, 10× (part of CircLigase ssDNA Ligase, Epicentre, cat. no. CL4111K)
  • ATP, 1 mM (supplied with CircLigase ssDNA Ligase, Epicentre, cat. no. CL4111K)
  • MnCl 2, 50 mM (supplied with CircLigase ssDNA Ligase, Epicentre, cat. no. CL4111K)
  • CircLigase ssDNA Ligase (100 U/µl; Epicentre, cat. no. CL4111K)
  • Phusion HF Buffer, 5× (supplied with Phusion High‐Fidelity DNA Polymerase, NEB, cat. no. M0530S)
  • Phusion DNA Polymerase (2,000 U/ml; NEB, cat. no. M0530S)
  • 6× DNA loading dye (unit 10.2; Gallagher, )
  • TBE gels, 8% (w/v) (Life Technologies, cat. no. EC62152BOX)
  • DNA soaking buffer (see recipe)
  • Qubit dsDNA HS Assay Kit (Life Technologies, cat. no. Q32851)
  • High Sensitivity Bioanalyzer DNA Analysis Kit (Agilent Technologies, cat. no. 5067‐4626)
Table 4.9.1   MaterialsDNA and RNA Oligos Required for the Preparation of Subcellular RNA‐Seq Libraries

DNA oligos
RNA oligos
oGAB11 (control oligo) agucacuuagcgauguacacugacugug
oGAB11‐P f agucacuuagcgauguacacugacugug/3Phos/

 a5rApp: 5′‐riboadenylate.
 b3ddC: 3′‐dideoxycytidine.
 cCommercially available from Integrated DNA Technologies.
 d5Phos: 5′‐phosphate.
 eiSp18: internal 18‐atom hexa‐ethylenglycol spacer.
 f3Phos: 3′‐phosphate.
  • Refrigerated centrifuge
  • Thermomixer
  • Thermal cycler
  • Blue or UV light source
  • Scalpels (Electron Microscopy Sciences, cat. no. 72042‐11)
  • 0.5‐ml and 1.5‐ml RNase/DNase‐free non‐stick microcentrifuge tubes
  • 20‐G needle (BD, cat. no. 305175)
  • Microcentrifuge tube filter: Costar Spin‐X centrifuge tube filters (Sigma, cat. no. CLS8162‐96EA)
  • 0.2‐ml PCR tubes
  • Additional reagents and equipment for polyacrylamide gel electrophoresis (unit 10.2; Gallagher, )
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