Identification of Neural Programmed Cell Death Through the Detection of DNA Fragmentation In Situ and by PCR

Yun C. Yung1, Grace Kennedy2, Jerold Chun2

1 University of California, San Diego School of Medicine, San Diego, California, 2 Helen L. Dorris Child and Adolescent Neuropsychiatric Disorder Institute, The Scripps Research Institute, La Jolla, California
Publication Name:  Current Protocols in Neuroscience
Unit Number:  Unit 3.8
DOI:  10.1002/0471142301.ns0308s48
Online Posting Date:  July, 2009
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Programmed cell death is a fundamental process for the development and somatic maintenance of organisms. This unit describes methods for visualizing both dying cells in situ and for detection of nucleosomal ladders. A description of various current detection strategies is provided, as well as support protocols for preparing positive and negative controls and for preparing genomic DNA. Curr. Protoc. Neurosci. 48:3.8.1‐3.8.24. © 2009 by John Wiley & Sons, Inc.

Keywords: cell death; apoptosis; ISEL; TUNEL; nucleosomal ladder

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Detection of Programmed Cell Death by In Situ End‐Labeling Plus (ISEL+)
  • Support Protocol 1: Preparation of Thymocyte Cell Cultures for ISEL+
  • Basic Protocol 2: Detection of Nucleosomal Ladders Associated with Programmed Cell Death by Ligation‐Mediated Polymerase Chain Reaction (LMPCR)
  • Support Protocol 2: Isolation of Genomic DNA from Tissues and Cultures
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Detection of Programmed Cell Death by In Situ End‐Labeling Plus (ISEL+)

  • Pregnant mice or tissue culture cells grown on 12‐mm glass coverslips coated with an appropriate adhesive (e.g., poly‐L‐lysine, appendix 2A, or Cell‐Tak from Becton Dickinson)
  • DMEM or other dissection medium, 4°C
  • OCT compound (e.g., Tissue‐Tek II from Sakura) or other water‐soluble embedding medium, 4°C
  • Appropriate controls (see step 1 annotation)
  • Liquefied Histo‐Freeze (Fisher Sci), CryoKwik (Damon), or liquid nitrogen
  • Dry ice, finely crushed (optional)
  • Fixative (see recipe)
  • 2× SSPE ( appendix 2A)
  • 2× SSPE/0.6% Triton X‐100 (see recipe)
  • 0.1 M triethanolamine (TEA; see recipe)
  • Acetic anhydride (Sigma, cat. no. 91204)
  • DNase‐free water
  • 30%, 50%, 70%, 95%, and 100% ethanol, prepared with DNase‐free water
  • ISEL+ TdT solution (see recipe)
  • Parafilm
  • MABS buffer (see recipe)
  • Blocking buffer (see recipe)
  • AP‐conjugated sheep anti‐DIG antibody (Roche, cat. no. 11093274910)
  • Alkaline phosphate buffer (see recipe)
  • Alkaline phosphatase color substrate buffer (see recipe)
  • Nuclear fast red solution (see recipe)
  • Permanent mounting medium (e.g., Crystal Mount from Biomeda and DPX from Fluka)
  • Unconjugated sheep anti‐DIG antibody (Roche, cat. no. 11333089001)
  • Phosphate‐buffered saline ( appendix 2A)
  • Fluorescent tagged anti‐sheep antibody (e.g., AlexaFluor 488 tagged; Invitrogen, cat. no. A‐11015)
  • 4′,6‐diamidino‐2‐phenylindole (DAPI; Sigma, cat. no. D9542)
  • Fluorescence mounting medium (e.g., Vectashield from Vector Labs)
  • Dissecting instruments including:
    • Fine forceps
    • Fine scissors
    • Blunt forceps and spatula
  • Freezing molds (Fisher Scientific, optional)
  • Cryostat
  • Superfrost Plus glass slides (Fisher Scientific)
  • Slide‐warmer (Barnstead Thermolyne), 50°C
  • Slide‐processing holders and vessels
  • 80°C vacuum oven with house vacuum/pump
  • 24‐well microtiter plates (if using coverslip‐mounted cells as controls)
  • Airtight containers for slide storage with desiccant (Tupperware)
  • Humidified chamber for microscope slides
  • Coverslips
  • Microscope, preferably equipped for brightfield, DIC, and/or fluorescence
CAUTION: Paraformaldehyde, triethanolamine, acetic anhydride, and potassium cacodylate (in the TdT buffer) are toxic and must be used in accordance with safety standards.

Support Protocol 1: Preparation of Thymocyte Cell Cultures for ISEL+

  • 4‐week‐old mice
  • DMEM/F‐12 ( appendix 2A), containing 0.0025% trypsin
  • DMEM/F‐12/5% FBS ( appendix 2A)
  • 12‐mm diameter round glass coverslips coated with poly‐L‐lysine ( appendix 2A) or Cell‐Tak (Collaborative Research)
  • Dexamethasone stock solution: 2 mM dexamethasone in 100% ethanol
  • Long‐nose Pasteur pipet, flame polished
  • 24‐well microtiter dishes
  • Additional reagents and equipment for tissue culture (for cultured cells; see appendix 3B)

Basic Protocol 2: Detection of Nucleosomal Ladders Associated with Programmed Cell Death by Ligation‐Mediated Polymerase Chain Reaction (LMPCR)

  • Isolated and quantified genomic DNA (see protocol 4)
  • Oligonucleotides for ligation, unphosphorylated:
    • 12‐bp: 5′‐TGCGGTGAGAGG‐3′
  • 10× T4 DNA ligase buffer (prepared fresh; see recipe)
  • T4 DNA ligase (Roche; store up to 1 month at −20°C)
  • DNase‐free water
  • PCR buffer (see recipe)
  • Oligonucleotides for single‐copy‐gene PCR controls: e.g., for mouse engrailed:
  • Taq DNA polymerase
  • Agarose gels, analytical grade (see appendix 1N), prepared in TBE buffer ( appendix 2A)
  • Ethidium bromide staining solution ( appendix 2A)
  • 0.5‐ml microcentrifuge tubes
  • Thermal cycler
  • Gel photographic setup
  • Additional reagents and equipment for agarose gel electrophoresis ( appendix 1N)
CAUTION: Ethidium bromide is a mutagen and should be handled, stored, and disposed of with appropriate care.

Support Protocol 2: Isolation of Genomic DNA from Tissues and Cultures

  • Mice or tissue culture cells (see appendix 3B) grown on 12‐mm glass coverslips coated with an appropriate adhesive (e.g., poly‐L‐lysine, appendix 2A, or Cell‐Tak, Collaborative Research)
  • Sodium dodecyl sulfate (SDS)/proteinase K buffer (see recipe)
  • Molecular biology–grade 25:24:1 (v/v/v) phenol/chloroform/isoamyl alcohol equilibrated with Tris⋅Cl, pH 8.0 ( appendix 2A)
  • 24:1 (v/v) chloroform/isoamyl alcohol
  • 3 M sodium acetate, pH 5.0 ( appendix 2A)
  • 100% ethanol, −20°C
  • 70% ethanol
  • TE buffer, pH 8.0 ( appendix 2A)
  • RNase A solution, DNase‐free ( appendix 2A; optional)
  • Ceramic mortar and pestle, precooled with liquid nitrogen
  • 15‐ and 50‐ml polypropylene tubes with caps
  • 50°C oven with rocker platform
  • Fluorometer or spectrophotometer
  • Additional reagents and equipment for DNA quantitation using a spectrophotometer (see appendix 1K)
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Key References
   Blaschke et al., 1996. See above.
  First use of ISEL+ and the detection of programmed cell death in the embryonic cortex.
   Gavrieli et al., 1992. See above.
  First technique to utilize labeling of DNA ends to detect programmed cell death.
   Raff et al., 1993. See above.
  An informative discussion of nervous system programmed cell death.
   Staley et al., 1997. See above.
  First use of ligation‐mediated PCR to demonstrate apoptotic ladders in normal tissues.
   Wyllie, 1981. See above.
  First demonstration of nucleosomal ladders associated with apoptosis.
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