[Methods in Molecular Biology] Chromatin Immunoprecipitation Assays Volume 567 || Fish’n ChIPs: Chromatin Immunoprecipitation in the Zebrafish Embryo

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  • Chapter 5

    Fishn ChIPs: Chromatin Immunoprecipitationin the Zebrafish Embryo

    Leif C. Lindeman, Linn T. Vogt-Kielland, Peter Alestrom,and Philippe Collas


    Chromatin immunoprecipitation (ChIP) is arguably the assay of choice to determine the genomiclocalization of DNA- or chromatin-binding proteins, including post-translationally modified histones, incells. The increasing importance of the zebrafish, Danio rerio, as a model organism in functional genomicshas recently sparked investigations of ChIP-based genome-scale mapping of modified histones on pro-moters, and studies on the role of specific transcription factors in developmental processes. ChIP assaysused in these studies are cumbersome and conventionally require relatively large number of embryos.To simplify the procedure and to be able to apply the ChIP assay to reduced number of embryos, were-evaluated the protocol for preparation of embryonic chromatin destined to ChIP. We found thatmanual homogenization of embryos rather than protease treatment to remove the chorion enhancesChIP efficiency and quickens the assay. We also incorporated key steps from a recently published ChIPassay for small cell numbers. We report here a protocol for immunoprecipitation of modified histones frommid-term blastula zebrafish embryos.

    Key words: Chromatin immunoprecipitation, ChIP, embryo, histone modification, zebrafish.

    1. Introduction

    The importance of zebrafish as a model system for studyingvertebrate embryogenesis or even human disease has been stronglyestablished (14). Advantages of zebrafish are that several hun-dreds of synchronized embryos can be produced from a fewfemales, generation interval is short (34 months), embryos aretransparent, and development is rapid (1,000 cell-stage at 3 hpost-fertilization, hpf) and external, so all developmental stagesare accessible for manipulation and observation, in contrast to

    Philippe Collas (ed.), Chromatin Immunoprecipitation Assays, Methods in Molecular Biology 567,DOI 10.1007/978-1-60327-414-2_5, Humana Press, a part of Springer Science+Business Media, LLC 2009


  • most other vertebrate models. Zebrafish are also well suited forfunctional genomics investigations (4). Large-scale mutagenesisscreens can be undertaken and stable transgenic lines are easy toestablish. The seventh assembly of the zebrafish genome (Zv7)reports 1, 563, 441, 531 bp with 24,147 protein-coding genes(www.sanger.ac.uk/Projects/D_rerio). Although not finallyannotated, access to the genome sequence allows the identificationof gene orthologs. Forward genetics has through positional clon-ing enabled discoveries of over 2,000 zebrafish developmentalgene relationships (4). Reverse genetics through antisenseMorpholino oligonucleotides (5), TILLING targeted mutagen-esis (6), and zinc finger nucleases (7, 8), and the emergence ofzebrafish expression arrays with probes from oligonucleotidelibraries based on transcription units predicted by improvedbioinformatics, places zebrafish functional genomics at a levelcomparable to that of mouse or human.

    Embryo development proceeds from a cascade of gene activa-tion and repression events in response to extracellular signals andlocal determinants. Resulting changes in gene expression in spe-cific cell types regulate differentiation. The coordinate activationand repression of genes requires intricate regulatory networks (9,10). These networks are controlled by binding of transcriptionalregulators to key gene regulatory sequences. Binding of thesefactors is itself modulated by modifications of DNA (DNA methy-lation) or chromatin (such as post-translational modifications ofhistones). Interactions between proteins and DNA, therefore, areessential to the regulation of gene expression.

    To date, the tool of choice for studying proteinDNA inter-actions and unraveling transcriptional regulatory circuits in cellsis chromatin immunoprecipitation (ChIP) [reviewed in (11)].ChIP has been widely used for mapping the positioning of post-translationally modified histones, transcription factors, or otherDNA-binding proteins on specific genomic regions in a variety ofcell types and species, including mouse blastocysts (12). In a ChIPassay, DNA and proteins are reversibly cross-linked, chromatin isfragmented, usually by sonication, to 500 bp fragments andantibodies to the protein of interest (e.g., a modified histone),are used to immunoprecipitate a specific proteinDNA complex.Immune complexes are washed, the chromatin is eluted, cross-links are reversed, and the ChIP DNA is purified. Genomicsequences associated with the precipitated protein can be identifiedby polymerase chain reaction (PCR), high-throughput sequencing(ChIP-seq), microarray hybridization (ChIP-on-chip), or othermethods (11).

    Only recently has ChIP been applied to zebrafish embryos.A whole embryo ChIP assay for zebrafish was published in2006 to establish a proof-of-concept that the procedure wasapplicable in this species for investigating the enrichment of

    76 Lindeman et al.

  • modified histones (acetylated histone H4) or c-Myc on specificpromoters (13). ChIP has also been used for identification oftranscriptionally active promoters bearing trimethylated H3 lysine4 (H3K4m3) in gastrula-stage embryos using a ChIP-on-chipapproach (14), and to investigate the role of the transcriptionfactor Trf 3 in the initiation of hematopoiesis in the zebrafishembryo (15). These protocols rely on protease (pronase) treat-ment to remove the chorion prior to preparing nuclei andisolating chromatin. We have found that pronase is detrimentalto the efficiency of ChIP and have re-evaluated the procedure forpreparation of chromatin. We also take advantage of critical stepsin our recently published miniaturized and quick (1 day) ChIPassays (1618) to produce a revised protocol for efficient immu-noprecipitation of modified histones from mid-term blastula(MBT) zebrafish embryos (Fig. 5.1).

    Fig. 5.1. Zebrafish embryo preparation for ChIP assays. (A) Breeding tank with a grid in the inner tank; the inner tank issubdivided into two compartments to separate fish of different sex. Marbles are added to the inner tank as enhancementof breeding behavior; marbles are added to both sides (not shown here). (B) Harvesting of newly fertilized embryos ina sieve. Embryos can be seen in the sieve. (C) Embryos are screened under a dissecting microscope to eliminateunhealthy eggs. (D) Selected MBT stage embryos. (E) Embryos are homogenized through a 21G needle using a 5 mLsyringe.

    Zebrafish Embryo ChIP 77

  • 2. Materialsand Reagents

    2.1. Materials

    2.1.1. Preparation

    of Zebrafish Embryos

    1. Zebrafish, e.g., AB strain (Zebrafish International ResourceCenter; http://zfin.org/zirc/).

    2. Reverse osmosis water production system with filters and UVsterilization (www.zebrafish.no for details).

    3. Breeding chambers (2 L) made from autoclavable, FDA-approved, food-grade polycarbonate (Aquatic Habitats,parts no. BTANK2, BINSERT2, BDIVIDER2 andBLID2).

    4. Glass marbles (purchased from toy store).

    5. Thermo Plate (TOKAI HIT, Model: MATS-U4020WF, orsimilar).

    6. Incubator set to 28C.7. Stereo microscope.

    8. Digital camera fitted to the microscope.

    9. 90 mm plastic Petri dishes.

    10. Sieve (purchased from drug store; see Fig. 5.1B).

    11. Glass Pasteur pipettes with glassfirm-pi-pump.

    2.1.2. ChIP Assay 1. Filter 10, 200, and 1,000 mL pipette tips.

    2. Magnetic rack suited for 200 mL tube strips (Diagenode).

    3. 200 mL PCR tubes in eight-tube strip format (Axygen).

    4. 0.6 and 1.5 mL centrifuge tubes.

    5. Magnetic holder for 1.5 mL tubes.

    6. Probe sonicator (e.g., Sartorius Labsonic M sonicatorwith 3 mm diameter probe at setting 0.5 cycle and 30%power).

    7. Rotator (e.g., Science Lab Stuart SB3) placed at 4C.8. Tabletop centrifuge.

    9. Minicentrifuge.

    10. Vortex.

    11. Thermomixer (e.g., Eppendorf).

    12. Heating block.

    13. Real-time thermal cycler.

    2.2. Reagents

    2.2.1. Preparation

    of Zebrafish Embryos

    1. Instant Ocean (Synthetic sea salt).

    2. 1 M HCl.

    78 Lindeman et al.

  • 2.2.2. ChIP Assay 1. 36.5% formaldehyde.

    2. Dynabeads1 Protein A (Invitrogen, cat. no. 100.02D). Beadsshould be well suspended before pipetting. Use Dynabeads1

    Protein A beads with rabbit IgGs and Dynabeads1 Protein G(Invitrogen, cat. no. 100.04D) with mouse IgGs.

    3. 5 M NaCl.

    4. 400 mM EGTA.

    5. 500 mM EDTA.

    6. 1 M TrisHCl, pH 7.5 and 1 M TrisHCl, pH 8.0.

    7. Glycine: 1.25 M stock solution in PBS.

    8. Acrylamide carrier.

    9. Proteinase K: 20 mg/mL solution in MilliQ water.

    10. Protease inhibitor mix (Sigma-Aldrich, cat. no. P8340).

    11. Phenylmethylsulfonyl fluoride (PMSF): 100 mM stock solu-tion in 100% ethanol.

    12. Na-butyrate: 1 M stock solution in MilliQ water.

    13. Phosphate buffered saline (PBS).

    14. PBS/Na-butyrate solution: 20 mM butyrate in 1X PBS. Makeimmediately before use.

    15. PBS/Na-butyrate/formaldehyde fixative: 20 mM butyrate,1 mM PMSF, and protease inhibitor mix in 1X PBS. Makeup immediately before use.

    16. Phenol:chloroform:isoamylalcohol (25:24:1).

    17. Chloroform:isoamylalcohol (24:1).

    18. 3 M NaAc.

    19. IQ SYBR1 Green (BioRad).

    20. Antibodies to the protein to be ChIPed, preferably ChIP-grade.

    2.3. Buffers

    and Solutions

    2.3.1. Preparation

    of Zebrafish Embryos

    1. System water for breeding and incubating embryos: purifywater by sterile filtration, UV sterilization, and reverse osmo-sis. Reconditioned by adding, per liter, 0.15 g Instant Ocean(Synthetic sea salt), 0.05 g Na-bicarbonate, and 0.035 gCaCl2. If necessary adjust pH to 7.5 with 1 M HCl.

    2. Egg water: 60 mg/L Instant Ocean salt in milliQ water.Autoclave.

    2.3.2. ChIP Assay 1. Lysis buffer: 50 mM TrisHCl, pH 8.0, 10 mM EDTA, 1% (wt/vol) SDS, protease inhibitor mix (1:100 dilution from stock), 1mM PMSF, 20 mM Na-butyrate. Protease inhibitor mix, PMSF,and Na-butyrate should be added immediately before use.

    2. RIPA buffer: 10 mM TrisHCl, pH 7.5, 140 mM NaCl,1 mM EDTA, 0.5 mM EGTA, 1% (vol/vol) Triton X-100,0.1% (wt/vol) SDS, 0.1% (wt/vol) Na-deoxycholate.

    Zebrafish Embryo ChIP 79

  • 3. RIPA ChIP buffer: 10 mM TrisHCl, pH 7.5, 140 mM NaCl,1 mM EDTA, 0.5 mM EGTA, 1% (vol/vol) Triton X-100,0.1% (wt/vol) SDS, 0.1% (wt/vol) Na-deoxycholate, pro-tease inhibitor mix (1:100 dilution from stock), 1 mMPMSF, 20 mM Na-butyrate. Protease inhibitor mix, PMSF,and Na-butyrate should be added immediately before use.

    4. TE buffer: 10 mM TrisHCl, pH 8.0, 10 mM EDTA.

    5. Elution buffer: 20 mM TrisHCl, pH 7.5, 5 mM EDTA, 50 mMNaCl, 20 mM Na-butyrate, 1% (wt/vol) SDS, 50 mg/mL pro-teinase K. Na-butyrate, SDS, and proteinase K should be addedjust before use.

    3. Methods

    3.1. Preparation

    of Zebrafish EmbryosIn this protocol, the ChIP assay is described for embryos at thelate MBT stage (>1,000 cells), i.e., between the high andoblong stages defined on http://www.neuro.uoregon.edu/k12/Table%201.html. At 28C, this corresponds to 3.5 h post-fertilization (hpf).

    1. Set up breeding tanks on the day before you want embryos.

    2. Breeding in 2 L tanks with one fish pair. Set up a breedingtank by placing an inner tank with a bottom grid into the 2 Lfish tank; the inner tank is divided by a separator into twocompartments to separate the fish by sex. Add marbles toboth sides of the inner tank and place a lid on top (Fig. 5.1A).

    3. On the next morning, remove the separator in the 2 L breedingtanks. Avoid stressing the fish and do not feed.

    4. After 3060 min, collect embryos (see Note 1); pour theembryos from the 2 L tank into an embryo sieve (Fig. 5.1B).

    5. Thoroughly rinse the embryos in the sieve with system waterand transfer them into a 90 mm Petri dish containing roomtemperature (2128C range) system water (see Note 2).

    6. Incubate the embryos for 1 h at 28C.7. Using a dissection microscope, select, count, and transfer all

    healthy embryos to a new 90 mm Petri dish containing systemwater (Fig. 5.1C).

    8. To harvest late MBT stage embryos, prolong incubation inthe Petri dish for another1.5 h at 28C on a thermoplate orin an incubator (see Note 2).

    9. Document state of embryo development and level of synchro-nization by a camera fitted to the microscope (Fig. 5.1D).

    80 Lindeman et al.

  • 3.2. Cross-Linking

    of DNA and Proteins

    1. Using a transfer pipette, transfer 500 MBT embryos in PBScontaining 20 mM Na-butyrate, protease inhibitors, andPMSF into a 5 mL syringe fitted with a 21G needle (Fig. 5.1E).

    2. Let the embryos sink to the bottom of the syringe and removethe PBS with the pipette, leaving 0.5 mL buffer on top ofthe embryos.

    3. Push the piston and force the embryos through the needleinto a 1.5 mL tube. This one-step lysis is usually sufficient tobreak all the embryos. Wash the needle with a small volumePBS/Na-butyrate, PMSF, and protease inhibitors to collectany leftover in the syringe.

    4. Immediately cross-link the cells by adding formaldehyde to1% vol/vol final concentration, vortexing, and incubating forexactly 8 min at room temperature. Briefly spin (12 s) in theminicentrifuge to collect the liquid from the lid.

    5. Add glycine to 0.125 M to quench the formaldehyde. Vortex,place the tube on ice, and incubate for 5 min. From this steponward, handling of chromatin is carried out on ice.

    6. Centrifuge the tube at 470g for 10 min at 4C to sedimentcells and fragments from the chorion; carefully remove anddiscard the supernatant with a 1 mL pipette.

    7. Add 500 mL ice-cold PBS/Na-butyrate, PMSF, and proteaseinhibitors and resuspend the cells by vortexing. Centrifuge at470g for 10 min at 4C and discard the supernatant.

    8. Add another 500 mL PBS/Na-butyrate, PMSF, and proteaseinhibitors. Transfer to a 0.6 mL tube and centrifuge at 470gfor 5 min.

    9. Remove all the supernatant with a pipette. The cells can bestored as a dry pellet at 80C for several weeks.

    3.3. Preparation

    of AntibodyBead


    1. Prepare a slurry of Dynabeads1 Protein A or G, depending onthe origin of the antibody. For each ChIP to be performed,place 10 mL of well-suspended bead stock solution in a 1.5 mLtube. Place beads in an additional tube for a no-antibody(bead only) control. Work on ice for all steps.

    2. Place the tubes in a magnetic holder, capture the beads,remove the supernatant, and add 2.5 volumes of RIPA buffer.

    3. Vortex, spin briefly in a minicentrifuge, capture the beads,remove the buffer, and add one volume of RIPA buffer.

    4. Repeat Step 3.

    5. For each ChIP reaction, add 90 mL RIPA buffer to each 200 mLtube. We find it convenient to use eight-tube PCR strips fromAxygen.

    6. Add 10 mL of well-dispersed slurry of Dynabeads1 Protein.

    Zebrafish Embryo ChIP 81

  • 7. Add a titrated amount of antibody (we routinely use 2.4 mgof anti-modified histone ChIP-grade antibody) (see Note 3).

    8. Incubate on a rotator at 40 rpm at 4C for 2 h, or overnight ifsuitable.

    3.4. Preparation

    of Chromatin

    1. To a tube containing cells, add lysis buffer to a total volume300 mL. Resuspend the pellet with a pipette without makingbubbles. We found that starting with a frozen or fresh cross-linked cell pellet has no noticeable influence on ChIP efficiencyor results.

    2. Cut the end of a 1 mL pipette tip and transfe...


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