Name: cell-specific paired interrogation of the mouse ovarian epigenome and transcriptome
Uploaded: 2023-02-24T12:50:00
Description: Watch this Scientific Journal Video about Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome at JoVE.com

This work was supported by grants from the National Institutes of Health (NIH) (R01AG070035, R01AG069742, T32AG052363), BrightFocus Foundation (M2020207), and Presbyterian Health Foundation. This work was also supported in part by the MERIT award I01BX003906 and a Shared Equipment Evaluation Program (ShEEP) award ISIBX004797 from the United States (U.S.) Department of Veterans Affairs, Biomedical Laboratory Research and Development Service. The authors would also like to thank the Clinical Genomics Center (OMRF) and Imaging Core Facility (OMRF) for assistance and instrument usage.

All animal procedures were approved by the Institutional Animal Care and Use Committee at the Oklahoma Medical Research Foundation (OMRF). Parent mice were purchased from the Jackson Laboratory (Bar Harbor, ME) and bred and housed under SPF conditions in a HEPA barrier environment on a 14 h/10 h light/dark cycle (lights on at 6:00am) at the OMRF.
NOTE: In this demonstration, we use a Cyp17iCre+/&#8722;(Strain # 028547, The Jackson Laboratory) male paired with a NuTRAP female (Strain...

<ol>
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The NuTRAP mouse model6&#160;is a powerful transgenic labeling approach for the paired interrogation of the transcriptome and epigenome from specific cell types that can be adapted to any cell type with an available Cre driver. Here, we demonstrate the specificity of the Cyp17-NuTRAP mouse model in targeting ovarian theca and stromal cells. The Cyp17-NuTRAP model can be used to further elucidate the theca and stromal cell-specific epigenetic mechanisms involved in ovarian aging, cancer, and diseas...

The ovaries are major players in somatic aging1, with distinct contributions from specific cell populations. The cellular heterogeneity of the ovary makes it difficult to interpret molecular results from bulk, whole-ovary assays. Understanding the role of specific cell populations in ovarian aging is key to identifying the molecular drivers responsible for fertility and health decline in aged women. Traditionally, the multi-omics assessment of specific ovarian cell types was achieved by techniques such as laser microdissection2, single-cell approaches3, or cell sorting4. However, microdissection can be expensive and difficult to perform, and cell sorting can alter cellular phenotypic profiles5.
A novel approach to assess ovarian cell-type-specific epigenomic and transcriptomic profiles uses the nuclear tagging and translating ribosome affinity purification (NuTRAP) mouse model. The NuTRAP model allows the isolation of cell-type-specific nucleic acids without the need for cell sorting by using the affinity purification methods: translating ribosome affinity purification (TRAP) and isolation of nuclei tagged in specific cell types (INTACT)6. The expression of the NuTRAP allele is under the control of a floxed STOP cassette and can be targeted to specific ovarian cell types using promoter-specific Cre lines. By crossing the NuTRAP mouse with a cell-type-specific Cre line, the removal of the STOP cassette causes eGFP-tagging of the ribosomal complex and biotin/mCherry-tagging of the nucleus in a Cre-dependent manner6. The TRAP and INTACT techniques can then be used to isolate mRNA and nuclear DNA from the cell type of interest and proceed to transcriptomic and epigenomic analyses.
The NuTRAP model has been used in different tissues, such as adipose tissue6, brain tissue7,8,9, and the retina10, to reveal cell-type-specific epigenomic and transcriptomic changes that may not be detected in whole-tissue homogenate. The benefits of the NuTRAP approach over traditional cell sorting techniques include the following: 1) the prevention of ex vivo activational artifacts8, 2) the minimized need for specialized equipment (i.e., cell sorters), and 3) the increased throughput and decreased cost of cell-type-specific analyses. In addition, the ability to isolate cell-type-specific DNA and RNA from a single mouse allows for paired analyses that increase the statistical power. Since recent studies have implicated ovarian stromal cells in driving premature aging phenotypes11,12,13, we targeted the NuTRAP expression system to stromal and theca cells using a Cyp17a1-Cre driver. Here, we demonstrate that the induction of the NuTRAP construct is specific to ovarian stromal and theca cells, and sufficient DNA and RNA for sequencing studies are obtained from a single ovary. The NuTRAP model and methods presented here can be used to study any ovarian cell type with any available Cre line.
For the generation of a cell-type-specific ovarian NuTRAP mouse line, the nuclear tagging and translating ribosome affinity purification (NuTRAP) allele has a floxed STOP codon that controls the expression of BirA, biotin ligase recognition peptide (BLRP)-tagged mCherry/mRANGAP1, and eGFP/L10a. When crossed with a cell-type-specific Cre line, the expression of the NuTRAP cassette labels the nuclear protein mRANGAP1 with biotin/mCherry and ribosomal protein L10a with eGFP in a Cre-dependent manner. This allows for the isolation of nuclei and mRNA from specific cell types without the need for cell sorting. The NuTRAPflox/flox can be paired with a cell-type-specific Cre relevant to ovarian cell types to assess this.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.1 M Spermidine</td>
			<td>Sigma-Aldrich</td>
			<td>05292-1ML-F</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M MgCl2</td>
			<td>Thermo Scientific</td>
			<td>AM9530G</td>
			<td></td>
		</tr>
		<tr>
			<td>10% NP-40</td>
			<td>Thermo Scientific</td>
			<td>85124</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mg/mL Cycloheximide</td>
			<td>Sigma-Aldrich</td>
			<td>C4859-1ML</td>
			<td></td>
		</tr>
		<tr>
			<td>2-mercaptoethanol</td>
			<td>Sigma-Aldrich</td>
			<td>M3148</td>
			<td></td>
		</tr>
		<tr>
			<td>30 &#181;m cell strainer&#160;</td>
			<td>Miltenyi Biotec</td>
			<td>130-098-458</td>
			<td></td>
		</tr>
		<tr>
			<td>All Prep DNA/RNA Mini Kit</td>
			<td>Qiagen</td>
			<td>80204</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-GFP antibody</td>
			<td>Abcam</td>
			<td>Ab290</td>
			<td>For TRAP and IHC (Rabbit polyclonal to GFP)</td>
		</tr>
		<tr>
			<td>Buffer RLT</td>
			<td>Qiagen</td>
			<td>79216</td>
			<td>RNA Lysis Buffer in protocol</td>
		</tr>
		<tr>
			<td>cOmplete, mini, EDTA-free protease inhibitor tablet</td>
			<td>Roche</td>
			<td>11836170001</td>
			<td>For TRAP Homogenization Buffer</td>
		</tr>
		<tr>
			<td>Cyp17iCre mouse model</td>
			<td>The Jackson Laboratory</td>
			<td>28547</td>
			<td>B6;SJL-Tg(Cyp17a1-icre)AJako/J</td>
		</tr>
		<tr>
			<td>DynaMag-2 magnet</td>
			<td>Invitrogen</td>
			<td>12321D</td>
			<td></td>
		</tr>
		<tr>
			<td>Genotyping Primers</td>
			<td>IDT</td>
			<td>Custom</td>
			<td>Generic Cre - Jackson Laboratory protocol 22392, Primers: oIMR1084, oIMR1085, oIMR7338, oIMR7339</td>
		</tr>
		<tr>
			<td>&#160;&#160;</td>
			<td>&#160;&#160;</td>
			<td>&#160;&#160;</td>
			<td>Cyp17iCre - Jackson Laboratory protocol 30847, Primers: 21218, 31704, 31705, 35663</td>
		</tr>
		<tr>
			<td>&#160;&#160;</td>
			<td>&#160;&#160;</td>
			<td>&#160;&#160;</td>
			<td>NuTRAP - Jackson Laboratory protocol 21509, Primers: 21306, 24493, 32625, 32626</td>
		</tr>
		<tr>
			<td>Halt Protease Inhibitor cocktail (100X)</td>
			<td>Thermo Scientific</td>
			<td>1861278</td>
			<td>For NPB Buffer</td>
		</tr>
		<tr>
			<td>M-280 Streptavidin Dynabeads&#160;</td>
			<td>Invitrogen</td>
			<td>11205D</td>
			<td>2.8 &#181;m bead diameter</td>
		</tr>
		<tr>
			<td>MixMate</td>
			<td>Eppendorf</td>
			<td>5353000529</td>
			<td></td>
		</tr>
		<tr>
			<td>Nuclei Isolation Kit: Nuclei EZ Prep</td>
			<td>Sigma-Aldrich</td>
			<td>Nuc101</td>
			<td>Contains Nuclei Lysis Buffer and Nuclei Storage Buffer</td>
		</tr>
		<tr>
			<td>1 M HEPES</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>5 M NaCl</td>
			<td>Thermo Scientific</td>
			<td>AM9760G</td>
			<td></td>
		</tr>
		<tr>
			<td>2M KCl</td>
			<td>Thermo Scientific</td>
			<td>AM9640G</td>
			<td></td>
		</tr>
		<tr>
			<td>0.5 M EDTA</td>
			<td>Thermo Scientific</td>
			<td>AM9260G</td>
			<td></td>
		</tr>
		<tr>
			<td>0.5 M EGTA</td>
			<td>Fisher Scientific</td>
			<td>50-255-956</td>
			<td></td>
		</tr>
		<tr>
			<td>NuTRAP mouse model</td>
			<td>The Jackson Laboratory</td>
			<td>29899</td>
			<td>B6;129S6-Gt(ROSA)26Sortm2(CAG-NuTRAP)Evdr/J</td>
		</tr>
		<tr>
			<td>Pierce DTT No-Weigh Format</td>
			<td>Thermo Scientific</td>
			<td>A39255</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein G Dynabeads</td>
			<td>ThermoFisher</td>
			<td>10004D</td>
			<td>For TRAP</td>
		</tr>
		<tr>
			<td>RNaseOUT</td>
			<td>Invitrogen</td>
			<td>10777019</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Heparin</td>
			<td>Fisher Scientific</td>
			<td>BP2425</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultrapure 1M Tris-HCl, pH 7.5</td>
			<td>Invitrogen</td>
			<td>15567-027</td>
			<td></td>
		</tr>
		<tr>
			<td>VWR Tube Rotator</td>
			<td>Fisher Scientific</td>
			<td>NC9854190</td>
			<td></td>
		</tr>
	</tbody>
</table>

cell-specific paired interrogation of the mouse ovarian epigenome and transcriptome

Assessing cell-type-specific epigenomic and transcriptomic changes are key to understanding ovarian aging. To this end, the optimization of the translating ribosome affinity purification (TRAP) method and the isolation of nuclei tagged in specific cell types (INTACT) method was performed for the subsequent paired interrogation of the cell-specific ovarian transcriptome and epigenome using a novel transgenic NuTRAP mouse model. The expression of the NuTRAP allele is under the control of a floxed STOP cassette and can be targeted to specific ovarian cell types using promoter-specific Cre lines. Since recent studies have implicated ovarian stromal cells in driving premature aging phenotypes, the NuTRAP expression system was targeted to stromal cells using a Cyp17a1-Cre driver. The induction of the NuTRAP construct was specific to ovarian stromal fibroblasts, and sufficient DNA and RNA for sequencing studies were obtained from a single ovary. The NuTRAP model and methods presented here can be used to study any ovarian cell type with an available Cre line.

A schematic of the TRAP and INTACT protocols is shown in Figure 1. Here the specificity of the Cyp17-NuTRAP mouse model to ovarian stromal/theca cells is demonstrated by immunofluorescent imaging and RNA-Seq from TRAP-isolated RNA. First, immunofluorescence imaging of the eGFP signal in the ovary and localization of the eGFP signal to the theca and stromal cells were performed. Briefly, 5 &#181;m sections were deparaffinized with a xylene and ethanol gradient. For better eGFP signaling, the ...

Watch this Scientific Journal Video about Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome at JoVE.com

Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome

In this protocol, the translating ribosome affinity purification (TRAP) method and the isolation of nuclei tagged in specific cell types (INTACT) method were optimized for the paired interrogation of the cell-specific ovarian transcriptome and epigenome using the NuTRAP mouse model crossed to a Cyp17a1-Cre mouse line.

Assessing cell-type-specific epigenomic and transcriptomic changes are key to understanding ovarian aging. To this end, the optimization of the ...

This method provides a technique to isolate nucleic acids from specific ovarian cell populations from the same mouse without the need for cell sorting. This technique can help identify how specific cell populations are changing under a variety of conditions. For example, with aging.The main advantage of this technique is that it allows for paired epigenomic and transcriptomic analysis from a specific ovarian cell type without the need for cell sorting. This significantly increases the throughput, decreases the cost, and eliminates the need for specialized equipment when performing cell type-specific analysis from ovarian tissue. Here, our goal is to identify the cell type-specific changes that occur with ovarian aging prior to reproductive senescence, which has implications in treating female infertility.This method can be applied to any cell type across body systems for which a cell type-specific Cre driver is available. The most difficult part of this technique is choosing an appropriate Cre line for your cell type of interest. Extensive validation of the cell specificity is recommended.To begin, collect one ovary from the euthanized mouse in 500 microliters of nuclei lysis buffer and chop the ovary into eight parts within the buffer using self-opening micro scissors. Transfer the minced ovary and the lysis buffer into a glass dounce homogenizer on ice and homogenize the ovary 10 to 20 times with the loose pestle A.Add 400 microliters of lysis buffer to the dounce homogenizer washing pestle A.And then homogenize the ovary with tight pestle B 10 to 20 times. Transfer the homogenate to a two-milliliter round bottom tube and centrifuge at 200 g for 1.5 minutes at four degrees Celsius to remove the undissociated tissue and blood vessels.After pre-wetting a 30-micrometer cell strainer with 100 microliters of lysis buffer, filter the supernatant through the strainer into a 15-milliliter conical tube. Transfer the nuclei containing mixture to a two-milliliter round bottom tube. Centrifuge the sample at 500 g for five minutes at four degrees Celsius and discard the supernatant.Resuspend the nuclei pellet in 250 microliters of ice cold lysis buffer by vortexing briefly at moderate to high speed. Bring the volume up to 1.75 milliliters by adding 1.5 milliliters of lysis buffer. Mix gently and rest the nuclei suspension on ice for five minutes.Pellet the nuclei by centrifugation at 500 g for five minutes at four degrees Celsius. And carefully discard the supernatant without disturbing the nuclei pellet. Resuspend the pellet in 200 microliters of ice cold storage buffer and vortex briefly to completely resuspend the nuclei pellet.Reserve 10%of the resuspended pellet as an input nuclei sample for downstream analysis. Take the resuspended nuclei pallet and make up the volume to two milliliters with ice cold nuclear purification buffer, or NPB. Add 30 microliters of resuspended beads for each sample into a two-milliliter round bottom tube.Then add one milliliter of NPB and resuspend well by pipetting. Place the tube on the magnetic rack for one minute to separate the beads. Discard the supernatant and remove the tube from the magnet.Resuspend the washed magnetic beads in one milliliter of NPB. Repeat the wash step for a total of three washes. And after the final wash, resuspend the beads in the initial volume of NPB.Add 30 microliters of the washed beads to two milliliters of the nuclear suspension and resuspend the beads nuclei mixture well by pipetting and gently inverting the tube. Place the tubes on a rotating mixer in a cold room or refrigerator for 30 minutes at low speed and incubate the input samples without beads in the same conditions. Place the tubes with the nuclei suspension and beads on the magnet for three minutes to separate the biotinylated nuclei bound to streptavidin beads from the negative fraction of nuclei.Remove the supernatant. Pass the negative fraction to a fresh two-milliliter tube and reserve it on ice. For each positive fraction tube, remove the tube from the magnet and resuspend the contents in one milliliter of NPB.Place the tube on the magnet for one minute and discard the supernatant. Resuspend the positive fraction bead nuclei mixture in 30 microliters of NPB. Transfer the ovary and 100 microliters of homogenization buffer into a glass dounce homogenizer and homogenize 10 to 20 times with the loose pestle A.Add 400 microliters of TRAP homogenization buffer to washing pestle A and transfer the homogenate to a two-milliliter round bottom tube.Wash the homogenizer with an additional one milliliter of TRAP homogenization buffer and transfer the washed volume to the two-milliliter round bottom tube. Centrifuge the homogenate at 12, 000 g for 10 minutes at four degrees Celsius. And transfer the cleared supernatant to a fresh two-milliliter round bottom tube.After discarding the pellet, transfer 100 microliters of the cleared homogenate to a fresh two-milliliter round bottom tube and reserve it as input on ice. Incubate the remainder of the cleared homogenate with five micrograms per milliliter anti-GFP antibody for one hour at four degrees Celsius while rotating in an end-over-end mixer. Incubate the input sample in the same condition.Transfer 50 microliters of the protein G magnetic beads for each sample into a two-milliliter round bottom tube. Add 500 microliters of low-salt wash buffer to the beads and pipette gently to mix. Place the tube into a magnetic stand for one minute to collect the beads against the side of the tube.After discarding the supernatant, remove the tube from the magnetic stand and add one milliliter of low-salt wash buffer to the tube. Pipette gently to mix. Again, place the tube into the magnetic stand and repeat the step for a total of three washes.After the final wash, resuspend the beads in the initial volume of low-salt wash buffer. Transfer the resuspended washed beads to the antigen sample antibody mixture and incubate at four degrees Celsius overnight while rotating in an end-over-end mixer. Incubate the input samples overnight in the equivalent conditions.After that, separate the positive fraction or the magnetic beads with the target ribosomes RNA from the negative fraction or the supernatant using the magnetic stand for 2.5 to 3 minutes. Aspirate the negative fraction. Place it in a fresh two-milliliter round bottom tube, and set it aside on ice.Add 500 microliters of high-salt wash buffer to the tube with the positive fraction and gently pipette to mix. Place the tube on a magnetic stand maintained on ice for one minute to separate the beads. After discarding the supernatant, remove the tube from the magnet and repeat the step for a total of three washes.After the final wash, resuspend the beads in 350 microliters of RNA lysis buffer supplemented with 3.5 microliters of 2-mercaptoethanol. Incubate the tubes at room temperature while mixing for 10 minutes at 900 RPM in a digital shaker. Separate the beads from the solution that now contains the target ribosomes RNA with a magnetic stand for one minute at room temperature.Collect the eluted positive fraction in a fresh 1.5 milliliter tube. Immunofluorescence imaging was performed on the paraffinized ovaries of Cyp17-Cre positive NuTRAP flox and Cyp17-Cre negative NuTRAP flox mice. EGFP protein was stained using goat anti-GFP primary antibody and Alexa 488 donkey anti-goat secondary antibody, and the nuclei was stained with DAPI.Images were taken on a fluorescence microscope at 20x magnification. The input and TRAP positive fraction RNA was isolated from Cyp17-Cre positive NuTRAP flox mouse ovaries and sequenced in a paired end manner. The principal component analysis of all the expressed genes showed a separation of the TRAP input and positive fractions in the first component.The volcano plot of differentially expressed genes between the input and positive fractions is shown here. The comparison of the TRAP positive fraction to the input showed an overall enrichment of the stroma/theca cell marker genes and the depletion of the oocyte, granulosa, immune, and smooth muscle cell marker genes in the TRAP positive fraction. After the first centrifugation of the nuclear suspension to remove undissociated blood vessels, the nuclei are in the supernatant.Make sure to keep the supernatant and discard the pellet at this point. Following the intact method, several epigenomic techniques can be conducted, including assays for chromatin accessibility or DNA modifications among others. Following the TRAP method, RT-qCPR or RNA sequencing can be conducted to assess the translatome.This is the first application of the NuTRAP method in the mouse ovary. This allows for high throughput epigenomic and transcriptomic analysis from specific ovarian cell types, which may be used to study ovarian aging or cancer.

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