Rapid, single-tube method for quantitative preparation and analysis of RNA and DNA in samples as small as one cell
© Hartshorn et al; licensee BioMed Central Ltd. 2005
Received: 28 September 2004
Accepted: 13 January 2005
Published: 13 January 2005
Current methods for accurate quantification of nucleic acids typically begin with a template preparation step in which DNA and/or RNA are freed of bound proteins and are then purified. Isolation of RNA is particularly challenging because this molecule is sensitive to elevated temperatures and is degraded by RNases, which therefore have to be immediately inactivated upon cell lysis. Many protocols for nucleic acids purification, reverse transcription of RNA and/or amplification of DNA require repeated transfers from tube to tube and other manipulations during which materials may be lost.
This paper introduces a novel and highly reliable single-tube method for rapid cell lysis, followed by quantitative preparation and analysis of both RNA and/or DNA molecules in small samples. In contrast to previous approaches, this procedure allows all steps to be carried out by sequential dilution in a single tube, without chemical extraction or binding to a matrix. We demonstrate the utility of this method by quantification of four genes, Xist, Sry and the two heat-inducible hsp70i (hsp70.1 and hsp70.3), as well as their RNA transcripts in single mouse embryos and in isolated blastomeres.
This method virtually eliminates losses of nucleic acids and is sensitive and accurate down to single molecules.
Real-time polymerase chain reaction (PCR) in combination with reverse transcription (RT) provides a powerful tool for accurate quantification of DNA and RNA copy numbers and has opened the way to the study of subtle modulations of gene expression in small numbers of cells, as well as small-scale genetic analyses aimed at establishing chromosome numbers, the presence of mutations, or allele dropout. The reliability of these measurements, however, depends on the accuracy of each step, including preparation and recovery of RNA and/or DNA, reverse transcription of RNA into cDNA, and quantifiable and specific amplification of all desired sequences. The importance of optimizing each of these steps is well recognized , as is the need to minimize the number of tube-to-tube transfers in order to avoid the loss of templates and decrease the risk of contamination. This risk is posed by environmental RNases, material carried over from sample to sample, as well as previously generated amplicons present on laboratory equipment. Sequential performance of several steps in a single-tube is therefore highly desirable, especially when starting with small numbers of target molecules, such as chromosomes of individual cells or a few virus particles [2–5].
Our laboratory has already demonstrated that bound proteins prevent reliable PCR amplification of genomic DNA and that a thorough proteolytic digestion followed by heat inactivation solves this problem . For accurate gene expression studies, RNA molecules also need to be released intact and free of proteins from all subcellular compartments, but proteases cannot be used both because they are not fast enough to inhibit the RNases (particularly endogenous RNases, released in the sample upon cell disruption) and because RNA is sensitive to the high temperatures required for protease inactivation . Commercial kits for RNA purification therefore commonly employ either chaotropic agents or lysis buffers containing strong detergents, or a combination of the two, in order to achieve rapid denaturation of proteins. Nucleic acids are then extracted to remove these chemicals, because their presence interferes with subsequent enzymatic reactions. Alternatively, some RT-PCR kits bypass nucleic acid purification in favor of a simple dilution step, but in this case only a small aliquot of the lysed sample can be added to the RT mixture, due to volume restrictions. This approach introduces imprecision of its own and makes single cell analysis impossible. On the other hand, gentler lysis conditions that are compatible with single-tube analysis of a whole small sample do not remove proteins completely, resulting in substandard template preparations. For instance, protocols involving simple freeze-thaw cycles to produce cell lysis do not generate protein-free RNA or DNA. Similarly, mild detergents that do not lyse the nuclear membrane preclude quantification of DNA or RNA located in the nucleus, and are unlikely to completely remove proteins bound to cytoplasmic RNA.
The chaotropic agent guanidine isothiocyanate (GITC) has long been the chemical of choice for nucleic acid preparation. It is particularly useful for RNA studies [8, 9], because it rapidly denatures all cellular proteins, as well as serum proteins, including RNases, added to culture media. GITC has also proven superior to all other tested methods for the recovery of either DNA or RNA extracted from mummified tissue . Due to its strong chemical action, GITC at high concentrations offers the further advantage of allowing safe storage of the samples until they are processed for quantification. For the same reason, however, all traditional protocols require removal of GITC prior to RT and PCR to avoid inactivation of the enzymes involved. Typically GITC is removed by extraction with phenol-chloroform and purification of the nucleic acids through alcohol precipitation cycles , or by absorption of the freed RNA to a matrix such as glass fiber filters, silica-gel membranes, magnetic beads or proprietary compositions, usually followed by elution in a relatively large volume. Both these approaches are time-consuming and involve a number of steps that can lead to incomplete RNA recovery.
In view of these limitations we devised an alternative strategy in which the sample is collected and denatured in a minimal volume of a GITC solution, briefly heated to allow dry storage, and, when needed, is directly analyzed in the same tube by performing quantitative RT-PCR in a volume large enough to lower GITC concentration to negligible levels. This new procedure, hereafter referred to as PurAmp (patent pending) and described here in full for the first time, is the only available method that allows a whole sample, such as a single embryo or cell, to be processed from lysis to RT-PCR in the same tube, under conditions that permit precise quantification of both RNA and genomic DNA copy numbers. This fully optimized method is sensitive enough to detect specific sequences within a single chromosome in one cell, yet robust enough to measure the presence of thousands of RNA molecules released from hundreds of cells.
PurAmp has made it possible for us to conveniently investigate expression levels of two gene types essential for early mouse embryo development: Xist, responsible for X-inactivation and dosage compensation in female cells [11–13], and the heat-shock inducible hsp70.1 and hsp70.3, jointly called hsp70i [14, 15]. Xist RNA is a noncoding transcript that exerts its particular function of gene-silencer by coating the inactive X-chromosome. Unlike hsp70i RNA and most other mRNAs, it is therefore localized in the cell nucleus and particularly challenging to extract. Besides their biological relevance, both Xist and the hsp70i genes offer the advantage of naturally-occurring unambiguous controls for the specificity of transcripts amplified with RT-PCR. Xist RNA is, in fact, virtually absent from male cleavage stage embryos [16–19], while hsp70i RNA is predominantly synthesized in response to stress although minimal levels of hsp70i transcripts are normally present in embryonic cells. A careful quantitative analysis of hsp70i heat and culture stress-response in preimplantation embryos at different developmental stages, and its implications for development, will be presented elsewhere (C. Hartshorn, A. Anshelevich and L. J. Wangh, in preparation). In addition, we have been able to detect and quantify the genomic sequences of Xist, the hsp70i and the male sex-determining gene Sry . Because the number of these sequences is known and very low in samples comprised by an identifiable number of cells, such as early embryos that have undergone few cleavages, their precise quantification provided an optimal internal control to demonstrate the strength of this novel technique. The quick and reliable detection of DNA (or RNA) in very low copy number is, however, not limited to the role of internal control, but holds much wider utility for a variety of applications such as genetic studies and detection of viral sequences in a sample. Further, this method can be successfully employed for the study of individual cells, as shown by the present report, and is easily adaptable to analysis of subcellular fractions or aliquots from bodily fluids; it also minimizes the use of toxic chemicals and the possibility of contamination, while allowing dry storage of the collected samples. All these features concur to render PurAmp ideally suitable for fast but highly sensitive gene and gene expression screening of multiple samples, including small whole specimens or fractions of larger ones.
Single-tube Xist RNA, Xist DNA and SryDNA quantification in individual male and female blastocysts
The PurAmp method presented in this study is performed in a single tube from cell lysis to cDNA or genomic DNA amplification, thus eliminating possible loss of template molecules due to procedures such as phase separation and recovery, repeated washing and re-suspension of nucleic acid pellets, elution from binding matrices and vessel-to-vessel transfer. This strategy offers an immediate improvement in the precision of gene expression analyses, at the same time shortening considerably the experimental protocol compared to traditional methods.
In order to validate our method, we initially measured the Xist RNA content of a group of female mouse embryos at the blastocysts stage and quantified Xist and Sry DNA copy numbers in their male counterparts. Our previous analysis of these parameters in single female and male mouse embryos at different developmental stages provided us with an ample pool of data obtained with commercially available nucleic acids preparation methods [17–19], which we used as a reference for comparison with our new results.
Quantification of low-to-high XistRNA and DNA copy numbers in single embryos and blastomeres
Hsp70iRNA and DNA measurements in heat shocked and non-heat shocked single embryos and blastomeres
In order to more extensively test the validity of the PurAmp approach to template quantification in single cells, we measured transcript levels of the heat shock-inducible genes hsp70.1 and hsp70.3 in blastomeres isolated from embryos at the pre-compaction 8-cell stage, when cells can be easily counted and separated. The sequences of these two genes are almost entirely identical, they are located on the same chromosome and they encode the same protein [14, 15]. For this reason, there has been some confusion in their identification and nomenclature in past studies. Heat-inducible hsp70 transcription, previously indicated as hsp70.1 expression, is now more precisely designated as the sum of hsp70.1 and hsp70.3 (hsp70i) RNAs.
Comparison of hsp70i copy numbers measured in single blastocysts: multistep/multitube versus PurAmp method
hsp70iDNA + RNA copies
No Heat shock, + RT
512 ± 69 (3)a
967 ± 548 (4)
Heat shock, + RT
2240 ± 1184 (3)
Correlation between hsp70i copy numbers in single blastomeres and whole 8-cell embryos, ± heat shock
hsp70i DNA copies
No-heat shock, No RT
Whole embryos (4)a
Per blastomere average ± s.d.
5 ± 2
hsp70i DNA + RNA copies
No-heat shock, + RT
Whole embryos (4)
Per blastomere average ± s.d.
19 ± 7
Heat shock, + RT
Per blastomere average ± s.d.
488 ± 134
701 ± 325
Whole embryosb (6)
Per blastomere average ± s.d
500 ± 172
Whole embryosc (2)
Per blastomere average
Expression of hsp70i RNA increased sharply after a 30-minute heat treatment, followed by a recovery period of either 2 or 3 hours necessary for transcripts synthesis and accumulation. Some of the heat-shocked embryos were harvested intact, while others were dissociated in single blastomeres. The average numbers of hsp70i template copies per blastomere were calculated from the isolated cells (not all cells of dissected 8-cell embryos could be recovered) and compared to the average per blastomere values obtained from whole embryos. The results show that the amount of hsp70i RNA + genomic DNA per cell calculated by these two approaches is very similar. A post-heating recovery period of 3 hours rather than 2 hours increased the hsp70i RNA levels only slightly, indicating that the onset of transcription and the major build-up in RNA occur quickly. Single cells derived from non-heated embryos contained only trace amounts of hsp70i RNA, consistent with whole embryo measurements, and PCR efficiency was, again, unaffected by the PurAmp components (not shown).
Efficiency of DNase treatment within the PurAmp protocol
It is increasingly clear that individual cells in a population do not exhibit identical patterns of gene expression and, hence, that expression profiling is more informative if it is quantitative and carried out at the single cell level [25–27]. This consideration is particularly relevant to current efforts aimed at understanding early mammalian embryogenesis in which totipotent cells generated during the first few cell divisions gradually become committed to particular lines of development. The mechanisms of this process are under intensive scrutiny and appear to be rooted in differential gene expression resulting from epigenetic modifications. It is in this context that we have been measuring RNA levels in single cells of cleaving embryos [18, 19] and it is to increase the reliability of these measurements that we have now developed the PurAmp method. This completely single-tube approach is easy to use, eliminates loss of material, and improves the quantitative accuracy of gene and gene expression studies.
First, cell lysis and protein denaturation occur very rapidly upon delivery of the sample to crystalline GITC, thus ensuring both protein removal from DNA and RNA and inactivation of cellular nuclease that would otherwise quickly degrade RNA . Transcripts localized in the nucleus, such as Xist RNA, are freed and made available to reverse transcription as well as cytoplasmic mRNA molecules, a result unattainable by mild detergent treatment that leaves nuclei intact . Second, the brief heating period after cell lysis enhances complete denaturation of proteins and also reduces the volume of the sample, thereby further increasing the guanidine concentration. The semi-dry sample can then be safely stored without risk of nuclease activity. Third, carrying out cell lysis in nanoliter volumes allows a manifold dilution of the chaotropic agent after addition of the RT cocktail, so that RT can be performed on the whole sample and in the same vessel in which it was collected without inhibition of the enzymatic activity. Finally, RT and PCR can be carried out immediately after cell lysis, rather than after cumbersome and lengthy nucleic acid preparation procedures, thereby further reducing the time required to process many samples, as well as the risk of contamination.
Individual blastomeres of pre-compaction mouse embryos are easily harvested due to their size, and laser zona drilling efficiently preserves RNA pools allowing dependable single-cell analysis . We thus used measurements of Xist and hsp70i RNA levels in single blastomeres to further validate the quantitative accuracy and reliability of the PurAmp method, as shown by the fact that transcript levels in individual cells are comparable to average RNA levels per cell calculated from whole embryos. Based on these results we anticipate that PurAmp will prove useful for quantification of RNA levels in small pieces of tissue from many sources, as well as single cells and even fractions of cells such as neuronal dendrites and axons . The small volume in which denaturation is carried out is also amenable to analysis of biological material isolated by laser capture microdissection or laser pressure catapulting .
Genomic DNA has recently been proposed as the optimal standard for gene expression studies  and it is the required internal standard when cDNA is quantified with the strategy of amplification competition . In this case, DNA and RNA are purified together, as in our experiments, and one set of primers is designed to co-amplify a genomic sequence that spans an intron as well as the corresponding intronless cDNA. The alternative strategy that we developed makes use of primer sets that do not span introns and therefore amplify genomic DNA sequences that have the same length and composition as their corresponding cDNA's, eliminating any possible difference in PCR efficiency for the two types of templates [[17–19]; C. Hartshorn, A. Anshelevich and L. J. Wangh, in preparation]. We have found it very informative to measure genomic DNA copy numbers in addition to RNA levels of the genes under study, because this strategy provides a reliable internal control for primer specificity and for nucleic acids recovery, particularly when performing single-cell analyses. In the case of early mouse embryos, detection of the Sry gene, which is not expressed at those stages, has also allowed us to identify the sex of each embryo.
The recovery and quantification of genomic DNA together with RNA has previously enabled us to establish genome number averages for developing embryos [17, 19]. While these numbers are very similar to the number of cells in early embryos, measurements of DNA copies are more accurate because they indicate whether the cells have completed S phase. Genome quantification becomes even more critical after the late 8-cell stage, because the embryos compact making it very difficult to count individual cells. Moreover, endoreduplication takes place in trophoblasts at the blastocyst stage, greatly increasing the number of genome copies present in those cells . All these factors render the counting of DNA copy numbers important if gene expression data are to be calculated on a per-genome basis, independently from a cell's ploidy.
A further reason to preserve DNA molecules in preparations for RT-PCR is that all DNase digestion protocols currently available lead to partial hydrolysis of RNA when the enzyme is heat-inactivated in the presence of divalent cations at the end of the reaction . We have consistently found a decrease in amplified cDNA in DNase-treated samples, particularly when performing RNA isolation with traditional methods (unpublished results), even when a chelating agent was added prior to the heating step. Incomplete RNA recovery after DNase inactivation in the presence of EDTA was not evident in past reports, due to the use of non-quantitative methods of nucleic acids analysis . Our real-time PCR results, however, agree with numerous more recent findings [see ref.  for an overview of DNase-related problems]. Efforts have been made, therefore, to devise alternative ways to eliminate the DNase once digestion has occurred. These methods, however, depend on removal of the enzyme which, in turn, implies manipulations such as phenol extraction that may still generate nucleic acids loss.
For all of the above reasons as well as the fact that we are working with very small amounts of material, we prefer single-tube preparation-to-amplification of both RNA and DNA templates, an approach made possible for the first time by the procedure described in this paper. Previously reported single-tube template preparation protocols, in fact, have been aimed at measuring only specific RNAs and employ lysis buffers containing low concentrations of the mild detergent NP-40 [25, 37], or they bypass the lysis step altogether and are limited to neuron studies . While these methods are valuable for detection of protein-free RNA molecules, they utilize non-denaturing conditions, as clearly demonstrated by the addition of proteic RNase inhibitors to the extraction buffers, and therefore preclude quantitative analysis of DNA  as well as of protein-bound RNA pools.
Due to its ability to thoroughly remove proteins from both RNA and DNA molecules in a rapid and simple way, PurAmp is suitable to a wide variety of applications, including gene expression quantification, studies on genetic mutations, and viral detection. Because the presence of DNA is undesirable for certain applications, such as microarray-based expression profiling, we have also shown that a DNase digestion step can be easily included in the single-tube format. We anticipate that treatment with other enzymes, such as cellulase in the case of plant cells, can similarly be inserted into the PurAmp protocol to digest other "undesired" components of particular cells prior to amplification. Thus, PurAmp is a very flexible technique that affords the investigator a variety of ways of processing the contents of a lysed sample with a heightened level of precision (Fig. 6).
Embryo culture and single blastomere isolation
For most experiments, frozen late 2-cell stage embryos (B6C3F1 females bred with B6D2F1 males) were obtained from Embryotech Laboratories, Inc. (Wilmington, MA), and were cultured as previously described  until the desired stage of development. For the DNase experiment, frozen 8-cell embryos obtained from the same source were grown to the morula stage. Blastocyst stage embryos used for hsp70i measurements were also grown from frozen 8-cell embryos.
Single blastomeres were isolated from either 4-cell embryos (for Xist measurements) or pre-compaction 8-cell embryos (for hsp70i measurements) after drilling the zona using a ZILOS-tk™ zona infrared laser optical system (beam = 1480 nm) (Hamilton Thorne Biosciences, Inc., Beverly, MA), according to a procedure developed in our laboratory and described elsewhere [18, 19].
PurAmp multiplex measurements of Xist/SryRNA + DNA in individual embryos or blastomeres
Dried droplets of denaturing solution, hereafter called "LysoDots", were prepared prior to embryo collection by delivering 20-nl aliquots of the denaturing solution (see below) to the inside surface of the lids of PCR-grade reaction tubes (Applied Biosystems, Foster City, CA). Precise measurement of the droplets size was obtained following the method previously described by Wangh . The denaturing solution composition was: 0.25% sarcosyl, 2 M GITC, 100 mM β-mercapto-ethanol, 0.01 M sodium citrate, pH 7.0 (all reagents from Stratagene, La Jolla, CA), 1% (vol/vol) dimethylsulfoxide (Sigma Chemical Company, St. Louis, MO). LysoDots were prepared in advance, allowed to dry under sterile conditions, and then stored at room temperature in closed PCR tubes.
Immediately before harvesting, individual embryos were placed in 3 ml of Dulbecco's PBS devoid of calcium and magnesium chloride . Dulbecco's PBS containing 0.4% polyvinyl pyrrolidone (both products from Sigma) was used when isolating single blastomeres . After one wash in the same buffer, each embryo or cell was aspirated into a glass capillary having an internal diameter of 0.2 mm  and tapered at the end so that the inner volume of the tapered tip would contain about 20 nl. Tapering was obtained by pulling the glass capillaries in a Micro-Pipette Puller (Industrial Science Associates, Inc., Ridgewood, NY). The embryo (or cell) was expelled directly onto the LysoDot in a volume of PBS as close as possible to 20 nl. Microscope observation revealed that the GITC crystals dissolved instantly upon addition of the sample-containing PBS and, thus, that cell lysis occurred immediately. Tubes were closed upside down and heated at 75–77°C for 5 minutes, after which their content was once again dry or semi-dry. The samples were then stored at -20°C until the next step.
In order to perform reverse transcription, each sample was carefully re-solubilized in the lid by addition of 6 μl of Random Hexamers mixture (4.2 ng/μl) in DEPC-treated water (all RT reagents were from a ThermoScript™ RT-PCR System kit, Invitrogen, Life Technologies, Carlsbad, CA). Tubes were closed, inverted, briefly centrifuged and incubated for 5 minutes at 65°C in order to allow primer/RNA hybridization. The remaining reagents needed for RT were then added to the tube in a volume of 4 μl, and the reaction was carried out according to the protocol suggested by the manufacturer. As previously described [17–19], all RT reagents were used at the suggested concentrations except for the absence of DTT, but volumes were halved so that each assay was performed in just 10 μl, which increased to 10.5 μl after RNase H digestion.
The full volume of each sample was then mixed with 89.5 μl of complete PCR amplification cocktail containing sequence-specific molecular beacons as detection probes . Multiplex real-time PCR of Xist and Sry genomic DNA + cDNA templates was thus performed in a final volume of 100 μl, as detailed elsewhere, in the presence of 4 units of Taq DNA polymerase (Promega, Madison, WI) [18, 19]. Real-time PCR was carried out in an ABI Prism® 7700 Sequence Detector (Applied Biosystems, Foster City, CA) and fluorescence readings were taken at the annealing temperature.
PurAmp assay for hsp70iRNA and DNA measurements in individual embryos or blastomeres
Embryos were heat-shocked at 43°C for 30 minutes, followed by a recovery period of 30–40 minutes (blastocysts), or 2–3 hours (8-cell embryos, as indicated) at 37°C. The hsp70i assay was carried out similarly to the one for the Xist/Sry multiplex, by sequential dilutions of denaturant, RT and PCR reagents. The procedure for collection and lysis of the samples was the same. Dry samples were re-solubilized with 6 μl of random decamer primers (8.3 μM) in nuclease-free water (all RT reagents were from a Cells-to-cDNA™ II kit, Ambion, Inc., Austin, TX). After a 3 minute incubation at 75°C to optimize primer binding to RNA, all other reagents needed for RT were added to the sample and the reaction was carried out according to the manufacturer's instructions. As for the Xist/Sry assay, all RT mixture components were used at the suggested concentrations, but volumes were halved so that RT was performed in a final volume of 10 μl. An RNase H digestion step was included at the end of RT, as in the case of the Xist/Sry assay.
Real-time PCR was carried out in a final volume of 100 μl, by adding the PCR reagents to the sample after completion of RNase H digestion. The chosen hsp70i primers were localized at positions 1245/1305 of the hsp70.1 GenBank sequence with accession number M35021 (5' CCGCCTACTTCAACGAC 3', upstream primer; 5' ATCCGCAGCACGTTTA 3', downstream primer) and were identical to sequences within the hsp70.3 gene, previously known as hsp70A1 (GenBank sequence with accession number M76613) . Because the hsp70i was the only amplicon generated in this assay, it was not necessary to design a sequence-specific detection probe. In this case, SYBR® Green, a fluorescent dye that binds to double-stranded DNA, was used as fluorescent probe for real-time PCR. The specificity and purity of the amplicon was confirmed by both gel electrophoresis and analysis of the melt profile, as previously described . The composition of the cocktail for hsp70i PCR was the following: 50 mM Tris, pH 8.3, 3 mM MgCl2, 0.3 μM each primer, 0.25 mM each dNTP, 1:62,500 SYBR Green (from a "10,000X concentrate in DMSO" purchased from FMC BioProducts, Rockland, ME), and 4 units of Taq DNA polymerase (Promega, Madison, WI). The polymerase was incubated at a 1:1 (v/v) ratio with Platinum® Taq antibody (Invitrogen) for 5 minutes before addition to the reaction mixture (hotstart PCR). The cycling profile was: 95°C for 5 minutes; 10 cycles consisting of the following four steps: 95°C (20 sec), 64°C (30 sec), 72°C (30 sec), 84°C (15 sec); 35 cycles with the following four steps: 95°C (20 sec), 59°C (30 sec), 72°C (30 sec), 84°C (15 sec). Fluorescence readings were acquired at 84°C, in order to exclude fluorescent signals due to the possible formation of primer dimers late in the reaction.
A number of embryos were also processed as "No RT" controls, with the same protocol used for the other samples but without inclusion of reverse transcriptase in the RT mixture. These controls were used to quantify hsp70i genomic DNA copy numbers in the absence of cDNA .
Multistep/multitube nucleic acid extraction
For the preliminary studies on hsp70i expression in blastocysts, some of the embryos were processed using a commercially available multistep/multitube kit, as previously described . Briefly, nucleic acids (DNA and RNA) from each sample were purified using phenol:chloroform:isoamyl alcohol phase separation (Micro RNA Isolation Kit, Stratagene, La Jolla, CA) with a ratio of 100 μl of phenol and 45 μl of chloroform/isoamyl alcohol solution per assay. Transfer RNA (10 μg/assay; Sigma Chemical Company, St. Louis, MO) was added as a co-precipitant. Pellets were washed twice, once in isopropanol followed by overnight precipitation at -20°C and once in 75% ethanol, and then nucleic acids were reverse transcribed and analyzed by real-time PCR exactly as detailed above for the PurAmp-treated samples.
Quantification of Xist, Sry and hsp70iamplicons
Calculation of template copy numbers was based on the "threshold cycle" (CT) at which each fluorescent signal was first detected above background. CT values were compared to standard scales obtained from analysis of male mouse genomes at known copy numbers, as detailed previously [17–19] and further exemplified in the Result section. Briefly, a two-fold difference in the number of templates amplified results in a shift of one cycle between two CT determinations. A lower CT value indicates an earlier detection of the fluorescent signal and therefore more templates present at the start of the reaction [reviewed in ref. ]. One male mouse genome contains one copy of Sry (Y-chromosome), one copy of Xist (X-chromosome) and four copies of hsp70i (two of hsp70.1 and two of hsp70.3, both on chromosome 17).
Insertion of a DNase I digestion step within the Xist/SryPurAmp protocol
Embryos were grown to the morula stage and were individually harvested and lysed as detailed above. Controls were processed for multiplex detection of Xist/Sry with the described PurAmp protocol. RNA-only samples were prepared by inserting a DNase digestion step prior to RT, as follows. Lysed, dried samples were re-suspended with 4 μl of DNase mixture containing: 20 mM Tris-HCl, pH 8.4; 2 mM MgCl2, 50 mM KCl (Invitrogen's DNase I Reaction Buffer) and 1 unit of DNase I (Ambion) in nuclease-free water. After an incubation of 20 minutes at room temperature, the reaction was terminated by adding 1 μl of a 10 mM EDTA solution, pH 8.0 (Invitrogen). The nuclease was inactivated by heating the samples at 65°C for 10 minutes, according to the protocol recommended by Invitrogen. One μl of a 25 ng/μl RT primer solution was then added to the sample, so that the final primer concentration was now the same as in the assay without DNase (see above). RT and PCR were then carried out as detailed for the "No DNase" assay.
This work was funded by Brandeis University.
- Bustin SA: Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol. 2002, 29: 23-39. 10.1677/jme.0.0290023.View ArticleGoogle Scholar
- Fiorenza MT, Mangia F: Quantitative RT-PCR amplification of RNA in single mouse oocytes and preimplantation embryos. Biotechniques. 1998, 24: 618-623.Google Scholar
- Olmos A, Cambra M, Esteban O, Gorris MT, Terrada E: New device and method for capture, reverse transcription and nested PCR in a single closed-tube. Nucleic Acids Res. 1999, 27: 1564-1565. 10.1093/nar/27.6.1564.View ArticleGoogle Scholar
- Yan L, Kaczorowski G, Kohler M: One-tube protocol for single-cell reverse transcriptase-polymerase chain reaction. Anal Biochem. 2002, 304: 267-270. 10.1006/abio.2002.5623.View ArticleGoogle Scholar
- Callahan JD, Brown F, Osorio FA, Sur JH, Kramer E, Long GW, Lubroth J, Ellis SJ, Shoulars KS, Gaffney KL, Rock DL, Nelson WM: Use of a portable real-time reverse transcriptase-polymerase chain reaction assay for rapid detection of foot-and-mouth disease virus. J Am Vet Med Assoc. 2002, 220: 1636-1642.View ArticleGoogle Scholar
- Pierce KE, Rice JE, Sanchez JA, Wangh LJ: QuantiLyse™: reliable DNA amplification from single cells. Biotechniques. 2002, 32: 1106-1111.Google Scholar
- Eigner J, Boedtker H, Michaels G: The thermal degradation of nucleic acids. Biochim Biophys Acta. 1961, 51: 165-168. 10.1016/0006-3002(61)91028-9.View ArticleGoogle Scholar
- Chirgwin JM, Przybyla AE, MacDonald RJ, Rutter WJ: Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry. 1979, 18: 5294-5299.View ArticleGoogle Scholar
- Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987, 162: 156-159. 10.1016/0003-2697(87)90021-2.View ArticleGoogle Scholar
- Konomi N, Lebwohl E, Zhang D: Comparison of DNA and RNA extraction methods for mummified tissues. Mol Cell Probes. 2002, 16: 445-451. 10.1006/mcpr.2002.0441.View ArticleGoogle Scholar
- Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnaud D, Capra V, Grompe M, Pizzuti A, Muzny D, Lawrence C, Willard HF, Avner P, Ballabio A: Characterization of a murine gene expressed from the inactive X chromosome. Nature. 1991, 351: 325-329. 10.1038/351325a0.View ArticleGoogle Scholar
- Brockdorff N, Ashworth A, Kay GF, Cooper P, Smith S, McCabe VM, Norris DP, Penny GD, Patel D, Rastan S: Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature. 1991, 351: 329-331. 10.1038/351329a0.View ArticleGoogle Scholar
- Kay GF, Penny GD, Patel D, Ashworth A, Brockdorff N, Rastan S: Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell. 1993, 72: 171-182. 10.1016/0092-8674(93)90658-D.View ArticleGoogle Scholar
- Christians E, Michel E, Renard JP: Developmental control of heat shock and chaperone gene expression. Hsp 70 genes and heat shock factors during preimplantation phase of mouse development. Cell Mol Life Sci. 1997, 53: 168-178.View ArticleGoogle Scholar
- Huang L, Mivechi NF, Moskophidis D: Insights into regulation and function of the major stress-induced hsp70 molecular chaperone in vivo: analysis of mice with targeted gene disruption of the hsp70.1 or hsp70.3 gene. Mol Cell Biol. 2001, 21: 8575-8591. 10.1128/MCB.21.24.8575-8591.2001.View ArticleGoogle Scholar
- Sheardown SA, Duthie SM, Johnston CM, Newall AE, Formstone EJ, Arkell RM, Nesterova TB, Alghisi GC, Rastan S, Brockdorff N: Stabilization of Xist RNA mediates initiation of X chromosome inactivation. Cell. 1997, 91: 99-107. 10.1016/S0092-8674(01)80012-X.View ArticleGoogle Scholar
- Hartshorn C, Rice JE, Wangh LJ: Developmentally-regulated changes of Xist RNA levels in single preimplantation mouse embryos, as revealed by quantitative real-time PCR. Mol Reprod Dev. 2002, 61: 425-436. 10.1002/mrd.10037.View ArticleGoogle Scholar
- Hartshorn C, Rice JE, Wangh LJ: Differential pattern of Xist RNA accumulation in single blastomeres isolated from 8-cell stage mouse embryos following laser zona drilling. Mol Reprod Dev. 2003, 64: 41-51. 10.1002/mrd.10223.View ArticleGoogle Scholar
- Hartshorn C, Rice JE, Wangh LJ: Optimized real-time RT-PCR for quantitative measurements of DNA and RNA in single embryos and blastomeres. A-Z of Quantitative PCR. Edited by: Bustin SA. 2004, La Jolla: International University Line, 675-702. [IUL Biotechnology series, vol. 5]Google Scholar
- Koopman P: Sry and Sox9: mammalian testis-determining genes. Cell Mol Life Sci. 1999, 55: 839-856. 10.1007/s000180050338.Google Scholar
- Edgar BA, Orr-Weaver TL: Endoreplication cell cycles: more for less. Cell. 2001, 105: 297-306. 10.1016/S0092-8674(01)00334-8.View ArticleGoogle Scholar
- Graham CF, Lehtonen E: Formation and consequences of cell patterns in preimplantation mouse development. J Embryol Exp Morphol. 1979, 49: 277-294.Google Scholar
- Zuccotti M, Boiani M, Ponce R, Guizzardi S, Scandroglio R, Garagna S, Redi CA: Mouse Xist expression begins at zygotic genome activation and is timed by a zygotic clock. Mol Reprod Dev. 2002, 61: 14-20.View ArticleGoogle Scholar
- Christians E, Campion E, Thompson EM, Renard JP: Expression of the HSP 70.1 gene, a landmark of early zygotic activity in the mouse embryo, is restricted to the first burst of transcription. Development. 1995, 121: 113-122.Google Scholar
- Dixon AK, Richardson PJ, Lee K, Carter NP, Freeman TC: Expression profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Res. 1998, 26: 4426-4431. 10.1093/nar/26.19.4426.View ArticleGoogle Scholar
- Dixon AK, Lee K, Richardson PJ, Bell MI, Skynner MJ: Single cell expression analysis – pharmacogenomic potential. Pharmacogenomics. 2002, 3: 809-822. 10.1517/146224126.96.36.1999.View ArticleGoogle Scholar
- Levsky JM, Singer RH: Gene expression and the myth of the average cell. Trends Cell Biol. 2003, 13: 4-6. 10.1016/S0962-8924(02)00002-8.View ArticleGoogle Scholar
- Brockdorff N: X-chromosome inactivation: closing in on proteins that bind Xist RNA. Trends Genet. 2002, 18: 352-358. 10.1016/S0168-9525(02)02717-8.View ArticleGoogle Scholar
- Helbig R, Fackelmayer FO: Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain. Chromosoma. 2003, 112: 173-82. 10.1007/s00412-003-0258-0.View ArticleGoogle Scholar
- Steward O, Schuman EM: Compartmentalized synthesis and degradation of proteins in neurons. Neuron. 2003, 40: 347-359. 10.1016/S0896-6273(03)00635-4.View ArticleGoogle Scholar
- Fink L, Seeger W, Ermert L, Hanze J, Stahl U, Grimminger F, Kummer W, Bohle RM: Real-time quantitative RT-PCR after laser-assisted cell picking. Nat Med. 1998, 4: 1329-1333. 10.1038/3327.View ArticleGoogle Scholar
- Talaat AM, Howard ST, Hale W, Lyons R, Garner H, Johnston SA: Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res. 2002, 30: e104-10.1093/nar/gnf103.View ArticleGoogle Scholar
- Gerdes JC, Marmaro JM: Quantitation of RNA transcripts using genomic DNA as the internal amplification competitor. United States Patent 6,258,543. 2001Google Scholar
- Bickler SW, Heinrich MC, Bagby GC: Magnesium-dependent thermostability of DNase I. Biotechniques. 1992, 13: 64-66.Google Scholar
- Wiame I, Remy S, Swennen R, Sagi L: Irreversible heat inactivation of DNase I without RNA degradation. Biotechniques. 2000, 29: 252-256.Google Scholar
- Getting Rid of Contaminating DNA and the DNase Used to Destroy it. [http://www.ambion.com/techlib/tn/83/836.html]
- Tietjen I, Rihel JM, Cao Y, Koentges G, Zakhary L, Dulac C: Single-cell transcriptional analysis of neuronal progenitors. Neuron. 2003, 38: 161-175. 10.1016/S0896-6273(03)00229-0.View ArticleGoogle Scholar
- Lambolez B, Audinat E, Bochet P, Crepel F, Rossier J: AMPA receptor subunits expressed by single Purkinje cells. Neuron. 1992, 9: 247-58. 10.1016/0896-6273(92)90164-9.View ArticleGoogle Scholar
- Wangh LJ: Injection of Xenopus eggs before activation, achieved by control of extracellular factors, improves plasmid DNA replication after activation. J Cell Sci. 1989, 93: 1-8.Google Scholar
- Tyagi S, Kramer FR: Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996, 14: 303-308. 10.1038/nbt0396-303.View ArticleGoogle Scholar
- Walker NJ: A technique whose time has come. Science. 2002, 296: 557-559. 10.1126/science.296.5567.557.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.