analysis ofthe c-value paradoxbymolecular hybridization

5
Proc. Nat. Acad. Sci. USA Vol. 71, No. 9, pp. 3746-3750, September 1974 Analysis of the C-Value Paradox by Molecular Hybridization (complementary DNA/reiteration frequency/Amphibia) MICHAEL ROSBASH*t, PETER J. FORDt, AND JOHN 0. BISHOP* * Institute of Animal Genetics, and t Department of Molecular Biology, King's Buildings, University of Edinburgh, Edinburgh EH9 3JN, Scotland Communicated by Roy J. Britten, July 10, 1974 ABSTRACT Poly(A)-containing RNA was isolated from ovaries of Xenopus laevis laevis and Triturus cristatus car- nifex and used as a template for the synthesis of radioactive complementary DNA with RNA-dependent DNA polymer- ase. When annealed with an excess of homologous DNA, the complementary DNA is rendered double-stranded with kinetics that suggest that the coding sequences are single- copy in both these organisms. In Triturus, these sequences are distinct from the majority of the genome, which con- sists of repeated sequences, and distinct from the ribo- somal cistrons, which are present in proportion to the in- crease in C-value relative to the Xenopus genome. More- over, the number of different poly(A)-containing molecules in the ovary (sequence complexity) is the same in Xenopus and in Triturus. There exists an enormous variation in C-value (DNA content per haploid genome) among eukaryotic organisms (1). Even within a single class of organisms, large differences have been detected. These are most striking in the class Amphibia, in which C-values vary by two orders of magnitude (2). In particular, the Urodeles contain large amounts of DNA per haploid genome, e.g., Triturus crustatus carnifex has about 21 pg while Amphiuma and Necturus contain more than 100 pg of DNA per haploid genome (2). These values can be contrasted with Xenopus laevis laevis and most mammals, which have about 3 pg of DNA per haploid genome (3, 4). On the basis of this range of DNA values and cytological evidence from various sources, Callan proposed that chromo- somal DNA, and in particular genetically significant DNA, is arranged in tandemly repeated sequences (5). These repeated sequences consist of a "master" sequence and "slave" se- quences; the "master" sequence would be subject to muta- tional and recombinational events while the "slave" sequences would be corrected once per life-cycle to reflect the sequence of the "master" sequence. The formation of extended lampbrush loops during meiotic prophase was proposed as the stage at which this correction process takes place. In order to test this proposal, and in order to understand the organization of the eukaryotic genome in Urodeles of high C-value, we have examined the reiteration frequency of DNA sequences complementary to poly(A)-containing RNA iso- lated from ovaries of Triturus cristatus carnifex. This fraction of the cellular RNA, assumed to be enriched for coding se- quences, was transcribed with RNA-dependent DNA poly- merase to make a radioactive DNA copy. This cDNA was Abbreviations: cDNA, complementary DNA; phosphate buffer, equimolar Na2HPO4 and NaH2PO4; Cot, product of DNA concen- tration and time in mol-sec/liter. t Present address: Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Mass. 02154. 3746 annealed with an excess of unlabeled Triturus DNA in order to measure the reiteration frequency of the fraction of the genome corresponding to these sequences (6). The data, when compared to identical experiments performed on material from Xenopus taevis, strongly suggest that the coding sequences in Triturus occur once per haploid genome (single-copy), in con- trast to the greater part of Triturus DNA. Moreover, kinetic experiments indicate that the number of different poly(A)-con- taining molecules present in the ovary (sequence complexity) is very similar, if not identical, in Triturus and Xenopus. MATERIALS AND METHODS Xenopus laevis laevis were obtained from the South African Snake Farm, Fish Hoek, South Africa, and Triturus cristatus carnifex from Haig and Co., U.K. Ovaries were removed and washed in Barth X medium. Nucleic acid was prepared by the method of Kirby, with the addition of 0.5% sodium lauryl sulfate to the aqueous phase, as described (7). High- molecular-weight RNA was prepared by homogenizing the pelleted nucleic acid in 3 M NaOAc (pH 6) to solubilize DNA, transfer RNA, and 5S RNA (8). The RNA precipitate was resuspended in "binding" buffer [0.4 M NaCl, 1 mM EDTA, 0.1% sodium lauryl sulfate, 10 mM Tris * HCl (pH 7.4), 10% glycerol] and passed over oligo(dT)-cellulose (9). The poly- (A)-containing RNA was eluted in "elution" buffer [10 mM Tris * HCl pH 7.4, 0.1 % sodium lauryl sulfate], and the RNA spectrum was measured in the Unicam SP800A spectro- photometer. The amount of poly(A) in this eluate was rou- tinely assayed by hybridization with radioactive poly(U), as described (7). By comparing the amount of poly(A) with the total RNA bound by the column, it was estimated that the eluted RNA contained 20-50% ribosomal RNA. This was verified by sucrose gradient sedimentation of the RNA. RNA was precipitated and resuspended three times to remove sodium lauryl sulfate, and finally resuspended at a final con- centration of 0.4 mg/ml in distilled H20 and stored at -20° . DNA was purified as described from Xenopus erythrocytes and from Triturus erythrocytes, liver, and sperm (10). The DNA was sonicated in 15 mM NaCl-1.5 mM sodium citrate or sheared in a Sorvall French Press at 50,000 lbs./inch2 at 10- 150 and passed over a Sephadex SP-50-Chelex-100 column developed with 0.3 M NaCl-0.01 M NaOAc (pH 5). DNA prepared in this way was 450-550 nucleotides long if sonicated and 300(400 nucleotides long if sheared, as measured by the method of Studier in an analytical ultracentrifuge (11). RESULTS The reassociation of Triturus and Xenopus DNA was analyzed optically under standard conditions (Fig. 1). About 75% of Downloaded by guest on November 26, 2021

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Page 1: Analysis ofthe C-Value ParadoxbyMolecular Hybridization

Proc. Nat. Acad. Sci. USAVol. 71, No. 9, pp. 3746-3750, September 1974

Analysis of the C-Value Paradox by Molecular Hybridization(complementary DNA/reiteration frequency/Amphibia)

MICHAEL ROSBASH*t, PETER J. FORDt, AND JOHN 0. BISHOP*

* Institute of Animal Genetics, and t Department of Molecular Biology, King's Buildings, University of Edinburgh,Edinburgh EH9 3JN, Scotland

Communicated by Roy J. Britten, July 10, 1974

ABSTRACT Poly(A)-containing RNA was isolated fromovaries ofXenopus laevis laevis and Triturus cristatus car-nifex and used as a template for the synthesis ofradioactivecomplementary DNA with RNA-dependent DNA polymer-ase. When annealed with an excess ofhomologous DNA, thecomplementary DNA is rendered double-stranded withkinetics that suggest that the coding sequences are single-copy in both these organisms. In Triturus, these sequencesare distinct from the majority of the genome, which con-sists of repeated sequences, and distinct from the ribo-somal cistrons, which are present in proportion to the in-crease in C-value relative to the Xenopus genome. More-over, the number of different poly(A)-containing moleculesin the ovary (sequence complexity) is the same in Xenopusand in Triturus.

There exists an enormous variation in C-value (DNA content

per haploid genome) among eukaryotic organisms (1). Evenwithin a single class of organisms, large differences have beendetected. These are most striking in the class Amphibia, inwhich C-values vary by two orders of magnitude (2). Inparticular, the Urodeles contain large amounts of DNA per

haploid genome, e.g., Triturus crustatus carnifex has about 21pg while Amphiuma and Necturus contain more than 100 pg ofDNA per haploid genome (2). These values can be contrastedwith Xenopus laevis laevis and most mammals, which haveabout 3 pg of DNA per haploid genome (3, 4).On the basis of this range of DNA values and cytological

evidence from various sources, Callan proposed that chromo-somal DNA, and in particular genetically significant DNA, isarranged in tandemly repeated sequences (5). These repeatedsequences consist of a "master" sequence and "slave" se-

quences; the "master" sequence would be subject to muta-tional and recombinational events while the "slave" sequences

would be corrected once per life-cycle to reflect the sequence ofthe "master" sequence. The formation of extended lampbrushloops during meiotic prophase was proposed as the stage atwhich this correction process takes place.

In order to test this proposal, and in order to understandthe organization of the eukaryotic genome in Urodeles of highC-value, we have examined the reiteration frequency of DNAsequences complementary to poly(A)-containing RNA iso-lated from ovaries of Triturus cristatus carnifex. This fractionof the cellular RNA, assumed to be enriched for coding se-

quences, was transcribed with RNA-dependent DNA poly-merase to make a radioactive DNA copy. This cDNA was

Abbreviations: cDNA, complementary DNA; phosphate buffer,equimolar Na2HPO4 and NaH2PO4; Cot, product of DNA concen-

tration and time in mol-sec/liter.

t Present address: Rosenstiel Basic Medical Sciences Research

Center, Brandeis University, Waltham, Mass. 02154.

3746

annealed with an excess of unlabeled Triturus DNA in orderto measure the reiteration frequency of the fraction of thegenome corresponding to these sequences (6). The data, whencompared to identical experiments performed on material fromXenopus taevis, strongly suggest that the coding sequences inTriturus occur once per haploid genome (single-copy), in con-trast to the greater part of Triturus DNA. Moreover, kineticexperiments indicate that the number of different poly(A)-con-taining molecules present in the ovary (sequence complexity)is very similar, if not identical, in Triturus and Xenopus.

MATERIALS AND METHODS

Xenopus laevis laevis were obtained from the South AfricanSnake Farm, Fish Hoek, South Africa, and Triturus cristatuscarnifex from Haig and Co., U.K. Ovaries were removed andwashed in Barth X medium. Nucleic acid was prepared bythe method of Kirby, with the addition of 0.5% sodiumlauryl sulfate to the aqueous phase, as described (7). High-molecular-weight RNA was prepared by homogenizing thepelleted nucleic acid in 3 M NaOAc (pH 6) to solubilize DNA,transfer RNA, and 5S RNA (8). The RNA precipitate was

resuspended in "binding" buffer [0.4 M NaCl, 1 mM EDTA,0.1% sodium lauryl sulfate, 10 mM Tris * HCl (pH 7.4), 10%glycerol] and passed over oligo(dT)-cellulose (9). The poly-(A)-containing RNA was eluted in "elution" buffer [10 mMTris * HCl pH 7.4, 0.1% sodium lauryl sulfate], and the RNAspectrum was measured in the Unicam SP800A spectro-photometer. The amount of poly(A) in this eluate was rou-

tinely assayed by hybridization with radioactive poly(U), as

described (7). By comparing the amount of poly(A) with thetotal RNA bound by the column, it was estimated that theeluted RNA contained 20-50% ribosomal RNA. This was

verified by sucrose gradient sedimentation of the RNA. RNAwas precipitated and resuspended three times to remove

sodium lauryl sulfate, and finally resuspended at a final con-

centration of 0.4 mg/ml in distilled H20 and stored at -20° .DNA was purified as described from Xenopus erythrocytes

and from Triturus erythrocytes, liver, and sperm (10). TheDNA was sonicated in 15mM NaCl-1.5mM sodium citrate or

sheared in a Sorvall French Press at 50,000 lbs./inch2 at 10-150 and passed over a Sephadex SP-50-Chelex-100 columndeveloped with 0.3 M NaCl-0.01 M NaOAc (pH 5). DNAprepared in this way was 450-550 nucleotides long if sonicatedand 300(400 nucleotides long if sheared, as measured by themethod of Studier in an analytical ultracentrifuge (11).

RESULTS

The reassociation of Triturus and Xenopus DNA was analyzedoptically under standard conditions (Fig. 1). About 75% of

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Proc. Nat. Acad. Sci. USA 71 (1974)

2 3 4

FIG. 1. Optical renaturation of Xenopus and Triturus DNA.Denatured DNA was annealed in 0.30 M NaCl-0.030 M sodiumcitrate at 700. At various Cot values, aliquots were removed andquenched in ice-cold 15 mM NaCl-1.5 mM sodium citrate. Theabsorbance was monitored at 500 and 900 as described (12, 13).A complete gain of initial hypochromism was defined as 35%(100% duplex). All DNA samples were sheared. The arrows in-dicate the expected range of C ti/, (3500-7000) of single-copyTriturus DNA. *, Xenopua; 0, Tr*uru8.

the Xenropus genome reassociates with a Cot,/, of between500 and 1000 in 0.24 phosphate buffer M. Under identicalconditions, single-copy Triturus DNA (with C-value seven

times that of Xenopus) should reassociate at a rate seven timesslower than Xenopus, or with a Cot,/, of between 3500 and7000. These values are indicated by the arrows in Fig. 1.There is relatively little detectable single-copy DNA in theTriturus genome; most of the Triturus DNA is present as

repeated DNA. Moreover, there is no discrete class of repeti-

80-

x 60. o,-°

ae a///

40~~~~~~~

20

0 co0 1 2 3

Cot

FIG. 2. DNA excess hybridization with ribosomal RNA. 18Sribosomal ["2P]RNA was prepared by standard procedures (7).Briefly, Xenopus kwvis kidney cells were incubated for 3 days in1/3 normal concentration of phosphate, with 0.2 mCi/ml of 32P(carrier-free, Amersham). RNA was prepared and passed over

oligo(dT)-cellulose to remove poly(A)-containing sequences.The 18S region from a sucrose gradient was pooled, precipitated,and repurified by acrylamide gel electrophoresis. The 18S peakwas eluted, precipitated, and suspended in distilled H2O. Thespecific activity was 0.5 X 106 cpm/pg. DNA excess hybridizationwas performed as described (12) with a DNA/RNA ratio in excess

of 3 X 104 (DNA > 3 mg/ml; RNA = 0.1 ug/ml). Aliquotswere removed at the indicated Cot values and assayed for the per-

centage of RNase-resistant "2P as described (12). The arrow indi-cates the Cot,/, = 6. 0, Xenopus; 0, Triturus.

fraction no.

FIG. 3. Alkaline sucrose gradient sedimentation of DNA.Complementary DNA was synthesized using poly(A)-containingRNA from Xenopus and Triturus ovaries as template RNA. Thecomplete reaction mixture and methods of synthesis and purifica-tion were as described (6), except that the RNA-dependent DNApolymerase was purified through the carboxymethyl-Sephadexstep (16), the substrate was ['H]dCTP (13.3 Ci/mmole, Amer-sham), and 100 Mg/ml of actinomycin D was present (17). Soni-cated DNA and [3H]cDNA were resuspended in 0.25 ml of 0.1 MNaOH, 0.5% sodium lauryl sulfate and sedimented in a 5-20%sucrose gradient (0.1 M NaOH, 0.5% sodium lauryl sulfate) at38,000 rpm for 15.5 hr in a Spinco SW 41 swinging-bucket rotor,at 250. Fractions were collected .and the absorbance was moni-tored. Radioactivity'was assayed by the addition of 3 ml of Insta-gel (Packard) to each 0.45-ml fraction. A 500-nucleotide-long"P-labeled marker (gift of Dr. E. Southern) was included in thegradients and sedimented coincident with the absorbance peak inboth cases. (A) Xenopus; (B) Triturus. Broken line, 3H; solid line,Ace.s

tion frequencies. This is in agreement with the report ofStraus (31), which presented similar data on DNA fromvarious other Urodeles, as analyzed with hydroxyapatite.

In principle, a small amount of radioactive nucleic acidadded to a vast excess of nonradioactive DNA can be used as

a tracer in order to follow the reassociation of the portion ofthe genome complementary to the radioactive sequences (13,14). The kinetics of this reassociation can be used to estimatethe reiteration frequency of this subset of the genome. In Fig.2, Xenopus ribosomal [2P]RNA is hybridized in-vast DNAexcess to both Xenopus and Triturus DNA. Despite the 7-folddifference in C-value, the Cott/,, and therefore the kinetics ofhybridization, of the two reactions is very similar. EachTriturus genome, therefore, has about seven times as manyribosomal cistrons as Xenopus. This is in good agreement witha published report in which the number of ribosomal genes inthese two organisms was measured by RNA excess filter hy-bridization (15).DNA complementary to total ovary poly(A)-containing

RNA was used in order to measure the reassociation kineticsof a fraction of the DNA that acts as a template for informa-tional RNA transcription. Poly(A)-containing RNA was iso-lated from ovaries of both Xenopus and Triturus. In thepresence of the primer (pT)lo, this RNA fraction is a goodtemplate for RNA-dependent DNA polymerase. The size ofcDNA was analyzed on alkaline sucrose gradients; XenopuscDNA and Triturus cDNA had S-values of 6.5 and 7.3 or

weight-average sizes of about 500 nucleotides and 600 nu-

cleotides, respectively (Fig. 3).

60xa,

e40

20k

.A.0

i ,~~~~~~~~~., I

-2 -1 1log Cot

C-Value Paradox 3747

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3748 Cell Biology: Rosbash et al.

xt

Q

log Cot

FIG. 4. Renaturation experiments with an excess of unlabeledDNA. DNA renaturation was performed as described (13) with0.24 M phosphate-EDTA (equimolar Na-phosphate buffer with 1mM EDTA) at 700. DNA concentration was greater than 10

mg/ml, and the DNA to cDNA ratio was at least 3 X 10'. Sam-ples were diluted to 0.12 M phosphate buffer. Fractionation on

hydroxyapatite was as described (6). Fractionation with nucleaseS1 (18) was as follows: Samples were diluted to a final DNAconcentration of 250-300 ,ug/ml in a solution with the final com-position: 48 mM phosphate buffer, 0.2 mM EDTA, 20 mMNaCl, 30 mM NaOAc (pH 4.5), 0.6 mM ZnSO4, 52 mM aceticacid. Samples were divided into two aliquots, one of which was

treated with nuclease S1. Both aliquots were incubated at 500for 40 min, precipitated with trichloroacetic acid, filtered, andcounted in toluene-based scintillant as described (13). The per-

centage of cDNA scored as double-stranded at Cot = -o was

subtracted from all subsequent values in each experiment. Thearrows indicate the average displacement of the curves. (A)Hydroxyapatite: 0, Xenopus, experiment 1, background =

11.5%; A, Xenopus, experiment 2, background = 8%; 0, Triturusexperiment 1, background = 17%; A, Triturus, experiment 2,background = 8%. (B) Nuclease: *, Xenopus, experiment 1,background = 8%; A, Xenopus, experiment 2, background =

11%; 0, Triturus, experiment 1, background = 7%.

This cDNA was used as a radioactive tracer and annealedwith an excess of homologous DNA (Fig. 4). As analyzed on

hydroxyapatite (Fig. 4A), the Xenopus DNA complementaryto this radioactive cDNA appears to renature with second-order kinetics. The Cot'/2 was about 200 to 400 under theseconditions, faster than the single copy (final) transition oftotal Xenopus DNA (Fig. 1). This difference may be due tothe difference between an optical assay and an assay withhydroxyapatite. Alternatively, it may be due to. the presence

of a small repetitive component or the lack of precise terminalvalues. There is relatively little (<15%) renaturation ofXenopus cDNA at low Cot. Therefore, it appears likely thatmost of the cDNA is complementary to single-copy DNA.Triturus cDNA, when renatured in the presence of a vastexcess of Triturus DNA, also renatures with second-orderkinetics but five to eight times slower than Xenopus DNA. InTriturus as in Xenopus, there is little highly repetitive DNAcomplementary to the cDNA (<10% at Cot 100) .

The same reassociation experiments were analyzed withsingle-strand-specific nuclease S1 (Fig. 4B). The XenopuscDNA reassociates at a rate two to three times slower thanwhen assayed by hydroxyapatite. This difference is mostlikely a result of the fact that an assay with hydroxyapatiteregisters single-stranded regions adjacent to reassociatedDNA as duplex, while an assay with nuclease S1 does not.Triturus cDNA begins to reassociate in such a way as to sug-

100 *-

80-

0 60-

40-

20-

60 70 80

temp(0C)

FIG. 5. Thermal stability of cDNA* DNA duplex. Xenopusand Triturus cDNA were renatured in the presence of a vast excess

of homologous cellular DNA to a Cot of 7500 under conditionsgiven in the legend of Fig. 3. The two samples were diluted to 12mM phosphate buffer and divided into 16 aliquots. Duplicatesamples were placed at the indicated temperatures for 5 min,chilled, and assayed with hydroxyapatite as in the legend of Fig. 4.The control values correspond to 77% duplex for Xenopus and53% duplex for Triturus. *, Xenopus; 0, Triturus.

gest a 10-fold slower rate than Xenopus cDNA. The kineticdata strongly suggest that the sequences complementary tothe Triturus cDNA are present once, or at most twice, per

genome.

The effect of base mismatching on the rate of renaturationis relatively small (19). Nevertheless, were the TrituruscDNA DNA duplexes considerably mismatched, this wouldlower the rate of reassociation and therefore lower the ap-

parent reiteration frequency of these sequences. In order totest this possibility, the cDNA DNA duplexes were melted(Fig. 5). The Tm values of the complexes from both organismswere the same (65.5 + 0.50). The same Tm was obtained whenthe assay was performed with nuclease S1 instead of hydroxy-apatite (data not shown). Triturus DNA has a Tm 10 greaterthan Xenopus DNA (unpublished results). The similarity ofthe Tm values of the two cDNA DNA complexes suggeststhat mismatching of a magnitude sufficient to noticeablyaffect the rate of duplex formation is unlikely.cDNA, transcribed from poly(A)-containing RNA, can be

hybridized to its original template in RNA excess. If a largeexcess of RNA is used, the reaction is pseudo-first order andthe rate is RNA-dependent. Consequently, the first-order rate

constant (or constants) is interpretable in terms of the se-

quence complexity of the RNA in the reaction. To examine

the relative sequence complexity of the two ovary poly(A)-containing RNA populations, each cDNA population was

hybridized to its template, in RNA excess (Fig. 6). In both

cases, the hybridization takes place with similar, and perhapsidentical, kinetics. The data indicate that the sequence com-

plexity of the poly(A)-containing RNA is very similar in the

two cases.

The abscissa of Fig. 6 is proportional to Rot, where Ro is the

initial concentration of RNA based on the measured concen-

tration of poly(A). Since the cDNA is only 500-600 nucleo-tides long (on average) and its synthesis is completely depen-dent on priming by (pT)lo, it is likely that it represents limited

synthesis from the 3'-end of the poly(A)-containing RNA.

The number of potentially reactive RNA molecules should,

therefore, be proportional to the number of poly(A) termini

and not necessarily to the absolute concentration of poly(A)-containing RNA. Provided that the size of the average poly(A)

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Proc. Nat. Acad. Sci. USA 71 (1974)

80[

x 60IV

8e40

20

8

C. 6

xE0 4

2

- -0.5 0 1 2 3 4log time (min)

FIG. 6. Hybridization between cDNA and its template RNA.All four experiments were plotted on an equivalent time axis cor-responding to a poly(A) concentration of 5.45 gg/ml, which isequivalent to about 109 gg of poly(A)-containing RNA per ml.Samples were incubated at 700 in 0.24 M phosphate-EDTA.Poly(A)containing RNA concentration was measured by hybrid-ization with radioactive poly(U), as described in the text. cDNAwas present at a concentration of 1.8 X 10-2 pg/ml. At the indi-cated (equivalent) times, aliquots were removed from the incuba-tion and challenged with nuclease S1 in the presence of 50 ,g/mlof denatured Escherichia coli DNA, as in the legend of Fig. 4.Xenopus: *, exp. 1; A, exp. 2. Triturus: 0, exp. 1; A, exp 2.

segment is the same in the poly(A)-containing RNA of bothXenopus and Triturus, the concentration of RNA sequencescomplementary to cDNA will be proportional to the concen-tration of poly(A). The sizes of the poly(A) sequences weremeasured by acrylamide gel electrophoresis and found to bevery similar in the RNA from the two organisms (Fig. 7). Thisjustifies the use of poly(U) hybridization to measure "reac-tive" RNA concentration in the experiment shown in Fig. 6.

DISCUSSIONAlthough there is a general progression in C-value fromprimitive eukaryotes through nonchordate metazoa andchordates, there exists great variability within several phylo-genetic groups. This is particularly true for fish, insects, andamphibia. The latter group includes related organisms thatdiffer widely in their C-values; indeed, the family Pelobatidae(Order, Anura; Suborder, Anomocoela) contains genera thatdiffer by a factor of five in DNA content (2). It is unlikely thatthis difference is due to the high C-value organism being sub-stantially more complex than the corresponding low C-valueorganism. There is also no obvious reason to expect Triturusto be phenotypically seven times more complex than Xenopus.Our results strongly suggest that the sequence complexity ofovary mRNA is the same for these two organisms. The resultsalso suggest strongly that in each case mRNA is transcribedpreferentially from the single-copy fraction of the DNA.This is in agreement with previous work from this and fromother laboratories on mRNA sequences in various organisms(20-23). This result is particularly striking in Triturus, sincethe majority of the genome consists of repeated DNA. Incontrast, the majority of Xenopus DNA renatures with a Cot,/,consistent with the representation of these sequences once, orat most twice, per genome (Fig. 1). It should also be noted thatthe percentage of repeated DNA in the Xenopus genome issmaller as measured optically than as measured on hydroxy-apatite (about 25% as opposed to 45%) (Fig. 1 and ref. 25).

A

5S 4S dyeI 1~ 4

*.\i \

5 10 15 20 25

B

5S 4S dye1 15

5 1.0 15 20 25frachion

FIG. 7. Size of poly(A). About 1 lsg of poly(A)-containingRNA was degraded with pancreatic and T1 ribonuclease and sub-jected to electrophoresis on 15% acrylamide gels. The RNA was

eluted and hybridized with radioactive poly(U) as described (7).The poly(U) was 5 X 104 cpm/ug under the counting conditionsused. The positions of the absorbance markers were determined ona parallel gel in which the dye migrated to an identical position.(A) Xenopus; (B) Triturus.

This is most likely due to interspersed single-copy sequencesthat are bound to hydroxyapatite at low Cot through theduplexed repetitive sequences to which they are attached andare, therefore, fortuitously scored as repeated DNA by thismethod (26).Most mRNA species, with the exception of histone mRNA,

contain a 3' sequence of poly(A) (23, 27-29). It has beenshown by Perry that there exist substantial amounts of nuclearpoly(A) that do not act as precursor to cytoplasmic messengerRNA (30). It is possible, therefore, that a substantial frac-tion of the cDNA is not complementary to mRNA sequences.Nevertheless, we chose to use the poly(A)-containing RNAfrom these two organisms as a probe for a fraction of thegenome significantly enriched for protein-coding sequences.Previous work in this laboratory has demonstrated thatXenopus oocytes contain a large amount of poly(A)-contain-ing RNA, which is likely to be the product of lampbrushchromosome activity (7). A large proportion of this RNA isbonafide messenger RNA, as judged by its ability to stimulateamino-acid incorporation in various in vitro systems, and mostlikely represents masked messenger RNA inherited by thefertilized egg (C. M. Darnborough, P. J. Ford, and M.Rosbash, unpublished results). These earlier studies were per-formed with oocytes chemically stripped of follicle cells anddivided into various size classes. Triturus oocytes are sensi-tive to this treatment and lyse in the presence of Pronase andEDTA. As a result, it was necessary to prepare the RNA fromwhole ovaries.

Triturus cDNA reassociates with an excess of Triturus DNAfive to ten times.slower than Xenopus cDNA with XenopusDNA. Since Triturus has seven times as much DNA per cell as

Xenopus, there appears to be no repetition in Triturus of thesequences that are transcribed into poly(A)-containing RNA.If there were extensive mismatching in either of these cases,this conclusion would be more tenuous. The Tm values of thecDNA*DNA duplexes (65.5 4± 0.50 in both cases) suggest thatthere is little mismatching in these duplex structures. If one

applies the relationship Tm = 16.6 log [Na+] + 0.41 (G+C) +81.5 (32), the cDNA DNA duplexes would have a Tm valueof 82 ± 0.50 in 0.12 M phosphate buffer. This is similar to the

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3750 Cell Biology: Rosbash et al.

value (82.50) reported by Davidson and Hough (24) for theTm of reassociated nonrepetitive Xenopwu DNA. Certainly,there exists no mismatching of the extent necessary to affectrates of reassociation and affect the conclusion drawn fromthe experiment in Fig. 4 (19).The data in Figs. 6 and 7 suggest that the ovaries of "both

species contain the same sequence complexity of poly(A)-containing RNA. In RNA excess, the cDNA provides aneffective tracer of the frequency distribution of the poly(A)-containing RNA; the more complex an RNA population is,the lower the concentration of the individual RNA sequenceand the slower the hybridization of the homologous cDNA.The concentration of poly(A)-containing RNA was assayedby measuring the poly(A) content by hybridization withradioactive poly(U) (7). The advantage of this approach isthat it avoids three potential problems that are encounteredif measurements of this sort are made on the basis of RNA con-centration. These are: (a) genuine differences in the mean sizeof the poly(A)-containing RNA populations from the twospecies, (b) limited cleavage of the RNA during preparation,and (c) contamination of the poly(A)-containing RNA byRNA that does not contain poly(A) (which is not transcribedbut contributes to the absorbance of the RNA).The experiments presented in Figs. 3 and 6 strongly suggest

that the basic transcription patterns in Xenopus and Triturusovaries are very similar. In both cases, mRNA is transcribedpreferentially from the single-copy fraction of the genome, inagreement with previous results on other systerns (20-24).Second, the number of different RNA species present in theovaries of the two organisms is similar. It is however, possiblethat the first conclusion is valid only for transcription in theovary. Other cell types may synthesize larger percentages ofmessenger RNA from the repetitive portions of the genome.Also, the first conclusion depends on the relative efficiency ofdifferent mRNA molecules as templates for RNA-dependentDNA polymerase. Were the mRNA molecules transcribedfrom the repetitive fraction of the genome relatively poor tem-plates for the enzyme, we would tend to underestimate thecontribution of repetitive DNA transcripts in the mRNA pop-ulation. The second conclusion is subject to a similar criticism.If mRNA molecules of a particular frequency class were poortemplates or unable to act as templates for RNA-dependentDNA polymerase, this would change the relative contributionof the various frequency classes to the totalmRNA population.Within these limits, the data strongly suggest that the Tni-

turus genome contains single-copy DNA that can be detectedby use of radioactive cDNA as a tracer. This single-copy DNAis the preferential, if not exclusive, site for the synthesis of in-formational RNA in the Triturus genome. The data arguestrongly against any serial repetition of gene sequences and,therefore, argue strongly against the need for any correctionmechanism to maintain Mendelian inheritance of mutationalevents incurred through evolution (5). The data also renderall the more puzzling the function, if any, the enormous quan-

tity of repetitious DNA in Triturw and perhaps in all orga-nisms with a high C-value.

We are grateful to Prof. H. G. Callan for helpful discussion.We thank Fiona Gibson for excellent technical assistance. Thiswork was supported by an S.R.C. Grant to J.O.B. M.R. is a HelenHay Whitney Fellow. We are indebted to Dr. J. W. Beard, DukeUniversity, Durham, N.C., for supplying us with avian myeloblas-tosis virus.

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