129

Biochimica et Biophysica Acta, 4 2 5 ( 1 9 7 6 ) 1 2 9 - - 1 4 7 © E l sev ie r S c i e n t i f i c P u b l i s h i n g C o m p a n y , A m s t e r d a m - - P r i n t e d in T h e N e t h e r l a n d s

B B A 9 8 5 2 5

CHARACTERIZATION OF THE REPETITIOUS HUMAN DNA FAMILIES

KENNETH A. MARX *, JAMES R. ALLEN ** and JOHN E. HEARST ***

Department of Chemistry, University of California, Berkeley, Calif. 94720 (U.S.A.)

(Received April 25th, 1975) (Revised manuscript received October 27th, 1975)

Summary

Human DNA isolated from HeLa cells or human placental tissue has been fractionated on hydroxyapat i te at Cot 1.0. The 25% of total DNA isolated at Cot 1.0 is composed of 3% foldback DNA and 22% which renatures by second- order kinetics and can be resolved into five renatured DNA families banding at distinct densities in CsC1 gradients. The individual renatured DNA families were isolated and their physical properties including reassociation kinetics deter- mined. A two-component kinetic analysis was used to resolve kinetic heteroge- neity. The three lightest density DNA families possess satellite DNA-like prop- erties. The two heaviest density DNA families were shown to contain reasso- ciated highly repetitious DNA as well as single-stranded, middle-repetitious DNA sequences, suggesting interspersion. The middle repetitious DNA se- quences are thought to be related in these two DNA families.

Introduction

Reassociation kinetic studies of the DNA of higher organisms have played a crucial role in the evolution of our concepts of the information content and organization of higher-organism DNA. Considerable portions of the genomes of eukaryotic organisms are known to be comprised of simple-sequence, highly repetitious DNAs [1,2].. Furthermore, many studies have emphasized the ex- t reme molecular heterogeneity of the repetitious DNA classes of eukaryotic organisms [2,3,4,5] .

A prerequisite then to a knowledge of the organization of eukaryotic ge- nomes is the isolation and characterization of individual DNA sequences fami-

* Present address: Institute of Animal Genetics, University of Edinburgh, Edinburgh EH9 3JN, U.K. * * Present address: Department of Zoology Oregon State University, Corvallis, Oregonl U.S.A.

*** To whom requests for reprints should be addressed.

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lies. The technique of Ag ÷ or Hg 2÷ binding in Cs~SO4 gradients has permitted the isolation of a number of .human DNA families [3,6,7] . However, this technique is limited [8] to DNAs having unusual, satellite-like properties. An alternate method of fractionation using hydroxyapat i te utilizes DNA complexi- ty, a proper ty of primary interest, to effect separation. Although hydroxy- apatite discriminates kinetic classes of human DNA [9,10,11] , preliminary evidence by Hearst et al. [10] indicates the presence of many DNA families within a single kinetic class. Clearly, further fractionation of kinetic classes into DNA families is necessary.

In this s tudy the highly repetit ious Cot 0--1.0 class of human DNA is frac- t ionated into molecular families, which are then characterized individually•

Materials and Methods

DNA preparation HeLa $3 cells were grown in RPMI-1640 medium supplemented with 5%

fetal calf serum and 1% pen-streptomycin and 1% aureomycin at 37°C (Grand Island Biological). DNA was 3H-labelled and extracted from HeLa cells and human placenta essentially as described in Cech et a]. [12] with the following modifications. Human placentae were homogenized in 0°C hypotonic medium in a Virtis " 2 3 " homogenizer with macroblades at highest speed. After decant- ing the hemolysate the tissue was resuspended in 0°C nuclear buffer and ho- mogenized similarly until light microscopy revealed nuclei with no adherent cytoplasm. Before continuing the isolation the homogenate was filtered through cheesecloth which trapped the anucleated tissue clumps. Simultaneous- ly with the ribonuclease treatment, 0.2 mg/ml a-amylase (Sankyo) was added. The final DNA extraction mixture used was 24 : 1 chloroform/iso-octanol.

DNA molecular weight determination The DNA used in the experiments below was routinely sheared by sonication

as described in Cech et al. [12] s pH 1a.o values in 0.9 M NaC1, 0.1 M NaOH • 2 0 , w

were determined by boundary sedimentation. Molecular weights were calcu- lated according to Studier [13] .

Isolation of rapidly renaturing sequences DNA at a concentrat ion of Co (mol phosphate • 1 -~) in 0.05 M sodium

phosphate buffer pH 6.8 was denatured with 1 M NaOH at room temperature. The solution was brought to 60°C and an appropriate volume of 60°C 2 M NaH2PO4 solution was added to effect a final concentrat ion of 0.12 M phos- phate buffer (0.18 M Na +) pH 6.8. Upon renaturation at 60°C to the desired Cot the solution was thoroughly mixed with a slurry of hydroxyapat i te in 0.12 M phosphate buffer pH 6.8 at 65°C. Stepwise elutions continued at 65°C with a series of 0.12 M, 0.16 M and 0.45 M phosphate buffer pH 6.8 wash solutions. At each step the slurry pellet was resuspended in the buffer and equilibrated for 1 min at 65°C before pelleting in a clinical centrifuge at 65°C and decanting of f the supernatant. The yields in the phosphate buffer wash fractions were determined optically (A26onm) unless small 3H-labelled amounts were used, in which case the radioactivity was measured by counting a

131

small aliquot in 1 ml water plus 10 ml scintillation solution (1 part Triton X-100 to 2 parts Amersham-Searle PPO-POPOP fluor in toluene).

Equilibrium density gradient centrifugation Equilibrium density gradient centrifugation was carried ou t in a Beckman

Model E Analytical Ultracentrifuge with photoelectric scanner optics. Double- sector t i tanium center pieces were used [14] . Harshaw optical grade CsC1 was used and gradients were run to equilibrium in 3 days at 35 000 rev./min at 25 ° C. Buoyant densities were measured relative to Micrococcus lysodeikticus DNA, which has a density of 1.733 g/ml relative to Escherichia coli, P0 = 1.710 g/ml. Density differences relative to the marker were calculated from the densi- ty gradient ( ~ p / ~ r ) b o u y a n c y = 9.35 • 10 -1 °¢o2~ according to Schmid and Hearst [15] .

Preparative centrifugation was performed at 35 000 rev./min at 25°C in equilibrium CsC1 gradients (3 days) in the Spinco fixed angle 60 Ti rotor. Polyallomer tubes were used with 10 /~1 of 20% sarkosyl added to decrease adsorption of renatured DNA. By using large amounts of starting DNA and rebanding impure fractions up to five times, pure renatured DNA families were obtained. The criterion of purity was the analytical ultracentrifuge CsCl density profile.

Reassociation kinetics Reassociation kinetics were determined and analysed as described in Marx

[16] and Marx and Hearst [17] . All samples were studied in 0.12 M phosphate buffer pH 6.8 (0.18 M Na ÷) at 60°C. Reassociation curves for all DNA samples were determined twice, the curves being superimposable. Each sample returned to the original denatured absorbance after any period of renaturation.

Determination of melting spectra Thermal denaturation spectra of DNA samples were obtained in 0.12 M

phosphate buffer (0.18 M Na ÷) pH 6.8. A Beckman DU spectrophotometer fitted to a Gilford Multiple Sample Absorbance Recorder with automatic slit adjustment was used. A HAAKE Thermostatic bath programmed at a tempera- ture increase of 15 ° C/h heated the jacketed cuvette.

R e s u l t s

Reassociation of total nuclear DNA Fig. 1 shows a plot of the optical reassociation * of sonicated ** human

nuclear DNA. It can be seen that renaturation occurs over many decades in log Cot. This suggests considerable heterogeneity in the complexi ty and/or degree of repetition of ~ e renaturing DNA families, a finding consistent with that of most mammalian DNAs studied, Although no CsC1 density satellites were

* Al l D N A samples were studied in varying concentrat ions o f equimolar ( N a 2 H P O 4 • 7 H 2 0 / N a H 2 P O 4 • H 2 0 ) phosphate buf fer m i x t u r e s p H 6 .8 . Therefore , the [ N a +] is 1 . 6 - t i m e s t h e s t a t e d phosphate buf fer concentrat ion .

** Al l of the D N A samples in this s tudy were sonlcated t o a weight average molecular weight o f 3 0 0 - - 4 5 0 nucleot ides /s in~le strand.

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1.0

~0.5 g <I

r ' i r I

0 ~/ i i J 1 1 0 - 5 10 -3 10-2 I 0 - I I I 0

Cot ( tool x s e c / l i t e r )

Fig. 1. Opt ica l reassoc ia t ion of son ica ted h u m a n D N A samples . (~ ~) To t a l h u m a n D N A (0 .70 M Na +) r e n a t u r a t i o n da t a co r r e c t e d to the 0 . 1 8 M Na + ra te [ 2 1 ] ; (o o) Cot 1.0 D N A , isolated on h y d r o x y a p a t i t e , d e n a t u r e d and r e n a t n r e d in 0 .18 M Na+; (• D) F o l d b a c k D N A , isolated on h y d r o x y - apa t i t e at Co t = 10 "4, d e n a t u r e d and r e n a t u r e d in 0 .075 M Na +. T h e - d a t a is co r r ec t ed to the 0 .18 M Na + rate; (o . . . . . . e) This dep ic t s the f rac t iona l yield of D N A u p o n h y d r o x y a p a t i t e at var ious Cot values in 0 .18 M Na +. T he e x p e r i m e n t a l p r o c e d u r e has b e e n descr ibed in Materials and Methods . A ~ in the o rd ina t e co r r e sponds to the na t ive high m o l e c u l a r weight a b s o r b a n c e of the D N A , A 0 / 1 . 4 3 = Aoo for h u m a n D N A . A 0 has b e e n co r r ec t ed for t h e r m a l e xpa ns ion and for i n t r a m o l e c u l a r opt ica l a b s o r b a n c e changes [ 1 6 ] . The lines t h r o u g h all of the po in ts are no t t heo re t i ca l bu t m e r e l y c o n n e c t the sets of points .

found (see Fig. 3a), it can be seen that human nuclear DNA contains very rapidly renaturing main band DNA sequences.

The plateau in the Cot curve at Cot 1.0 indicates that about 16% of total human nuclear DNA is comprised of a class of DNA sequences of relatively low complexity. Of course, whether any particular DNA family of low complexity has renatured by Cot 1.0 is dependent upon its dilution in the genome.

The nature o f isolated total Cot 1.0 DNA (i) Reassociation kinetics and thermal denaturation. Routinely, 25% of the

nuclear DNA is retained on hydroxyapat i te at Cot 1.0. This is shown in Fig. 1, with the yield at a Cot of 10 -2. These values compare favorably with those presented by Saunders et al. [9]. Comparing the 25% hydroxyapat i te yield to the 16% optical reassociation value in Fig. 1, it can be estimated that 30--40% of the hydroxyapatite-isolated DNA is single stranded.

In Fig. 1 the optical reassociation of isolated Cot 1.0 DNA can be seen to have a Cot112 of 2 • 10 -2. The renaturation of Cot 1.0 DNA is second-order. Over a five-fold range in initial concentration the Cot112 was found to be invariant. The considerable breadth of the reassociation curve suggests the pres- ence of a number of DNA families possessing either different rate constants (k values) or different relative abundances in the genome. It is clear that some 40% of the Cot 1.0 DNA sequences remain unrenatured. This result was antici- pated from the difference already noted between the total DNA optical and hydroxyapat i te renaturation values in Fig. 1. The broad double-stranded melt- ing spectrum of Cot 1.0 DNA shown in Fig. 2 has a T m of 78°C. Relative to

133

Io00 I ) )

0.9C

0.80

I 0.70[, I I I

50 60 70 80 Tempe,'etu)e (%)

o

w >

I 90 IO0

Fig. 2. O p t i c a l m e l t i n g curves o f h u m a n D N A . (e

<

is) 1.73,3

1,700 (b)

~L 1.703 1733

1.687 A J ~ ~-" ~ 1

1.733

(c) /

1.714 , \

1,700 1 1.703

~ L714

P

-e). T o t a l u n s h e a r e d na t i ve h u m a n D N A in 0 . 1 8 M Na+; (4 - 4) Cot 1 .0 h u m a n D N A , i so l a t ed o n h y d r o x y a p a t i t e , d i a l y z e d i n t o 0 . 1 8 M Na + b e f o r e me l t i ng . T h e s a m p l e s h a d r e spec t i ve c o n c e n t r a t i o n s o f 1 .26 a n d 0 . 8 0 A l c m ~ 2 6 0 n m " T h e cu rves have b e e n c o r r e c t e d f o r t h e r m a l e x p a n s i o n a n d a re n o r m a l i z e d t o t h e h i g h t e m p e r a t u r e a b s o r b a n c e fo r d i r e c t

c o m p a r i s o n .

Fig. 3. A n a l y t i c a l u l t r a c e n t r i f u g a t i o n in n e u t r a l CsCI o f h u m a n D N A s : (a) T o t a l u n s h e a r e d na t i ve D N A ; (b) Cot 1 .0 D N A , i so l a t ed o n h y d r o x y a p a t i t e , a n d s t r i n g e n t r e n a t u r e d to C o t = 1 0 b e f o r e b a n d i n g ; (e) F o l d b a c k D N A , i so l a t ed a t CO t = 1 0 --4 a n d n o n - s t r i n g e n t r e n a t u r e d a t 0 . 1 0 A ~ n m b e f o r e b a n d i n g ; (d) C o t 1 0 - 4 - - 1 . 0 D N A , i s o l a t e d o n h y d r o x y a p a t i t e a t C o t = 1 .0 f o l l o w i n g r e m o v a l o f t h e f o l d b a c k s e q u e n c e s a t CO t = 1 0 -4 , w a s s t r i n g e n t r e n a t t t r e d t o CO t = 10 b e f o r e b a n d i n g . M. lysodeikticus D N A , P0 = 1 . 7 3 3 g /ml , w a s a d d e d as a d e n s i t y m a r k e r .

native nuclear DNA with a Tm of 84°C, isolated Cot 1.0 DNA has a ATm of 6°C, if similar G-C compositions are assumed. This ATm suggests considerable sequence heterogeneity within the Cot 1.0 DNA families with base mismatch- ing ranging from 4--9% [18,19] in the renatured DNA. The 65% of Cot 1.0 DNA which is double stranded by the thermal stability criterion in Fig. 2 agrees well with the previous observations on double strandedness. Taken together, these observations of approx. 40% single stranded regions in the Cot 1.0 DNA (300--450 nucleotides) isolated on hydroxyapatite suggest that the highly repe- titious human DNA sequences come, on the average, in relatively short lengths, and therefore may be interspersed with DNA sequences of much higher com- plexity [12,20].

(if) CsCl density profile Isolated Cot 1.0 DNA, banded in a CsC1 gradient, has a very broad density

prof i l e d u e to d i f fus iona l spreading. When the Cot 1.0 D N A tA1 cm > 1.0) ~ ' 2 6 0 n m

134

is allowed to continue renaturation at 68°C in 0.12 M phosphate buffer pH 6.8 for 20 h (stringent conditions), the density profile appears as in Fig. 3b. The very high molecular weight aggregates band at distinct and characteristic densi- ties. This phenomenon must be due to the reassociation of the 40% single- stranded regions in Cot 1.0 DNA during the stringent renaturation to Cot 10. The stringent conditions select for renatured aggregates containing DNA se- quence regions of good homology and allow the unequivocal identification of five distinct renatured DNA families in isolated Cot 1.0 DNA. Each individual renatured DNA family is designated by its renatured CsC1 density *. From preparation to preparation the densities and percentages of each renatured DNA family in the Fig. 3b distribution are invariant following the stringent renaturation. It was found that a Cot 1.0 DNA concentration of at least 1.0 A t cm is required for high molecular weight aggregate formation under strin- 2 6 O h m gent conditions. This is perhaps due to the fact that at higher DNA concentra- tions bimolecular aggregation is able to compete much more effectively with intramolecular aggregate cyclization.

(iii) Foldback DNA Foldback DNA is thought to renature by an extremely rapid intramolecular

process due to the presence of sequence inversions [21]. When foldback DNA is isolated from total nuclear DNA at Cot 10 -4 about 3% of total human DNA binds to hydroxyapat i te , in good agreement with the 3% estimated from opti- cal data [21] and the 5% isolated on hydroxyapat i te [22] at slightly higher molecular weight (600 nucleotide/single strand). As expected, the isolated Cot 10-4--1.0 DNA fraction comprises 22% of the total human genome DNA. The foldback DNA (Cot 10 -4) percentage of an isolated 3H-labelled Cot 1.0 DNA sample was found to be 10%. This can be seen to represent 2.5% of total human DNA.

To demonstrate that the foldback DNA fraction is not simply the product of a fast second-order reaction or adventitious binding the optical reassociation kinetics are shown in Fig. 1. The initial renaturation has occurred by Cot < 10 -s, which is below the low complexity limit of second-order DNA renatura- tion. This demonstrable A260nm loss within the foldback DNA fraction occurs at Cot values where only first-order intramolecular reassociation is possible.

The fact that 80% of foldback DNA remains single stranded at Cot 10 -3 is not inconsistent with its presence in the Cot 10 -4 fraction. It is known [12,21] that foldback DNA binds weakly to hydroxyapat i te . Cech et al. [12] consider one probable cause of this instability to be single strand nicking. The isolated foldback DNA sequences, subsequently nicked, now renature with second- order kinetics, which accounts for only 20% renaturation of foldback DNA at Cot 10 -3 in Fig. 1. As expected from the nicking of foldback DNA only 30% of the input foldback DNA bound to hydroxyapat i te after rechromatography to a Cot of 5" 10 -s. Cech et al. [12] have noted a variable 40--90% of mouse

* T h e m o r e c o m p a c t n o m e n c l a t u r e used h e r e s u p e r c e d e s that u s e d in a p r e v i o u s c o m m u n i c a t i o n [ 1 0 ] . F o r e x a m p l e , h . a . r . r . D N A 1 . 6 8 7 is n o w referred to as 1 . 6 8 7 D N A . T h e b u o y a n t d e n s i t i e s in th i s s t u d y s.re ca l cu l a t ed us ing a ( b p / ~ r ) B [ 1 5 ] s o m e w h a t d i f f e r e n t f r o m that used in m o s t s tud ie s [ 2 6 ] in the l i terature . T h e r e f o r e , t h e e q u i v a l e n t d e n s i t i e s axe p r e s e n t e d in Tab le I I .

135

foldback DNA bound to hydroxyapat i te upon rechromatography, somewhat higher than the value determined here.

The CsC1 density profiles of the isolated Cot 10 -4 foldback DNA and Cot 10-4--1.0 DNA are shown in Fig. 3c and d following stringent renaturation. The Cot 10 -4 foldback DNA density profile shows a broad featureless distribu- tion while the relative percentage of each renatured DNA family in Cot 10-4--1.0 DNA remains about the same as its percentage in total Cot 1.0 DNA. (The 1.687 DNA position is not evident in this gradient.) Therefore, human foldback DNA does not seem to be enriched in particular Cot 1.0 DNA families in the molecular weight range of 1 . 5 , 1 0 s.

Characterization of the isolated Cot 1.0 DNA families The data obtained in this section describe the sequence properties of indi-

vidual DNA families rather than the properties of multi-family kinetic classes of DNA [9,11] . The final criterion of purity was the CsC1 gradient density profile in the analytical ultracentrifuge. In all cases, no discernible bands could be found at any of the contaminating density positions.

Melting spectra and optical reassociation kinetics of the purified renatured DNA families are presented in Figs. 4 and 5. The kinetic heterogeneity of these DNA families (Fig. 7) is resolved into kinetic components by the method of Marx and Hearst [17] and is summarized in Table I.

(i) 1.687 DNA. The presence of this DNA family was overlooked for some time, due in part no doubt to its low percentage (1--2%) in the Cot 1.0 DNA and to its preferential extraction into the phenol phase during DNA purifica- tion (use of phenol has since been discontinued). It has not been determined whether the 1.687 DNA is completely extracted into the phenol phase, a

1.0C

0,90

~: 0.80

0.70 I I I I I 40 50 60 70 80 90 I00

Temperolure ('=C)

Fig. 4. OPtical me l t i ng curves o f purif ied renatured h u m a n D N A famil ies in 0 .18 M Na+: ( e =) 1 .687 D N A ; (~ ~) 1 ,700 D N A ; (o .. o) 1 ,708 D N A ; (o o) 1 .714 D N A . Th e me l t ing spec t ra were d e t e r m i n e d at D N A c o n c e n t r a t i o n s corxespondlng to nat ive absorbances in the range f r o m 0 . 0 8 t o 0 .13 A l e m 260nm" Prior to mel t ing , all D N A samples w e r e denatured and renatured for 2 h in 0 .18 M Na + a t 68°C. T h e r e f o r e , all o f the sam p le s s.re at a b o u t the s a m e C0L value o f 0.1. Th e curves have b e e n c o r r e c t e d for t h e r m a l expans ion and are n o r m a l i z e d to the high t e m p e r a t u r e absorbance for d irec t c o m p a r i s o n .

136

property which could identify it as poly [d(A,T)] -like [24] or simply an A • T rich satellite DNA [23].

It was noted that the percentage of 1.687 DNA in the total Cot 1.0 DNA varied from tissues of mixed sex. It is entirely missing from HeLa cell Cot 1.0 DNA, present to a slight extent in uterine muscle Cot 1.0 DNA and more abundant in WI-38 Cot 1.0 DNA (female embryonic lung cell line). Though the reasons for its absence in HeLa DNA are not understood, satellite DNA poly- morphism is a possibility [25].

The melting spectrum of the 1.687 DNA in Fig. 4 has a Tm of 72°C and a very sharp melting transition, very different than the other renatured DNA families. The sharp melting transition indicates well matched renatured du- plexes and therefore a DNA family with little sequence divergence.

The reassociation curve for the 1.687 DNA, presented in Fig. 5, has a Cot112 of about 1.1 • 10 -3. Any kinetic heterogeneity in this apparently homogeneous DNA family can be resolved by the two component kinetic analysis of Marx and Hearst [17] into two second-order renaturing DNA classes. The results in Table I, obtained from the replotted kinetic data in Fig. 6(a), indicate the presence of DNA sequences considerably lower in complexity than expected on the basis of conventional estimates (60 base pairs (f) component compared with 620 base pairs estimated from Cotl/2 = 1.1 • 10-3). Since there is no unambiguous way of assigning the kinetic heterogeneity present in DNA reasso- ciation data to a specific number of components, we may think of the (f) and (s) component result as a convenient way of characterizing those sub-popula- tions of sequences which renature respectively the fastest and slowest.

(ii) 1.696 DNA. This particular renatured DNA family, comprising 2% of the human genome, was not characterized due to a lack of material. However, from

1.0 ~ I I i

I o

o~

0 ] I I 10-4 10-3 10-2 i0 -I I0 I00

Cot (tool xsec/liter)

Fig. 5. Optica l r e a s s o c i a t i o n o f t h e pur i f i ed r e n a t u r e d h u m a n D N A fami l i es at s o n i c a t e d m o l e c u l a r weigh t and at t h e 0 .18 M Na + ra te : (~ @) 1 .687 D N A m e a s u r e d in 0 .18 M Na+; (Q D) 1 .700 D N A m e a s u r e d in 0 .18 M Na +. The 1 .703 D N A (= s ) w a s m e a s u r e d in 0 .18 M Na + and (o o) in 1 .02 M Na + c o r r e c t e d to t h e 0 .18 M Na ÷ rate. T h e 1 .714 D N A (4 A) w a s m e a s u r e d in 0 .18 M Na*

A 1 e m nat ive a h s o r h a n c e . and (~ ~) in 0 .81 M Na +. D N A c o n c e n t r a t i o n s r a n g e d f r o m 0 . 0 5 7 - - 0 . 1 0 ~ 2 6 0 n m C o r r e c t i o n s to t h e 0 .18 M Na + rate and the d e t e r m i n a t i o n s o f A 0 and Aoo w e r e m a d e as s ta ted in t h e l egend of Fig. 1. T h e lines are n o t t h e o r e t i c a l b u t m e r e l y c o n n e c t t h e set o f p o i n t s .

137

700

6 0 0

500 '

400, ?

~300.

200"

tO0-

300

q<~200.

tOO.

(b)

" 80-

)

t 70 ~o z~o --.~o

(S) tit 1260 see

0 0 500 K)O0 1500 I00 300 500 700 900 t (S.c) t (S~)

Fig. 6. T h e t w o c o m p o n e n t k i n e t i c a n a l y s i s o f t h e Co t 1 .0 r e n a t u r e d h u m a n D N A fami l ies . O n l y t h e 0 . 1 8 M Na + d a t a f r o m Fig. 5 has b e e n r e p l o t t e d he re . (a) 1 . 6 8 7 D N A (e . . . . e ) , A 0 is 0 . 0 8 0 A l ~ n n m a n d t h e e x t r a p o l a t e d Aoo is 0 . 0 6 7 ( 8 ) A l ~ n m ; 1 . 7 0 0 D N A (a &), A 0 is 0 . 1 2 ( 2 ) Al~nnm.,.v..~ a~l(l t h e e x t r a p o l a t e d Aoo is 0 . 1 0 ( 8 ) A l ~ n m . ~(b) 1 . 7 0 3 D N A ( , .... &). A 0 is 0 . 1 4 ( 2 ) A ~ n n m a n d t h e e x t r a p o l a t e d i o o is 0 . 1 2 ( 7 ) A~-~,,-.~' . T h e inse r t is a n e x p a n s i o n o f t h e in i t i a l r e g i o n o f th i s cu rve ; 1 . 7 1 4 D N A (o o) , A 0 is 0 . 1 4 ( 6 ) A ~ n n m a n d t h e e x t r a p o l a t e d Aoo is 0 . 1 3 ( 7 ) A26~nnm . T h e t w o c o m p o n e n t k i n e t i c ana lys i s w a s p e r f o r m e d as p r e v i o u s l y d e s c r i b e d b y Marx a n d H e a r s t [ 1 7 ] . E x t r a p o - la ted Aoo used he re is d i f f e r e n t f r o m the Aoo in Figs. 1 a n d 5 a n d i s o b t a i n e d b y a n e x t r a p o l a t i o n o f d a t a [ 1 7 ] . I t is v a l u a b l e in t h a t i t s u b t r a c t s o u t n o n - r e n a t u r i n g D N A classes o r t h o s e hav ing ve ry smal l r a t e c o n s t a n t s f r o m t h e t w o c o m p o n e n t ana lys i s . F o r e x a m p l e , in t he 1 . 7 1 4 . D N A d a t a in b , t h e e x t r a p o l a t e d Aoo c o r r e s p o n d s t o (A -- Aoo)/(A 0 - - Aoo) = 0 . 6 9 in Fig. 5. So, fo r t h e p u r p o s e o f t h e t w o c o m p o n e n t k i n e t i c a n a l y s i s o f t h e h i g h l y r e p e t i t i o u s D N A in t h e 1 . 7 1 4 D N A f a m i l y , t h e m i d d l e r e p e t i t i o u s D N A c o m p o n e n t (Cot1~ 2 = 7 .2 in Fig. 5) r e n a t u r e s so s l owly as to b e negl ig ib le a n d is e x c l u d e d b y t h e c h o i c e o f e x t r a p o l a t e d Aoo. T h e p o s i t i o n s o f t h e Cot1~ 2 values o f t h e c a l c u l a t e d p u r e (f) a n d (s) c o m p o n e n t s d i l u t ed i n to t h e t o t a l r e n a t u r e d D N A fami ly a re i n d i c a t e d b y t h e a r r o w s . T h e l ines d r a w n t h r o u g h t h e e x p e r i m e n t a l d a t a are n o t t h e o r e t i c a l cu rves c o m p u t e d f r o m (f) a n d (s) c o m p o n e n t s , b u t m e r e l y serve to c o n n e c t t h e d a t a po in t s .

the data presented in Fig. 7, an inference can be made concerning its kinetic behavior. Cot 10 -2 DNA and Cot 10-5--1.0 DNA isolated on hydroxyapatite and incubated under stringent conditions are banded in CsC1 gradients. The 1 .696 DNA can be seen to have renatured to an appreciable extent (perhaps 80%) by a Cot of 10 -2. This suggests that its Cot112 in total DNA is somewhat less than 10 -2. Corrected for its dilution in total DNA, the Cot1/2 of the pure D N A family would be expected to be about 2 • 10 -4.

(iii) 1.700 DNA. This renatured DNA family, comprising some 4% of total human DNA, shows a broad melt with a Tm of 74 ° C. From its density and the fact that about 40% of the DNA remains unrenatured (Fig. 5) we can estimate the native buoyant density to be 1 .694 g/ml by the fol lowing relation: (Op + 4 (p + 0 . 0 1 6 ) ] / 1 0 = 1.700. This suggests a native Tm of 83°C and, therefore, a ATm ~- 9°C indicating quite extensive mismatching (10% using the data of Bonnet et al. [27] ).

The reassociation of the 1 .700 DNA extends over a wide Cot range consis- tent with the considerable mismatching seen in the melting spectrum. Kinetic heterogeneity is obvious in the more pronounced curvature of the replotted

138

T A B L E I

S U M M A R Y O F K I N E T I C P R O P E R T I E S O F R E N A T U R E D H U M A N D N A F A M I L I E S

T h e r e n a t u r e d T m v a l u e s i n c o l u m n I were d e t e r m i n e d f r o m t h e m e l t i n g s p e c t r a p r e s e n t e d in F ig . 4.

C o l u m n II s u m m a r i z e s t h e y i e ld (as a p e r c e n t a g e o f t o t a l n u c l e a r D N A ) o n h y d r o x y a p a t i t e o f each

r e n a t u r e d D N A f a m i l y and i t s c o n s i t u e n t k i n e t i c subc las ses . T h e e x t r a p o l a t e d A (F ig . 6, l e g e n d ) is u sed

t o d e t e r m i n e t h e y i e l d ; t h e r e f o r e , t h e s u m o f y i e l d s o f t h e k i n e t i c s u b c l a s s e s o f a g i v e n f a m i l y is less t h a n

t h e y i e l d c a l c u l a t e d fo r t h e w h o l e r e n a t u r e d D N A f a m i l y ( w h i c h i n c l u d e s s i n g l e - s t r a n d e d r e g i o n s ) f r o m

t h e CsC1 d e n s i t y p r o f i l e (F ig . 3b ) . A v e r a g e D N A c o m p l e x i t i e s in c o l u m n I I I w e r e c a l c u l a t e d f r o m t h e

Cot1~ 2 v a l u e s u s i n g Escherichia coli D N A (4 .5 - 1 0 6 base p a i r s / g e n o m e : Cot1~ 2 = 8) as a s t a n d a r d . T h e

Cot1/2 v a l u e s in c o l u m n IV are r e p r e s e n t a t i v e o f t h e p u r e D N A or D N A c o m p o n e n t . T h e p u r e m i d d l e

r e p e t i t i o u s D N A s u b c l a s s e s h a v e Cot1/2 v a l u e s d e t e r m i n e d f r o m t h e i r F ig . 5 Cotl/2 v a l u e a n d t h e i r d i l u t i o n in t h e t o t a l r e n a t u r e d D N A f a m i l y . F r o m t h e t w o c o m p o n e n t k i n e t i c a n a l y s i s k i va lues , C O t 1 / 2 =

( k i / 2 ) - l . T h e d e f i n i t i o n o f k i [ 4 1 ] u sed he re is t w i c e t h a t o f B r i t t e n a n d K o h n e [ 1 ] . C o l u m n V p r e s e n t s

t h e r e p e t i t i o n f r e q u e n c y p e r d i p l o i d n u c l e u s b a s e d u p o n a r e p e a t u n i t o f s t a t e d ave rage c o m p l e x i t y

( c o l u m n IV) a n d t h e c o r r e s p o n d i n g p e r c e n t a g e o f t h e g e n o m e in c o l u m n II. S o m e o f t h e d a t a i n t h i s t a b l e

h a s a p p e a r e d i n a p r e v i o u s c o m m u n i c a t i o n [ 1 0 ] . A n y d i f f e r e n c e i n t h e n u m b e r s t h a t a p p e a r h e r e r e s u l t s f r o m r e f i n e m e n t s i n d a t a p r o c e s s i n g .

I I I I I I IV V

T m Y i e l d Cotl/2 f o r A v e r a g e corn- R e p e t i t i o n (o C) (% o f t o t a l p u r e D N A or p l e x i t y o f p u r e f r e q u e n c y

h u m a n n u c l e a r D N A c o m p o - D N A or D N A ( c o p i e s pe r

D N A ) n e n t ( t oo l P X c o m p o n e n t d i p l o i d n u c l e u s )

2/1) (base p a i r s )

1 . 6 8 7 D N A 7 2 0 .4 1.1 • 1 0 -3 6 2 0 39 0 0 0

f - - 0 . 0 7 3 .8 • 1 0 -4 6 0 70 0 0 0

s - - 0 . 1 7 9 .4 • 10 -4 5 9 0 17 0 0 0

1 . 6 9 6 D N A - - 2 . 0 (8 • 1 0 - 5 ) _ ( 4 5 - - 1 1 0 ) 1 1 0 0 0 0 0 - -

2 • 1 0 -4 ) 2 7 0 0 0 0 0

f . . . . .

S . . . . . .

1 . 7 0 0 D N A 7 4 4 . 0 2 .4 • 1 0 -3 1 3 5 0 1 7 8 0 0 0

f - - 0 .7 6 .3 • 1 0 -5 1 4 0 3 0 0 0 0 0

s - - 1.1 1 .2 • 1 0 -3 8 8 0 7 5 0 0 0

1 . 7 0 3 D N A 7 6 7 .0 - - - - - -

H i g h l y r e p i t i t i o u s f - - 0 . 1 4 2.1 • 10 -5 1 5 5 6 0 0 0 0

s - - 1 . 2 6 2 .7 • 1 0 -3 11 6 0 0 6 5 0 0 0

M i d d l e r e p i t i t i o u s 3 .7 14 7 .9 • 106 3 0

1 . 7 1 4 D N A 8 0 9 . 0 - - - - - -

H i g h l y r e p i t i t i o u s f - - 1.7 5 .4 • 1 0 -5 3 2 3 2 0 0 0 0 0

s - - 1 .4 1 .6 • 1 0 -3 1 1 0 0 7 6 0 0 0

M i d d l e r e p i t i t i o u s 4 .7 7 .2 4 . 2 • 106 7 0

kinetic data in Fig. 6(a) compared to that for the 1.687 DNA. The two compo- nent kinetic analysis results in Table I once again describe a subpopulation having a complexity (140 base pairs, (f) component) which is considerably lower than would be calculated conventionally (1350 base pairs, Cot1/2 = 2.4 • 10-3).

(iv) 1. 703 DNA. This DNA family, some 7% of human DNA, bands invari- antly at 1.703 g/ml in CsC1 gradients after stringent renaturation. The melting spectrum of the 1.703 DNA in Fig. 4 has a Tm of about 76°C and is very broad. In its breadth and in the substantial fraction of single-stranded DNA present it resembles the melt of the 1.714 DNA and differs from the 1.687 DNA and 1.700 DNA melts already discussed. The width of the transition does

139

1.714 (a)

Lzoo / \ ~.6,~?~ ~.To3 j \ 1.733

(b) 1.703

1.700 ~'~', ,~ / \ 1.714

P Fig. 7. Analytical ultracentrifugation of human DNAs in neutral CsCI gradients. (a) Cot 10 -2 DNA, isolated on bydroxyapatite and stringent renatured to Cot = 10 before banding. (b) Cot 10-2--1.0 DNA, isolated on hydroxyapatite following the Cot 10 -2 isolation, was stringent renatttred to Cot = 10 before banding. M. lysodeikticus DNA, P0 = 1.733 g/ml, was added as a density mazjer.

suggest a large ATm. However, this is obscured by the large single-stranded DNA melt and more than a single DNA kinetic class. The reassociation kinetics in Fig. 5 show a number of distinct DNA kinetic classes. In this respect it resembles the 1.714 DNA and is unlike the two previous DNA families consid- ered. It will be noted that only 20% of the DNA sequences comprising this DNA family are renatured by a Cot = 3.0, the approximate Cot reached by these DNA sequences in total Cot 1.0 DNA during the stringent renaturation before banding in CsC1. Therefore, the buoyant density and melting spectrum reflect the presence of a large port ion of single-stranded DNA.

Approx. 80% of the 1.703 DNA renatures as a single kinetic class of Cot1/2 = 14 (Fig. 5, Table I). This DNA is nearly three orders of magnitude more complex than the 20% of DNA sequences which are covalently attached and renatured well before Cot = 0.1. Thus, on the average, only 80 nucleotides/400 nucleotide single-stranded piece are of the highly repetitive type. Since both kinetic classes are isolated at Cot 1.0 the most likely interpretation is that the highly repetit ious sequences are interspersed with middle repetit ious Co t l /2 = 14 sequences. If the 3.7% middle repetit ious DNA represents a distinct and complete DNA family (that is not necessarily so), then its Cot1/2, diluted in total DNA, would be close to 380, representing DNA repeated only 30 times per cell. Clearly, this should be viewed only as an approximate repeti t ion frequency.

When the 1.703 DNA kinetic data at Cot values less than 0.1 is replot ted in Fig. 6b, the result strongly suggests the presence of two distinct renaturing components in the highly repetit ious DNA class. The two component kinetic analysis results in Table I show a pure (f) component of 15 base pair complexi- ty responsible for the steep initial slope of the Fig. 6b curve and present in about 5.6 • 10 s copies /d iploid human genome.

(v) 1. 714 DNA. This DNA family comprises 9% of human DNA and bands invariantly at 1.714 g/ml in a CsC1 gradient following stringent renaturation. As already noted, its properties are similar to those of the 1.703 DNA. The melt-

140

ing spectrum has a renatured Tm ~- 80°C, somewhat higher than that of the 1.703 DNA, but nearly identical in its fraction of single-stranded DNA and breadth, suggesting a highly diverged family of DNA sequences.

The reassociation kinetics resemble that of the 1.703 DNA exhibiting two distinct DNA kinetic classes. By a Cot of 3.0 only the highly repetitious 25% of the 1.714 DNA sequences have renatured. This is reflected in the large single- stranded DNA fraction in the melting spectrum and in the rather high CsC1 buoyant density.

About 75% of the 1.714 DNA renatures as a single kinetic class of Cot112 = 7.2. Nearly 3 orders of magnitude separate the complexities of the highly repe- titious sequences and these middle repetitious DNA sequences in this renatured DNA family. Similar to the 1.703 DNA an interspersion of the two DNA kinetic classes can be considered the most likely way that two sequence classes can exist contiguously and be co-isolated on hydroxyapat i te . If this middle repetitious sequence class (4.7%) represents a distinct and complete DNA fami- ly, then its diluted CoQ/2 ~ - 175 represents some 70 copies per diploid cell, again only an approximate estimate of the repetition frequency.

When the 1.714 DNA reassociation data for Cot <<- 10 -1 is replotted in Fig. 6b the presence of two kinetic classes of highly repetitious DNA is strongly suggested as is the case for the 1.703 DNA. The two component kinetic analy- sis (f) component , having a complexity of some 30 base pairs, is present in about 3.2 • 106 copies/diploid human cell. The respective Cot1/2 values of the pure (f) and (s) components, when diluted in total 1.714 DNA, are about 4 • 10 -4 and 1.6 • 10 -2. These agree well with the Cot curve in Fig. 5.

The presence o f the human DNA families in Cot 10 .5 DNA and Cot 10-2--1.0 DNA

Based upon the detailed reassociation behavior of each individual DNA fami- ly, an estimate can be made of the percentage of each DNA family renatured in total human DNA by any given Cot. In Fig. 7 we have examined the CsC1 gradient distributions of Cot 10 -2 DNA and Cot 10-2--1.0 DNA after stringent renaturation. The Cot1/2 of any pure DNA family or kinetic component may be multiplied by the appropriate correction factor (the inverse of its fraction of total human DNA, see Table I) to determine the Cotl/2 at which it will rena- ture in total human DNA.

The 1.687 DNA will renature with a Cotl/2 of 0.1 in total human DNA, so that no more than about 20% should be present in the Cot 10 -2 DNA. How- ever, it can be seen that the 1.687 DNA does not band distinctly in either Fig. 7a or b. We have already estimated an approximate CoQ/2 of about 2 • 10 .4 for the pure 1.696 DNA. The 1.700 DNA will renature with a Cot 112 of 3.1 • 10 -2 in total human DNA. By Cot 10 -2 this DNA family would be about 30% renatured, approximately the percentage of the total 1.700 DNA which appears in the Cot 10 -2 DNA profile.

For the 1.703 DNA each repetitious DNA class will be considered individual- ly. By a Cot of 10 -2 in total DNA, essentially none of the (s) component highly repetitious sequences or middle repetitious sequences are renatured. The pure (f) component highly repetitious sequences, however, are about 40% reasso- ciated, indicating that approximately 4% of the highly repetitious DNA se-

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.

142

quence class has renatured at a total DNA Cot of 10 -2. From Fig. 7a, it is obvious that no significant port ion of the 1.703 DNA sequences are present, as we expect.

For the 1.714 DNA, the (s) component highly repetitious sequences and middle repetitious sequences will not be appreciably renatured by a total DNA Cot of 10 -2. However, the (f) component highly repetitious DNA will be about 80% renatured, meaning almost 50% reassociation of the highly repetitious DNA sequences. Comparison of Fig. 7a and b shows that a substantial fraction of the 1.714 DNA, perhaps close to 50%, has renatured by a total DNA Cot of 10 -2. Thus, the Cot 10 .2 DNA and Cot 10-2--1.0 DNA density profiles general- ly support the detailed kinetic analyses developed in the earlier sections.

Sequence homology of 1.703 DNA and 1.714 DNA (i) E[[ects o[ renaturation stringency. In the discussions above a number of

similarities in the physical properties of the 1.703 DNA and 1.714 DNA fami- lies have been noted. It is not entirely surprising then, to find that these two DNA families share sequence homology. When Cot 1.0 DNA from either HeLa cells or human placenta (in this case Cot 1.0 HeLa DNA) is isolated and then submitted to nonstringent renaturation (1.5 M Na~; 63°C for 20 h) before banding in a CsC1 density gradient, the profile reported in Fig. 8a is found. The 1.687 DNA, as expected, is absent from the Cot 1.0 HeLa DNA (but appears normally in non-stringent renatured Cot 1.0 placental DNA). The 1.696 DNA and 1.700 DNA families band at their usual densities and in the normal amounts in non-stringent renatured Cot 1.0 HeLa DNA.

However, comparing Fig. 3a with Fig. 8a it is immediately apparent that changes have occurred at the 1.703 and 1.714 g/ml density positions with the relaxation of renaturation stringency. The density of the 1.703 DNA becomes variable, ranging from 1.703 to 1.711 g/ml (this material will be referred to as "hybr id" DNA). With the density increase, there is concomitant increase in the amount of material banding at this density. On the other hand, the 1.714 DNA remains invariant in density but is diminished in amount in direct relation to the gain in material at the "hybr id" DNA density position.

(ii) The nature o[ the "hybrid" DNA. The differences noted above suggest that the 1.703 DNA and 1.714 DNA are primarily involved in the formation of the "hybr id" DNA. If we assume momentari ly that only 1.703 DNA and 1.714 DNA sequences are capable of cross-hybridization, then the percentage of the combined 1.703 DNA and 1.714 DNA in stringent renatured Cot 1.0 DNA will equal the percentage of "hybr id" DNA and 1.714 DNA in non-stringent rena- tured Cot 1.0 DNA. From Table I the 1.703 DNA and 1.714 DNA comprise 74% of stringent renatured Cot 1.0 DNA while from Fig. 8a 76% of non-strin- gent renatured Cot 1.0 DNA is "hybr id" DNA and 1.714 DNA, in good agree- ment with our assumption.

To provide a direct test of which sequences axe involved in the formation of "hybr id" DNA a purified sample was denatured and renatured under stringent conditions (see Fig. 8b, legend) before banding in a CsC1 gradient. The result, seen in Fig. 8b, clearly demonstrates the presence in "hybr id" DNA of only 1.703 DNA and 1.714 DNA. This observation is reversible (double arrow Fig. 8b); by denaturing and renaturing under non-stringent conditions "hybr id"

143

$:

1.0 O. I I00

T I

o

t I I I0

Cot (tool x sec/liter)

Fig. 9. Kine t ics of " h y b r i d " DNA f o r m a t i o n . The f rac t ion of " h y b r i d " D N A (of the to t a l op t ica l dens i ty of t he g rad ien t ) r e f o r m e d at its dens i ty pos i t ion in CsC1 equi l ib r ium gradien ts as a f u n c t i o n of Cot. Iso la ted " h y b r i d " D N A (0 .65 A1 c m ~ in 0 .18 M Na + was d e n a t u r e d and r e n a t u r e d at 6 3 ° C to Cot = 0.7 , ~ 2 6 O n m p the Cot value it wou ld n o r m a l l y r each u p o n isolat ion at Cot on h y d r o x y a p a t i t e . Th e D N A so lu t ion was t hen m a d e 1.5 M Na + and r e n a t u r a t i o n c on t i nue d at 63°C. Al iquots were r e m o v e d at var ious t imes for band ing in t he ana ly t ica l u l t racen t r i fuge . At equ i l ib r ium, pho toe l ec t r i c opt ica l scanner t races of the cells w e r e ob ta ined and the " h y b r i d " D N A f rac t ion of the to t a l cell ab so rbance d e t e r m i n e d b y m a n u a l in t eg ra t ion of peak areas. The po in t whe re " h y b r i d " D N A has r e n a t u r e d ( the highly r epe t i t i ous se- quences ) to CO t = 0.7 in 0 .18 M Na + is t a k e n to be Cot = O, since we have a l ready s h o w n (Fig. 8c) t ha t p ro longed i n c u b a t i o n u n d e r s t r ingent cond i t ions does no t allow " h y b r i d " D N A to fo rm . Th e CO t axis in this f igure has b e e n co r r ec t ed to the 0 .18 M Na + ra te [ 2 1 ] .

DNA of the original density may be obtained. There are two ways to interpret the above phenomena. The first is that the

relaxed conditions of stringency during the non-stringent incubation allow du- plex formation between highly diverged single stranded regions of the partially renatured (at Cot 1.0) 1.703 DNA and 1.714 DNA. These duplex regions would not exist under stringent conditions. The second possibility is that the homologous sequences renaturing to form "hybr id" DNA are not extensively mismatched but simply renature tenfold faster due to the effect of higher [Na ÷] on the non-stringent renaturation rate [21] . The differences in the Cot 1.0 DNA CsCI density profiles then would be due entirely to a trivial kinetic effect and at a tenfold higher Cot Fig. 8b would resemble Fig. 8a.

In order to determine the correct interpretation, "hybr id" DNA was non- stringent renatured to a tenfold reduced Cot (see Fig. 8d legend). This repre- sents a final Cot approximately equivalent to that reached by the total 1.703 DNA and 1.714 DNA sequences during stringent renaturation. At this equiva- lent Cot, any differences in the CsC1 density distribution are solely a manifesta- tion of the differential [Na*] selection conditions upon helix formation. As is evident in Fig. 8d a substantial port ion of "hybr id" DNA appears at its density position, supporting our first interpretation of differential stringency.

If this interpretation is correct it may be tested further by varying the above experiment. "Hybr id" DNA was denatured and stringent renatured (Fig. 8c) to Cot ~- 30, tenfold higher than would normally be reached and equivalent to that reached in non-stringent conditions. The Fig. 8c profile of this material appears very similar to that in Fig. 8b; there is no peak at the "hybr id" DNA density. Again, this is supportive of the idea that "hybr id" DNA formation is

144

due to renaturation of partially homologous sequences in the 1.703 DNA and 1.714 DNA under non-stringent conditions rather than to a trivial differential reassociation rate effect.

(iii) Reassociation of "hybrid" DNA. The rate of formation of "hybr id" DNA at its density position was studied. The data, plotted in Fig. 9, behave as a second-order renaturation reaction with a Cot1/2 of about 4. These data, cor- rected to the 0.18 M Na ÷ rates, may be compared with the optical reassociation curves of 1.703 DNA and 1.714 DNA in Fig. 5. It will be remembered that the middle repetitious 1.703 DNA and 1.714 DNA sequences have corrected Cotl/2 values (0.18 M Na ÷ rate) of 14 and 7.2. Thus, it appears likely that the formation of "hybr id" DNA is due to the cross-hybridization of the middle repetitious 1.703 DNA and 1.714 DNA sequences. Although the Cot1/2 of 4 for the "hybr id" DNA formation reaction is slightly lower than the CoQ [2 values of the middle repetitious DNA fractions, a somewhat different parame- ter is being measured.

Fig. 8 includes a hypothetical molecular model which attempts to describe sequentially the formation of the renatured DNA families and "hybr id" DNA under stringent and non-stringent conditions in terms of the highly repetitious and middle repetitious DNA sequences discussed above.

Discussion

We have examined in detail the nature of the highly repetitious DNA se- quences in the human genome. About 25% of human DNA (400 nucleotides/ single strand) can be isolated on hydroxyapat i te at a Cot of 1.0. Some 3% of total human DNA is foldback DNA, while the remaining 22% isolated by Cot 1.0 is comprised of five DNA families which renature by second-order kinetics. The foldback DNA sequences do not seem to be related to any particular renatured Cot 1.0 DNA family, a result similar to that seen with Drosophila melanogaster foldback DNA [28]. Human foldback DNA has been more thor- oughly investigated by Wilson and Thomas [22].

The five renatured DNA families in Cot 1.0 human DNA band reproducibly in CsC1 density gradients after stringent renaturation. Each DNA family was isolated and the two component kinetic analysis [17] used to resolve the heterogeneity in reassociation. The results describe a fraction of highly repeti- tious sequences within each DNA family of very much lower complexity than would be estimated from conventional kinetic treatments.

The 1.687 DNA, 1.696 DNA and 1.700 DNA appear satellite DNA-like in properties (Table II). From these properties and some unpublished observations at higher DNA molecular weights, these three rather homogeneous DNAs are thought to occur in the genome in relatively long lengths. This idea is comple- mented by the in situ hybridization results which localized these DNAs to very small heterochromatic regions of a few chromosomes [10].

Considerable portions (80 and 75%) of the 1.703 DNA and 1.714 DNA families renature with Cot I/2 values of 14 and 7.2. These middle repetitious DNA sequences are well over three orders of magnitude more complex than the highly repetitious fractions (20 and 25%) of these two DNA families. This is suggestive of an arrangement in the genome in which the highly repetitious

TA

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d D

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fam

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g/m

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Cot

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= 1

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(0.4

%)

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stat

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1.6

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g/~

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r 1

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g/r

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1

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(1

.70

3 g

/ml)

9

, 1

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on

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co

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g/m

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2 g

/ml)

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1.0

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1

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5 g

/ml

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1 )

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hy

dro

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ap

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iso

late

d f

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dif

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nd

co

nd

en

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c

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(1,6

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g/m

l) 1

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4 g

/ml

I t.

,^

= 2

• 1

0 -

3)

74

° C

(0

.5%

) ~

-,

.C,,~

,,~

. .

.

pre

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nc

e [

or

x c

nro

mo

som

e

(1.6

93

g/m

1)

1.6

96

g/m

i II

(C

otl

l 2 =

2 •

10

-4 )

85

°C (

2.0

%)

I, 1

6,

9 se

co

nd

ary

co

nst

ruc

tio

ns

(1,6

96

g/m

l 1

.70

3 g

/ml

III)

(C

otl

/2

= 1

0 -3

•

10

-2

) 7

4°C

(--

2.0

%)

9 se

co

nd

ary

co

nst

ric

tio

ns

1 se

co

nd

ary

co

nst

ric

tio

n

C g

rou

p c

en

tro

me

res,

G g

rou

p,

Y

(1.6

96

g/m

l) 1

.70

5 g

/ml

HM

B

2 k

inet

ic c

om

po

ne

nts

(C

otl

/2 ~

5

• 1

0 -3

, C

ot I/

2 >

1

0)

loc

ali

ze

d t

o a

ll c

hro

mo

so

me

s

/~ c

om

po

ne

nt,

1.7

03

g/m

l (7

.0%

)

(1.6

96

g/m

l 1

.71

2 g

/ml

HM

B

2 k

inet

ic c

om

po

ne

nts

(C

otl/

2 ~

5-1

0

-3 ,

Cot

l/2

:> 1

0)

loca

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es

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en

t 1

.70

7 g

/ml

(10

%)

146

sequences, responsible for the isolation of these DNAs on hydroxyapat i te , are interspersed with the middle repetitious DNA sequences [12] . Results of in situ hybridization support this idea [10] ; hybridization occurs at all chromo- somes and chromosomal regions, although a statistical preference for hetero- chromatic areas was noted (Marx, K.A., Allen, J.R. and Hearst, J.E., unpub- lished). Evidence is mounting for such an arrangement being a general feature of eukaryotic genome structure [12,20,21,30,31] . The molecular weight de- pendence of the hydroxyapat i te yield of the Cot 1.0 renatured DNA families is now being studied to determine what sequence structure patterns exist.

Evidence has been presented for sequence homology between the 1.703 DNA and 1.714 DNA families. The appearance of a "hybr id" DNA density peak, comprised entirely of these two DNA families was found to depend upon non-stringent renaturation (high Na ÷ concentration) following isolation at Cot 1.0. The Cot1/2 of formation of the "hybr id" DNA was found to be about 4 when corrected to the 0.18 M Na ÷ rate, close to the CoQ/2 values of the middle repetit ious DNA fractions of the 1.703 DNA and 1.714 DNA. It is felt that these middle repetitious DNA fractions are a considerably diverged family of sequences sharing partial homology and cause the formation of "hybr id" DNA under non-stringent renaturation conditions.

Human DNA has been fractionated by a number of other workers [3,6,7,9, 11,25,26,32,34,35] . Table II compares the results of these studies. Saunders et al. [9] fractionated human DNA into kinetic classes. Their fast and intermedi- ate DNA classes, although somewhat poorly resolved, have CsC1 density profiles similar to the Cot 10 .2 and Cot 10-2--1.0 DNA fractions in Fig. 7. This investi- gation and the more brief studies [11,26,35] compared in Table II did not fractionate the DNA classes into molecular families for further study.

A number of human satellite DNA fractions [3,6,7] have been identified by Ag ÷ or Hg2÷-Cs2SO4 gradient techniques. Satellite III [6] has properties that strongly suggest its similarity to the 1.700 DNA of this study. These include identical in situ hybridization patterns [10,32] . Similarly, Satellite II has an in situ hybridization pattern [25] , renatured buoyant density and percentage in the genome [3] similar to that of the 1.696 DNA [10] .

The possible biological functions of repetit ious DNAs in higher organisms have been discussed in a number of studies [2 ,10,36,37,39] . Evidence is ac- cumulating which implicates repetit ious human DNA of varying complexi ty as well as foldback DNA sequences in post-transcriptional control (see refs. 38,39 for review). Jelinek et al. [38] have demonstrated the presence of both types of human DNA sequences in Hn RNA. Some of these sequences do not appear with the mRNA in the cytoplasm. Melli et al. [40] have recently obtained preliminary evidence suggesting clustering of the DNA sequences complementa- ry to highly repetitive HeLa cell nuclear RNA. Thus, a prerequisite to our understanding of the biological function of any given human DNA family is a knowledge of its pattern of occurrence in the genome. Studies to this end are in progress. Within this context , investigations of in vivo RNA could determine whether any of the particular DNA families are involved in the processing or control of transcribed information.

147

Acknowledgements

This work was supported by the United States Public Health Service Grant No. GM 11180.

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