GENOMICS

13,332-338

(1992)

Chromosome 16-Specific Repetitive DNA Sequences That Map to Chromosomal Regions Known to Undergo Breakage/ Rearrangement in Leukemia Cells RAYMOND

L. STALLINGS, * NORMAN A. DOGGETT, * hTSUZUMl OKUMURA, t AND DAVID C. WARDt

*Center for Human Genome Studies and Life Sciences Division, Los Alamos National laboratory, Los Alamos, New Mexico 87545; and tDepartment of Human Genetics, Yale University School of Medicine, New Haven, Connecticut 06510 Received

October

25, 1991;

Human chromosome 16-specific low-abundance repetitive (CHlGLAR) DNA sequences have been identified during the course of constructing a physical map of this chromosome. At least three CHlGLAR sequences exist and they are interspersed, in small clusters, over four regions that constitute more than 5% of the chromosome. CH16LAR sequences were observed in one unusually large cosmid contig (number 55), where the ordering of clones was difficult because these sequences led to false overlaps between noncontiguous clones. Contig 55 contains 78 clones, or approximately 2% of all the clones contained within the present cosmid contig physical map. Fluorescent in situ hybridization of multiple clones, including cosmid and YAC contig 55 clones, mapped the four CHlGLAR-rich regions to bands ~13, ~12, pll, and q22. These regions are of biological interest since the pericentric inversion and the interhomologue translocation breakpoints commonly found in acute nonlymphocytic leukemia (ANLL) subtype M4 fall within these bands. Sequence analysis of a 2.2-kb Hind111 fragment from a cosmid containing a CHlGLAR sequence indicated that one of the CHlGLAR elements is similar to a minisatellite sequence in that the core repeat is only 40 bp in length. Additional characterization of other repetitive elements is in progress. 0 1992 Academic Press, Inc.

INTRODUCTION

Numerous classes of interspersed repetitive DNA sequences (IRS) have been identified in the genomes of humans and other eukaryotes and represent substantial portions of the genome (see Singer, 1982, for review). Some classes of the most abundant IRS have proven extremely useful in the development of ordered cosmid and YAC contig maps of human chromosomes. For example, Ah, Ll, and (GT), are used as “signposts” to assist in the correct assembly of cosmid clones into contigs (Stallings et aZ., 1990; Wada et al., 1990). In the case of human chromosome 16, a cosmid contig map for the entire chromosome is being constructed by repetitive sequence fingerprinting (Stallings et al., 1990). The fingerprinting analysis of over 4000 cosmid clones containing O&38-7543/92 Copyright All rights

332

$5.00 Q I992 by Academic Press, of reproduction in any form

Inc. reserved.

revised

December

20, 1991

chromosome 16 inserts has not revealed any negative effects of these high-abundance repeats on the ability to identify and order overlapping clones. In contrast, the effect of low-abundance repetitive sequences, such as minisatellites, on various physical mapping schemes is unknown. However, low-abundance IRS have the potential of making the construction of physical maps difficult, especially ordered contig maps. This is especially true for hybridization-based approaches, where low-abundance IRS cannot be suppressed by preannealing with Cot1 fractionated DNA. In addition, low-abundance repeats could interfere with restriction enzyme-based fingerprinting approaches if they contain restriction sites for the enzyme employed in the fingerprinting scheme. In this report, we describe chromosome 16-specific low-abundance repeats that have complicated the task of assembling clones into contigs for some regions of this chromosome. One of these chromosome 16-specific lowabundance repeats (CHlGLARl) is described in detail. It is very similar to the minisatellite repetitive sequences because the core repeat is short and it is distributed in euchromatin. Minisatellite repetitive sequences have been identified on numerous human chromosomes and usually possessa core repeat unit approximately 14-40 bp in length (Buroker et al., 1987; Das et al., 1987; Jarmen et al., 1986; Simmler et al., 1987; Stoker et al., 1985). Some minisatellites, such as those possessing significant similarity to the MI3 minisatellite motif, appear to occur on all human chromosomes (Christmann et al., 1991). Others may be chromosome specific and highly clustered within a single band of a chromosome. The minisatellite observed near the apolipoprotein gene occurs at approximately 60 sites on chromosome 19, all within band q13.3 (Das et al., 1987). The biological significance of minisatellite sequences is currently unknown, but in experimental systems these sequences possess highly recombinogenic properties (Wahls et al., 1990). A possible involvement of CHlGLAR sequences in chromosome 16 breakpoints found in acute nonlymphocytic leukemias is discussed.

CHROMOSOME

TABLE Overabundant EcoRI

Restriction

REPETITIVE

1 Fragments

Hi&II

0.98 1.75 2.21 2.82

16SPECIFIC

in Contig

55

EcoRI/HindIII

1.19 1.56

1.18 1.35

1.89 4.65

MATERIALS

AND

METHODS

Southern blotting and DNA hybridizations. Southern blotting was performed as described (Stallings et al., 1990) using Biodyne membranes (Pall, Glen Cove, NY). Plasmid and cosmid probes were “P-labeled by nick-translation to a specific activity >lO* cpm/pg, and small oligomers were “P-end-labeled using T4 polynucleotide kinase. C,tl DNA (BRL, Gaithersberg, MD) was preannealed to “P-labeled probes to mask repetitive sequences under conditions recommended by the supplier. Hybridizations were performed at 65°C in a high salt buffer containing 6X SSC, 10 m&f EDTA, pH 8.0, 1.0X Denhardt’s, 1% SDS, and 0.1 mg/ml sonicated, denatured salmon sperm DNA. Membranes were washed briefly in 2X SSC, 0.1% SDS at room temperature, 15 min in 2~ SSC, 0.1% SDS at room temperature, 15 min in 0.1~ SSC, 0.1% SDS at room temperature, and twice for 30 min in 0.1~ SSC, 0.1% SDS at 50°C. In situ hybridization. Cosmid clones were labeled with biotin dUTP and hybridized to metaphase chromosomes as described (Lichter et al., 1990). Probes were preannealed to human genomic or C,tl fractionated DNA to block repetitive sequences. Experiments were evaluated and digitally imaged using either a Bio-Rad MRC-500 confocal laser scanner or a cooled CCD camera (Photometrics) as previously described (Boyle et al., 1990). DNA cloning. A 2.2-kb Hind111 fragment from cosmid 311C6 was separated by agarose gel electrophoresis, entrapped on DEAE paper, and purified by standard protocols (Sambrook et al., 1989). Cloning of this 2.2-kb Hind111 fragment into the Hind111 site of Bluescript KS+ (Stratagene) produced plasmid p311C6-H2.2. DNA sequencing. Plasmid p311C6-H2.2 was double digested with Sac1 and EcoRV, and progressive unidirectional deletions were performed with exonuclease III followed by mung bean nuclease digestion (Poncz et al., 1982). The digestion products were recircularized and used to transform XLl-Blue competent cells (Stratagene). Doublestranded sequencing of p311C6-H2.2 and the deletion clones was performed using the dideoxy chain termination method (Sanger et al., 1977) and Sequenase reagents (United States Biochemical). Sequence assembly and database searching was aided by the GCG (Devereux et al., 1984) software package (release 7.0). Inter-ALU PCR. Inter-ALU PCR was performed on YAC clones containing chromosome 16 inserts following methods described by Nelson et al. (1989). The PDJ34Alu consensus sequence oligomer (Pieter DeJong, Lawrence Livermore National Laboratory) was used as a primer.

RESULTS

A cosmid contig map of human chromosome 16. A contig map of human chromosome 16 is being developed by repetitive sequence fingerprinting of cosmid clones containing inserts from this chromosome (Stallings et al., 1990). To date, over 4000 cosmids have been fingerprinted and assembled into -550 contigs. In most instances, contig assembly has been straightforward. However, one contig in particular, contig 55, has proven to be highly unusual for several reasons. First, it contains

DNA

SEQUENCES

333

more clones than any other contig (78 clones or -2% of all clones fingerprinted), and many of these clones contain small restriction fragments (l-3 kb size range) whose abundance is approximately threefold greater than that found in the database as a whole. Table 1 lists the restriction fragments that are overabundant in some contig 55 clones. Second, contig 55 clones could not be assembled into a linear contig, as there was a great amount of branching and piling of clones upon each other. The difficulty encountered in assembling a linear contig indicated that many false overlaps between clones were being generated due to the existence of some unknown repetitive sequence. By deleting the overabundant fragments from the analysis and analyzing the clones based upon more unique restriction fragments, contig 55 could be broken into several smaller contigs and single cosmids (singletons). Detection of CHlGLAR sequencesby in situ hybridization of contig 55 clones. Confirmation of the existence of chromosome 16-specific low-abundance repeats (CHlGLAR) was provided by fluorescence in situ hybridization of contig 55 cosmid clones. A total of five clones from contig 55 were labeled with biotin dUTP, preannealed with either human genomic or C,tl fractionated DNA to mask repetitive DNA sequences, and hybridized to normal human metaphase chromosomes. The in situ hybridization signals were unusually intense, and some clones mapped to as many as three locations on chromosome 16 (Fig. 1A). Figure 2 summarizes the regions in which each clone was localized on chromosome 16. We also found one chromosome 16 YAC clone, Y16.7, whose inter-Alu PCR products had an in situ hybridization pattern similar to that of some of the clones from c55 (Fig. 2). In total, these clones mapped to bands 16~13, 16~12, 16~11, and 16q22, as determined by fractional length measurements (Lichter et al., 1990) and in some casesby Alu-PCR hybridization banding (Baldini and Ward, 1991). These results, along with additional results discussed below, indicate that these regions possesschromosome 16-specific, low-abundance, repetitive sequences. We call these sequences low abundant because they could not be masked by preannealing with human genomic or C,tl fractionated DNA. The hybridization patterns of different clones indicate that more than one repeat occurs in these regions. For example, the hybridization of 81B9, 60B10, and 303F2 to p13 and q22 and the hybridization of 13E7 and 46A3 to ~12, pll, and q22 indicate that there must be a minimum of three CHlGLAR sequences. Identification of a restriction fragment containing a CHl 6LAR sequence. Two features of YAC clone Y 16.7 made it useful for identifying a restriction fragment containing a CHlGLAR sequence from the contig 55 clones. First, Y16.7 contains one or more CHlGLAR sequences (determined by in situ hybridization), and second, Y16.7 does not overlap the regions from which any of the contig 55 clones were derived. The latter is’ true because

334

STALLINGS

ET AL.

CHROMOSOME

13.2

I

:t:i: 13.11 ::3 12.1

I 13E7

81 B9

16SPECIFIC

I

DNA

SEQUENCES

335

I 303F2

6OBlO

I

I

Y16.7

46A3

11.1

REPETITIVE

11.2 12.1 12.2 13 21 22.1 22.2 22.3 23.1 23.2 23.3 24.1 24.2 24.3

I 13E7

146A3

I,,,,

1’32G5

I6OBlO

(Y16.7

1303F2

3

16 FIG. 2. Idiogram locations of cosmid

summarizing clones from

the in situ hybridization contig 55 and YAC clone

mapping Y16.7.

cosmid subclones of Y 16.7 show no similarity in repetitive sequence fingerprint patterns to contig 55 cosmids (data not shown). We can therefore conclude that when inter-AZu PCR products from Y 16.7 are preannealed to CJl DNA and hybridized to gridded arrays of contig 55 cosmid clones, it is only the CHlGLAR sequences that are hybridizing. Hybridization of Y16.7 inter-Alu PCR products to Southern blots containing DNA from contig 55 clones should therefore allow the identification of restriction fragments containing CHlGLARs. Southern blots containing several contig 55 clones were hybridized with Y16.7 inter-AZu PCR products, and in each case only a single restriction fragment was positive. One of these hybridizations (Y16.7 Alu-PCR products to cosmid 311C6) is shown in Fig. 3. Only a single restriction fragment is positive in the EcoRI, HindIII, or EcoRI/ Hind111 digest lanes. The 2.2-kb Hind111 fragment from cosmid 311C6, which hybridized to Y16.7 inter-Alu PCR products (Fig. 3), was subcloned into Bluescript KS+ and designated p311C6-H2.2. In situ hybridization of p311C6-H2.2 to metaphase chromosomes (Fig. 1B) revealed a signal on both the p and the q arms of chromosome 16, thus confirming that the fragment contained a CHlGLAR sequence. The plasmid produced a less intense signal than cosmids from contig 55. Preannealing of unlabeled p311C6-H2.2 to cosmid DNA from contig 55 clones prior to in situ hybridization failed to block multiple hybridization signals occurring on chromosome 16 (Fig. IC). These results further support the conclusion that more than one

FIG. 3. Hybridization of inter-Alu PCR products from Y16.7 to a Southern blot containing EcoRI (left lane), EcoRI/HindIII (middle lane), and Hind111 (right lane) digested DNA from cosmid clone 311C6 (from contig 55). Right figure is the ethidium bromide-stained gel. A single fragment, containing a CHlGLAR sequence, showedpositive hybridization signal on a single restriction fragment in all three digests. The 2.2 kb Hind111 fragment was subsequently cloned and sequenced.

low-abundance repetitive sequence exists in contig 55 clones. Sequencing of a 2.2-kb HindIII fragment containing a CHlGLAR sequence. Sequence data from p311C6-H2.2 were obtained by sequencing both ends of the insert and by sequencing subclones that contained unidirectional deletions generated with a exonuclease III/mung bean nuclease digestion system. Figure 4 is a map showing the positions of Ah and non-Alu sequences and the position that contains CHlGLARl. Both DNA strands were sequenced for the region containing the CHlGLAR repeat (bp 45-374), and the concordance between the two independently derived sequences was 99%. A total of five Ah repeats were identified in the p311C6-H2.2 insert. Two gaps of unsequenced regions, totaling - 180 bp, also exist in the map (Fig. 4). A 40-bp sequence was repeated four times (and once partially) in the first 400 bp of the sequence from p311C6-H2.2 (Fig. 5A). The consensus sequence, illus-

FIG. 1. (A) In situ hybridization of biotinylated cosmid clone 13E7 to normal human metaphase spreads (FITC detection). The clone hybridizes to two regions on the p arm with great intensity and to one region of the q arm with less intensity. (B) In situ hybridization of biotinylated p311C6-H2.2 to normal human metaphase chromosomes. Two regions on the p arm and one region on the q arm show hybridization signal. (C) 1n situ hybridization of biotinylated cosmid clone 13E7 to metaphase chromosomes. Cosmid clone 13E7 DNA was preannealed with p311C6-H2.2 DNA prior to hybridization. Some blocking of the CH16LAR repeat may have occurred because the original intensity (especially on the q arm) is somewhat weaker, but p311C6-H2.2 failed to totally suppress the multiple signals, indicating the presence of more than one CHlGLAR. All three images were taken with a cooled CCD camera using identical image acquisition times to facilitate comparison of relative signal intensity. Chromosomes were counterstained with DAPI.

336

STALLINGS

ET AL.

3llC6T7 EX0215 IX029

~ fxo36 Exo33

EX027

---Ewq3:P= Exo45

Ex031 mm417

ExO47 311C5HR EX0311

I

0.0

I

I

I

I

I

I

I

I

0.2

0.4

0.6

0.6

1.0

1.2

1.4

1.6

I +... .......... .......

I 1.6

I 2.0

I

2.2

LOW ABUNDANCE REPEAT SINGLE COPY ALU REPEAT UNSEQUENCED GAP

FIG. 4. Map of regions sequenced from p311C6-HZ.2 The map at the top shows regions containing Ah sequences, along with the orientation of the Ah (designated with arrows); non-Alu regions (open boxes); minisatellite or CH16LAR region (black box); unsequenced gaps (dashed line); and regions from where oligomers were synthesized (+ signs and arrows) for use as hybridization probes. The amount of sequence information obtained from each exonuclease-digested clone is designated as horizontal lines below the map. The unidirectional deletions occur from right to left in each clone. Sequences 311C6T7 and 311C6HR were obtained from p311C6-H2.2 using the T7 and T3 oligomers as sequencing primers. The ends at which sequencing primers bound to the sequence are designated by the position (left or right) of the sequence designation.

trated in Fig. 5B, did not possess significant sequence homology to any previously described minisatellite core sequence contained in Genbank (data not shown). In this same 400-bp region, a 46-bp sequence was also repeated once with 91% fidelity (Fig. 5C). Both of these short, tandemly duplicated sequences are reminiscent of the minisatellite class of repetitive sequences. The other non-Alu sequences shown on the map in Fig. 4 did not contain any internally duplicated sequences. Identification and characterization of CHIGLAR sequences. The identification of repeated sequences in the first 400 bp of the p311C6-H2.2 insert indicated that this region might be the CHlGLAR sequence. To test this hypothesis, we synthesized an oligomer sequence for 35 bp of the most conserved region of the consensus sequence and for other non-ALU sequences found in p311C6-H2.2. The positions from which these oligomers were synthesized are noted on the map in Fig. 4. These oligonucleotides were hybridized to the gridded arrays of cosmid clones. The 35bp oligomer sequence hybridized to 45 out of the 78 cosmids from contig 55 while oligomers 2 and 3 hybridized to 5 and 9 cosmids, respectively. On the basis of these hybridization results, we can conclude that the minisatellite sequence is one of the CHlGLAR sequencespresent in over 50% of the cosmid clones originally assigned to contig 55. Oligomers 2 and 3 are either unique sequences or repetitive sequences less abundant than the 40-bp minisatellite sequence. Hybridization characterization of ~311 C6-H2.2. Quantitative slot blot hybridization (data not shown)

with the consensus sequence oligomer indicated that approximately 250 copies of this repeat occur in the human genome. High-stringency hybridization of p311C6-H2.2 to Southern blots containing human, old world monkey (Rhesus macaque), rat, mouse, dog, cow, rabbit, chicken, and yeast genomic DNA produced a smear in lanes containing human and monkey DNA and nothing in the other lanes (Fig. 6). Lowering the stringency of hybridization by reducing the temperature from 60 to 50°C allowed a very faint band to be observed in other mammalian species. These results indicate that the CHlGLARl sequence is primate specific and therefore could be relatively recent in origin. DISCUSSION

Exactly how many distinct CHlGLAR sequences exist on chromosome 16 is uncertain. That more than one exists is supported by the fact that four distinct regions of chromosome 16 show a hybridization signal with contig 55 cosmids; yet any single cosmid tested hybridizes to a maximum of only three regions. A group at Leiden has independently isolated cosmid clones containing CHlGLAR sequences, one of which hybridizes to only two blocks on the p arm of chromosome 16 (Dauwerse et al., 1992). The failure of p311C6-H2.2 to block multiple hybridization signals when preannealed to contig 55 cosmids indicates that more than one CHlGLAR sequence exists. Finally, the fact that there are at least four overabundant EcoRI and Hind111 restriction fragments in

CHROMOSOME

A

i 51

CCGCCAKCA

CC-CM

ClUACAACA

TKTATAACT

16-SPECIFIC

REPETITIVE

GATMC!CXC

+J)XGCCTCAA GACACCTCCC GAAlWKCP

101

v

151

~GTATiJ?XTCGTCCc'pcLTccICCCTCTCCTC

G-

CTxrcC

251 301

TTAGCTACTC AGGAGGCCGA GGCGGAAAAA CCACCCAAAC

351

AGGGTGGA~

ACGEGAACA

401

lGAGGT-.%AA

CAATCGCCCA AGCCCAAA

CAAGAGGTGG

ATTACCGAAA CCCAAGAGGC OGAGGVXGA

6 TCCT GTG KCT 2 GTATC KCT 4) 5) CTCT3TTITc TCCCT 1)

Consensus

Repeat

TCCC ‘TCCT KCCT KCT CTICCACCC TCCT XA

CTTGC GG

- KCT

CTKCACCCT CTKCACCCT CTKCACCCT CTPCCACCCT CTKCACCCT

CAGlCGA'I'.iA CAGlGGAlGA C CAGTGGATGA CAG-l%GATG

TAATUTXAG TAAXTGMG

GA GA

TAA'IC'TGMG ATAA7’3’ZM

GA -GA

X TCCT CTTCCACCCT CAG-KGATGA TAAXT

G MC C

GA

C 332 CACCCMACCCMGAGGTGGAGGGl"GGAlGAGGl'GGMCMKACC 376 III1 IIIIIIIIIIII llllll IIIIIIIIIIIIIIIIII II 373 CACCGAAACCCMGAGGCGGAGGGCGGA~AGGTGGAACAATCGCC 418

FIG. 5. The first 428 bp of p311C6-H2.2 is shown in (A). The positions of the 40-bp repeat are underlined. In (B), the regions containing the core repeats are aligned to show the sequence similarities. Preceding and following the first TCCT or TCCCT sequence are 0 to 11 bp of degenerate sequence that do not appear to have a significant pattern (other than CTT in lines 2 and 5). These degenerate sequences are represented by an X in the consensus repeat sequence. (C) A 46-bp sequence was repeated once with 91% fidelity in positions 332-376and373-418.

contig 55 clones suggests that there could be multiple CHlGLAR sequences. The nature of these other CH16LAR sequences remains to be determined. Several lines of evidence suggest that CHlGLAR sequences occur over a significant portion of chromosome 16. Analysis of Southern blots from pulsed-field gels (data not shown) indicated that the macrorestriction fragments that hybridized to contig 55 clones totaled between 2 and 6 Mb, depending on the restriction enzyme. Because of possible heterogeneity in the methylation of restriction sites, this type of analysis does not provide firm evidence for the size of the regions covered by CH16LAR sequences, but does indicate that these regions could be as large as 6 Mb. The size of contig 55 also suggests that CHlGLAR sequences occur over a substantial region of chromosome 16. Approximately 2% of the clones thus far fingerprinted occur in contig 55, and 2% of chromosome 16 is approximately 2 Mb. signal of contig 55 Finally, the in situ hybridization clones to chromosome 16 covers at least 5% or 5 Mb of the chromosome. Although the sequences are interspersed over substantial portions of chromosome 16, it is unlikely that they represent substantial portions of the genome if they, like CHlGLARl, are relatively short. It is quite likely that some gene sequences are located within the regions that contain CH16LAR sequences, given that these regions are relatively large and are in euchromatin. The physical mapping of these regions is therefore of interest. Alternative physical mapping strategies will have to be devised to map contigs from regions

DNA

SEQUENCES

337

containing CHlGLAR sequences. One such strategy might involve the isolation of unique sequences from contig 55 clones to be used as probes in pulsed-field gel analyses. The regions containing CHlGLAR sequences appear to overlap chromosome 16 breakpoints on the p and q arms commonly found in acute nonlymphocytic leukemia (ANLL) subtype M4 (Mittelman, 1986). One type of rearrangement found in ANLL M4 is a pericentric inversion with breakpoints in p13 and q22 (LeBeau et al., 1983). Other ANLL M4 rearrangements are interhomologue translocations between 16~13 and 16q22, aswell as deletions affecting 16q22 (Mittelman, 1986). Given the high rate of recombination associated with minisatellite sequences (Wahls et al., 1990), it is not unreasonable to consider that CHlGLAR sequences may be causally related to the inversions and translocations that occur in leukemia cells. Recombination occurring between CHLAR sequences on the p and q arm could perhaps lead to these pericentric inversions or translocations. Other minisatellite sequences have been found near the translocation breakpoints affecting the c-myc and bc12 oncogenes (Krowczynska et al., 1990).

FIG. 6. Zoo blot. Lanes contain EcoRI-digested DNA from the designated species. A smear of hybridization can be observed in human and monkey DNA (Rhesus macaque). p311C6-H2.2 was used as probe and was preannealed with C,tl fractionated DNA. We believe that the suppression of Ah was complete because in situ hybridization of p311C6-H2.2 to human chromosomes did not show additional hybridization to other chromosomes. Also, p311C6-H2.2 has been hybridized to other cosmid clones on Southern blots and only one restriction fragment was positive. Other fragments from these cosmid clones are known to contain Ah sequences and are completely negative.

338

STALLINGS

In addition to inversions and interhomologue translocations, translocations between 16~13 and other chromosomes, such as chromosome 6, have been observed in ANLL M4 cases (Lai et al., 1987). Wessels et al. (1991) have shown that the breakpoints occurring in a 16;8 translocation and the 16 (~13.2) pericentric inversion occurring in ANLL M4 are at different loci. They proposed that two distinct loci in 16~13, in addition to the locus at 16q22, are involved in ANLL M4. Other types of cancers, including hepatocellular carcinoma (Tsuda et al., 1990) and prostate adenocarcinoma (Carter et al., 1990), have involved the q22 region of chromosome 16. In these cases, the loss of heterozygosity for alleles locatedon 16q22 has been reported. The isolation of repetitive sequences common to bands 16~13 and 16q22 should facilitate the isolation of the breakpoint regions and any gene(s) that may reside at these breakpoints. ACKNOWLEDGMENTS This study was supported Grant GM-00272 to D.C.W. Mandy Ford, Cleo Naranjo, greatly appreciated. We thank for helpful discussions, Dr. analysis, and Dr. Mary-Kay

by grants from the USDOE and NIH The technical support of Judy Tesmer, Liz Saunders, and Lynne Duesing was Drs. Robert Moyzis and Ed Hildebrand David Torney for assistance with data McCormick for YAC clone Y16.7.

REFERENCES Baldini, A., and Ward, D. C. (1991). Z n situ hybridization banding human chromosomes with alu-PCR products: A simultaneous karyotype for gene mapping studies. Gerwmics 9: 770-774. Boyle, A. L., Ballard, S. G., and Ward, D. C. (1990). Differential bution of long and short interspersed element sequences mouse genome: Chromosome karyotyping by fluorescence hybridization. Proc. Natl. Acad. Sci. USA 87: 7757-7761.

of

distriin the in situ

Buroker, H., Bestwick, R., Haight, G., Magenis, R. E., and Litt, M. (1987). A hypervariable repeated sequence on human chromosome 1~36. Hum. Genet. 77: 175-181. Carter, B. S., Ewing, C. M., Ward, S., Treiger, B. F., Aalders, T. W., Schalken, J. A., Epstein, J. L., and Isaacs, W. B. (1990). Allelic loss of chromosomes 16q and 1Oq in human prostate cancer. Proc. Natl. Acad. Sci. USA 87: 8751-8755. Christmann, A., Lagoda, P. J., and Zang, K. D. (1991). Nonradioactive in situ hybridization pattern of the Ml3 minisatellite sequences human metaphase chromosomes. Hum. Genet. 86: 487-490.

on

Das, H. K., Jackson, C. L., Miller, D. A., Leff, T., and Breslow, J. L. (1987). The human apolipoprotein C-II gene sequence contains a novel chromosome 19-specific minisatellite in its third intron. J. Biol. Chem. 262: 4787-4793. Dauwerse, J. G., Jumelet, E. A., Wessels, J. W., Saris, J. J., Hagemeijer, G., Beverstock, G., Van Ommen, G. J. B., and Breuning, M. H. (1992). Extensive cross-homology between chromosome 16p and 16q may explain inversions and translocations. Blood, in press. Devereux, J., Haeberli, P., and Smithies, 0. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387-395. Jarmen, A. P., Nicholls, R. D., Weatherall, D. J., Clegg, J. B., and Higgs, D. R. (1986). Molecular characterization of a hypervariable

ET

AL.

region downstream of the human a-globin gene cluster. EMBO J. 5: 1857-1863. Krowczynska, A. M., Rudders, R. A., and Kronitis, T. G. (1990). The human minisatellite consensus at breakpoints of oncogene translocations. Nucleic Acids. Res. 18: 1121-1127. Lai, J. L., Zandecki, M., Jouet, J. P., Savary, J. B., Lambiliotte, A., Bouters, F., Cosson, A., and Demiatti, M. (1987). Three case of translocation (8;16)(pll;p13) observed in acute myelomonocytic leukemia. Cancer Genet. Cytogenet. 27: 101. LeBeau, M. M., Larson, R. A., Bitter, M. A., Vardiman, J. W., Golomb, H. M., and Rowley, J. D. (1983). Association of an inversion of chromosome 16 with abnormal marrow eosinophils in acute myelomonocytic leukemia: A unique cytogenetic-clinicopathologic association. N. Engl. J. Med. 309: 630. Lichter, P., Tang, C., Call, K., Hermanson, G., Evans, G., Housman, D., and Ward, D. (1990). High resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64-69. Mittleman, F. (1986). Clustering of breakpoints to specific chromosomal regions in human neoplasia. A survey of 5,345 cases. Hereditab- 104: 113-119. Nelson, D. L., Ledbetter, S. A., Corbo, L., Victoria, M. F., Ramirez-Solis, R., Webster, T. D., Ledbetter, D. H., and Caskey, C. T. (1989). Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA 86: 6686-6690. Poncz, M., Soloweijczyk, D., Ballantine, M., Schwartz, E., and Surrey, S. (1982). “Nonrandom” DNA sequencing analysis in bacteriophage Ml3 by the dideoxychain termination method, Proc. Natl. Acad. Sci. USA 79: 4298-4302. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). “Molecular Cloning: A Laboratory Manual,” Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463-5467. Simmler, M. C., Johnson, C., Petit, C., Rouyer, F., Vergnaud, G., and Weissenbach, J. (1987). Two highly polymorphic minisatellites from the pseudoautosomal region of the human sex chromosomes. EMBO J. 6: 963-969. Singer, M. F. (1982). Highly repeated sequences in mammalian genomes. Internat. Reu. Cytol. 76: 67-112. Stallings, R. L., Torney, D. C., Hildebrand, C. E., Longmire, J. L., Deaven, L. L., Jett, J. H., Doggett, N. A., and Moyzis, R. K. (1990). Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc. Natl. Acad. Sci. USA 87: 6218-6222. Stoker, N. G., Cheah, K. S., Griffin, J. R., Pope, F. M., and Solomon, E. (1985). A highly polymorphic region 3’ to the human type II collagen gene. Nucleic Acids Res. 13: 4613-4622. Tsuda, H., Zhang, W., Shimosato, Y., Yokota, J., Terada, M., Sugimura, T., Miyamura, T., and Hirohashi, S. (1990). Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma. Proc. Natl. Acad. Sci. USA 87: 6791-6794. Wada, M., Little, R. D., Abidi, F., Porta, G., Labella, T., Cooper, T., Della Valle, G., D’Vruso, M., and Schlessinger, D. (1990). Human Xq24-Xq28: Approaches to mapping with yeast artificial chromosomes. Am. J. Hum. Genet. 46: 95-106. Wahls, W. P., Wallace, L. J., and Moore, P. D. (1990). Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells. Cell 60: 95-103. Wessels, J. W., Mollevanger, P., Dauwerse, J. G., Cluitmans, F. H., Breuning, M. H., and Beverstock, G. C. (1991). Two distinct loci on the short arm of chromosome 16 are involved in myeloid leukemia. Blood 77: 1555-1559.

rearrangement in leukemia cells.

Human chromosome 16-specific low-abundance repetitive (CH16LAR) DNA sequences have been identified during the course of constructing a physical map of...
7MB Sizes 0 Downloads 0 Views