The border between the Ultrabithorax and abdominal-A regulatory

domains

in the Drosophila bithorax complex

Welcome Bender and Maura Lucas1

BCMP Department, Harvard Medical School

Boston, Massachusetts 02115

1present address: University of Massachusetts Medical School

Genetics: Advance Online Publication, published on January 3, 2013 as 10.1534/genetics.112.146340

Copyright 2013.

55 Lake Avenue North

Worchester, MA 01655 running title: The bxd/iab-2 Border

Key words: BX-C, Ultrabithorax, abdominal-A, Glut3, CTCF

Corresponding author: Welcome Bender

BCMP Department

Harvard Medical School

240 Longwood Avenue

Boston, MA 02115

ph: 617-432-1906

FAX: 617-738-0516

email: not used

Abstract

The bithorax complex in Drosophila melanogaster includes three homeobox-

containing genes, Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-

B), which are required for the proper differentiation of the posterior ten segments of

the body. Each of these genes has multiple distinct regulatory regions; there is one

for each segmental unit of the body plan where the genes are expressed. One

additional protein coding gene in the bithorax complex, Glut3, a sugar-transporter

homolog, can be deleted without phenotype. We focus here on the upstream

regulatory region for Ubx, the bithoraxoid (bxd) domain, and its border with the

adjacent infraabdominal-2 (iab-2) domain, which controls abdA. These two domains

can be defined by the phenotypes of rearrangement breakpoints, and by the

expression patterns of enhancer traps. In D. virilis, the homeotic cluster is split

between Ubx and abd-A, and so the border can also be located by a sequence

comparison between species. When the border region is deleted in melanogaster, the

flies show a dominant phenotype called Front-ultraabdominal (Fub); the first

abdominal segment is transformed into a copy of the second abdominal segment.

Thus, the border blocks the spread of activation from the bxd domain into the iab-2

domain.

Introduction

The ~300 kb expanse of the bithorax complex (BX-C) includes very little protein

coding information; there are three transcription units for homeobox transcription

factors, plus one open reading frame encoding a glucose transporter homolog (Martin

et al, 1995). Many mutations in the complex have been recovered because of their

segmental transformation phenotypes; most fall outside the known transcription units

(Maeda and Karch, 2006). However, such mutations fail to complement with

mutations in one of the three homeobox genes, and so they were suspected to alter

the regulation of these three major products. Indeed, many of these mutations alter

the patterns of expression of the three homeobox genes (Beachy et al., 1985, Karch

et al., 1990; Celniker et al., 1990; Sánchez-Herrero, 1991).

The regulatory mutations revealed a striking order to the complex; they are aligned

on the genetic map in the order of the most anterior segments (or, more precisely, the

parasegments) that they affect (Lewis, 1978). The lesions of recessive (loss-of-

function) mutants that affect a particular parasegment roughly define a segmental

domain; there appears to be one such domain for each parasegment. The domains

are named after the mutant names, in the order (proximal to distal): bithorax (bx,

affecting the posterior thorax or PS5), bithoraxoid (bxd, affecting the first abdominal

segment or PS6), and infraabdominal-2 through infraabdominal-9 (iab-2 through iab-9,

affecting the second through ninth abdominal segments, or PS7 through PS14)

(Lewis, 1078). It has been suggested that each of these segmental domains reflect a

large region of the chromosome that is either activated or repressed as a unit,

depending on the position of a cell along the body axis (Lewis, 1981; Peifer et al.,

1987). Support for this view has come from the study of insertions into the BX-C of

mobile elements (Bender and Hudson, 2000), and of other probes for DNA

accessibility (Fitzgerald and Bender, 2001).

Unfortunately, the extents of the segmental domains are not precisely mapped by

the mutant analysis, for several reasons. Many of the available mutations are

associated with rearrangement breakpoints, which can affect domains beyond the one

they interrupt, either by position effects or by polar effects. As an example of a polar

effect, a break in the iab-7 (PS12) domain separates the iab-6 (PS11) and iab-5

(PS10) domains from the Abd-B transcription unit, which all three domains regulate.

Thus, iab-7 breaks cause transformations in the 5th, 6th, and 7th abdominal

segments. Four regulatory domains (bx, iab-2, iab-8, and iab-9) lie partly or wholly

within the transcription units they regulate, and are thus more difficult to define,

especially with rearrangement breakpoints. In addition, transformations among the

second though fifth abdominal segments are difficult to discern, due to the similar

morphologies of these segments.

“Boundaries” between segmental regulatory domains have been proposed, based

on the phenotypes of several small deletions. The Fab-7 deletions were proposed to

define the boundary between the iab-6 and iab-7 domains (regulating PS11 and

PS12, respectively) (Gyurkovics et al., 1990). Likewise, the Mcp deletions were

thought to remove a boundary between the iab-4 and iab-5 domains (affecting PS9

and PS10) (Karch et al., 1994), Fab-8 deletions are associated with the iab-7 / iab-8

boundary (affecting PS12/PS13) (Barges et al., 2000), and Fab-6 deletions

correspond to the iab-5/iab-6 boundary (affecting PS10/PS11)(Iampietro et al., 2010).

In each case, these deletions cause a dominant gain-of-function phenotype, showing

a transformation of the more anterior parasegment towards the character of the more

posterior one. This has been interpreted as spreading of the activation from one

segmental domain into the normally-repressed adjacent domain, when the boundary

between them is deleted. However, the limits of the iab-4 through iab-8 domains are

not well defined, for the reasons described above, and so it is not clear that these

deletions fall at the borders between domains, if, indeed, there are discrete borders.

The assumption that these deletions remove boundaries has been inferred from their

dominant (gain-of-function) phenotypes, but there is no reason to predict what that

phenotype of a boundary deletion should be. It is not clear whether there must be a

discrete barrier between adjacent active and repressed domains, or whether the

spread of marks for activation and repression are short-range and graded (Hathaway

et al., 2012).

The definition of boundaries is complicated by the presence of PREs at, or very

near, the Mcp, Fab-6, Fab-7, and Fab-8 boundaries. Deletions of the best studied

PRE, in the middle of the bxd domain (far from any proposed boundary), cause a

dominant phenotype similar to those of the boundary deletions, a one-parasegment

posterior transformation (Sipos et al., 2007). Although the bxd PRE deletion

phenotype is weaker than those of the boundary deletions, it is possible that the latter

transformations result from the loss of PREs. Efforts have been made to distinguish

the boundary from the nearby PREs (Mihaly et al., 1997; Gruzdeva et al., 2005).

Mihaly et al. (1997) concluded that deletion of the Fab-7 boundary, but not the

associated PRE, resulted in both gain-of-function and loss-of-function phenotypes,

due to spreading of both activation and of repression. Deletions that define the Fab-6

boundary also show a mixture of gain-of-function and loss-of-function phenotypes

(Iampietro et al., 2010). However, these analyses rest on assumed phenotypes of a

minimal boundary deletion, or on assumed properties of PREs and boundaries on

transgenes. In particular, the test for boundaries as insulators (i.e. enhancer blockers)

on transgenes is not reliable. The Fab-7 boundary, for example, lies between the iab-

6 domain and the Abd-B transcription unit that it regulates; this boundary clearly does

not block those enhancer/promoter interactions. It has been proposed that “promoter

targeting sequences” or “promoter tethering elements” exist in the BX-C to bypass

Fab-7 and other boundaries (Chen et al., 2005; Akbari et al., 2008). However, Hogga

et al. (2001) converted prototypic insulators (binding sites for the suppressor of Hairy-

wing protein, or the scs element adjacent to the HSP70 locus) into the endogenous

BX-C, and showed that they are not bypassed and cannot substitute for the Fab-7

boundary.

The transition zone, or “border” between the bxd domain and the adjacent iab-2

domain presents a unique opportunity, because it can be precisely mapped by

multiple criteria. (We prefer the term “border” to “boundary” or “insulator” because

“border” does not imply a function.) Mutations with lesions proximal to the bxd/iab-2

border fail to complement with Ubx, and primarily affect the first abdominal segment

(PS6)(Bender et al., 1985). Mutations distal to the border fail to complement with abd-

A and affect the second abdominal segment (PS7)(Karch et al., 1985). Enhancer

traps proximal to the border drive reporter genes starting in PS6; distal traps mark

PS7 (Bender and Hudson, 2000). Finally, in Drosophila virilis, Ubx and its regulatory

regions are clustered with the genes of the Antennapedia complex, leaving abd-A and

Abd-B as a separate cluster (Von Allmen et al., 1996). Mapping the homologies from

the edges of the two D. virilis clusters should help to define the limits of the adjacent

bxd and iab-2 regulatory domains. If the border region, so defined, lacks a PRE, then

a deletion of the border might show whether it is required to separate the regulatory

signals of the two domains.

In this manuscript we consolidate studies carried out over many years, which

together map the functions and extent of the bxd regulatory domain, and which define

the position and function of the bxd/iab-2 border. Materials and Methods

Sequence coordinates

The D. melanogaster sequence coordinates follow the SEQ89E numbering of

Martin et al. (1995)(GenBank U31961). Base #1 of SEQ89E corresponds to base

#12,809,162 in Release 5.37 of the D. melanogaster genome; SEQ89E numbering

proceeds from distal (Abd-B) to proximal (Ubx); the assembled genome proceeds

proximal to distal. The genome sequence includes a 6134 bp insertion of the Diver

retroposon in the bxd domain, with a 4 bp target duplication of bases 220,924-220,927

in SEQ89E. The target chromosome used for gene conversion experiments includes

278 bp from the 3’ end of the jockey transposable element, with a duplication of the 10

bp target site of bases 184,640-184,649 in SEQ89E.

Derivation of synthetic deficiencies

Hm: This breakpoint is derived from the complex rearrangement T(2;3) Hm (new

order 100-89E/32-29/89E-88E/32-60; 61-88E/29-21). Both fusion fragments of the

translocation have been cloned, and the rearrangement interrupts the BX-C DNA map

at ~240,000 (SEQ89E coordinates) (W. B., unpublished results). The rearrangement

has a dominant phenotype of transformation of the wing blade to the capitellum of the

haltere (Lewis, 1982), but there are no dominant effects we have noticed in the

embryonic pattern of UBX protein , or on the embryonic cuticle. E. B. Lewis

generated an insertional translocation into the Y chromosome of the left part of the

complex through the Hm breakpoint (Dp(Y;2;3)Hm ); this insertion conferred the

dominant phenotype, and the altered Y chromosome was male sterile. This Y

insertion was used to generate embryos lacking BX-C DNA to the right of the Hm

breakpoint. Females Dp(3;1)68 / FM6 / Dp(Y;2;3) Hm were crossed to males

T(1;3)P115 / TM1. Female offspring of the genotype Dp(3;1)P115 / FM6 /

Dp(Y;2;3)Hm; Df(3R)P115 / + were mated to males with Df(3R)P9 / Sb Dp(3R)P5.

One eighth of the embryos from this cross had the desired genotype, Dp(Y;2;3)Hm;

Df(3R)P9 / Df(3R)P115. The Dp(Y;2;3)Hm stock has been lost since these

experiments were done.

bxd100 This breakpoint is from an insertional transposition of the proximal part of the

BX-C (89B5-6 to 89E2 into 66C); the resulting duplication and deficiency stocks are

available separately. The breakpoint has been located by in-situ hybridization and

genomic blots to the interval 227,500-230,500 (Bender et al., 1983). Males with

Dp(3:1)68 ; Dp(3)bxd100 Df(3R)P115 / TM1 were crossed to Df(3R)P9 / Sb Dp(3)P5

females. One eighth of the resulting embryos were the desired genotype, Dp(3)bxd100

Df(3R)P115 / Df(3R)P9.

bxd111 This breakpoint is from an insertional translocation of the distal part of the BX-

C into the X chromosome (89E3-4 to 90B2 into 4D). The breakpoint has been

assigned to the interval 213,000-216,000 by genomic blots and in-situ hybridizations

(Bender et al., 1983). T(3;1)bxd111 / TM1 males were crossed to Df(3R)P9 / Sb

Dp(3)P5 females. One eighth of the offspring were the desired genotype,

Df(3R)bxd111 / Df(3R)P9.

bxd1068 This is a translocation to 2R heterochromatin; the break in BX-C DNA is

between 201,000-203,500, as determined by genomic blotting (Bender et al., 1985).

To create a synthetic deficiency for BX-C DNA to the right of this breakpoint, this

rearrangement was combined with T(2;3)Abd-B1065 (called iab-71065 in Karch et al.,

1985), which is also a translocation to 2R heterochromatin breaking in the BX-C at

about 42,000 kb. The Abd-B1065 breakpoint is about 12 kb distal to the Abd-B

homeobox, and the synthetic deficiency is completely lacking both abd-A and Abd-B

function, as judged by the apparently uniform expression of Ubx protein in the 1st

through 8th abdominal segments. Males with T(2;3)bxd1068 / TM1 were crossed to

females with T(2;3)Abd-B1065 / Sb Dp(3)P5. Male offspring with T(2;3)bxd1068 /

T(2;3)Abd-B1065 were crossed to Df(3R)P9 / Sb Dp(3)P5 females. One eighth of the

embryos had the desired genotype of bxd1068-left Abd-B1065-right / Df(3R)P9.

Uab5 This rearrangement is a translocation to the tip of the X chromosome (1F); the

break is associated with recessive lethal and a dominant male sterile mutations,

presumably due to the X chromosome breakpoint. Both fusion fragments have been

cloned, and the breakpoint maps to 186,000 in the BX-C DNA (Barbara Weiffenbach

and W. B., unpublished results). The dominant Uab phenotype is associated with the

X/distal 3R fusion chromosome. Synthetic deficiencies for the right half of the BX-C

were generated with T(Y;3)B116, which breaks in 90E, distal to the BX-C. Females

with T(1;3)Uab5 / FM6 / Y were crossed to T(Y;3)B116 males. Nondisjunction in the

mothers leads to female offspring with T(1;3)Uab5 / T(Y;3)B116 / FM6; these were

crossed to Df(3R)P9 / Sb Dp(3)P5 males. One in twelve of the resulting zygotes that

were not grossly aneuploid were of the desired genotype, T(1;3)Uab5-left T(Y;3)B116-

right / Df(3R)P9.

P10 This is an insertional translocation of the proximal part of the BX-C into 2L

(89C1-2 to 89E1-2 into 29A-C). It breaks the BX-C DNA at 174,000, within the abd-A

transcription unit (Karch at al., 1985). Dp(3;2)P10 homozygous males were crossed

to T(3;1)P115 / TM1 females. Male offspring with Dp(3;1)P115; Dp(3;2)P10;

Df(3R)P115 were crossed to Df(3R)P9 / Sb Dp(3)P5 females. One eighth of the

zygotes were of the desired genotype, Dp(3;2)P10 / +; Df(3R)P9 / Df(3R)P115.

D. virilis clones.

Phage clones overlapping the D. virilis abd-A gene were obtained from François

Karch (Von Allmen et al., 1996). D. virilis clones homologous to the distal bxd region

of D. melanogaster were isolated by Barbara Weiffenbach, using a phage library

constructed by Ron Blackman (Charon 30 vector). Subclones from the virilis phage

clones were sequenced from both ends using primer walking. Sequences were

assembled and homologies were mapped using MacVector software; they are listed in

GenBank under accession numbers JX877552 (for virilis bxd) and JX877553 (for

virilis iab-2). These sequences are collinear with the comparable regions of the more

recent D. virilis genomic scaffold (Clark et al., 2007), with a 1-2% mismatch. The

genomic scaffold sequence is the more reliable, since our sequence was usually from

one strand, often with only single coverage. The genomic sequence was used for the

Glut3 protein prediction of Fig. 3.

Recombination between P elements

The “Homing Pigeon” P element was used to recover enhancer traps in the BX-C

(Bender and Hudson, 2000). It contains two FRT sites flanking the rosy+

transformation marker. When two such P insertions with the same chromosomal

orientation are in trans, recombination between them can be generated by a heat-

inducible flipase gene (Kopp et al., 1997). The resulting crossovers can generate

either a duplication or deletion for the chromosomal region between the insertion

sites, and the hybrid P element can have 0, 1, or 2 copies of the rosy+ marker (Bender

and Hudson, 2000). Flanking markers (Sb and Fab-7) were used to recognize

recombinants, and to indicate the direction of the crossover (i.e., duplication or

deletion).

Deletion of the bxd/iab-2 border

The donor plasmid diagramed in Figure 5 included three genomic fragments,

cloned by PCR from cn; ry flies (the background strain for the HC184B P element

insertion) into the Bluescript II KS+ vector (Strategene-Agilent). The fragments

covered sequence coordinates 189,407-186,680 (red), 182,352-181,405 (blue), and

186,670-183,675 (orange). A synthetic linker between the blue and orange fragments

included the following sites: HindIII/I-SceI/NheI/NotI/BamH1. A cassette containing

the Gal4-VP16 fusion gene flanked by I-SceI sites was recovered as a 2.4 kb XbaI

fragment from the plasmid psce-G4VP16 3L, a gift from László Sipos (Sipos et al.,

2007). This XbaI fragment was cloned into the NheI site of the synthetic linker.

The donor plasmid was injected into embryos derived from a cross of males

homozygous for the HC184B P element insertion with females of the genotype ry,

Ubx109, ∆2-3 (99B ry+)/ MKRS. G0 survivors were crossed to UAS-GFP

homozygotes, and resulting larvae were screened for expression of GFP, marking the

convertants. Adults carrying the conversion chromosome had unfolded wings and a

reduced tergite on the first abdominal segment; these phenotypes were likely due to

the toxicity of GAL4-VP16. Conversion heterozygotes were crossed to [hs-FLP][ hs-

ISceI] Sco / CyO; ry Fab-7, and offspring were heat-shocked as young larvae for 1h at

37º. Resulting adult males were crossed to UAS-GFP; pbx Fab-7 / MKRS females,

and non-Fab7, Sb progeny were screened for loss of GFP expression (indicating I-

SceI cutting and removal of GAL4-VP16). Selected adults, potentially containing

border deletions, were screened by PCR for the expected fusion of the deletion

endpoints, and PCR products were sequenced to confirm the expected junction.

Results

Mapping the bxd Domain by Mutant lesions

The PS6 regulatory domain was first defined by the mapping of bithoraxoid (bxd)

and postbithoraxoid (pbx) mutant lesions (Bender et al., 1983; Bender et al., 1985;

Karch et al., 1990). These mutations transform structures of PS6 to those of PS5

(posterior haltere transforms into posterior wing, and first abdominal tergite is

removed, and extra legs appear on the first abdominal segment (Lewis, 1963)).

These included primarily chromosomal rearrangements, although several alleles were

associated with insertions of the gypsy mobile element, and the pbx alleles were X-ray

induced deletions. Figure 1A illustrates some of these lesions, including previously

unreported rearrangement breakpoints associated with very weak bxd phenotypes.

They are spread across a 50 kb region upstream of the Ubx transcription unit.

Several of these bxd breaks were induced on a homozygous-viable inversion,

In(3R)1000, which breaks in 81F and 90C, and puts the BX-C near the centromere.

The breaks were recovered in a screen for the disruption of transvection between the

mutagenized chromosome, and a copy of In(3R)1000 with the Cbx1 and Ubx1

mutations (Celniker et al., 1990). For the weakest bxd breaks (the group from bxd266

through bxd551), hemizygous embryos show weak thoracic-like ventral pits on the

anterior abdominal segments, and hemizygous adults show only a slight reduction of

the first abdominal tergite. The rightmost break in the bxd series is associated with

the Uab5 rearrangement, which is a translocation between the BX-C and section 1F on

the X chromosome. The dominant Uab phenotype (transformation of the first

abdominal (A1) tergite to second abdominal (A2)), is likely due to misexpression of

abd-A. This transformation obscures any weak bxd phenotype in the adult, but when

Uab5 is tested over a deficiency, it also shows ventral pits in the abdominal segments.

By that criterion, Uab5 is the most distal break associated with a bxd phenotype.

Figure 1A also illustrates a variety of DNA elements that have been uncovered in the

bxd domain, including enhancers that drive PS6 expression in early embryos (Pirrotta

et al., 1995), a noncoding RNA that is transcribed in PS6 (Lipshitz et al., 1987), a

prominent Polycomb Response Element (PRE) (Sipos et al., 2007), and the coding

region for the glucose transporter homolog (Martin et al., 1995).

Three iab-2 mutations are shown on the right in Figure 1A. The iab-2S3

rearrangement breakpoint lies just a few kb distal to the Uab5 break (Karch et al.,

1985); homozygotes show a weak transformation of the A2 tergite towards A1, but the

A1 segment is normal in embryos and adults (Bender et al., 1985). The other iab-2

alleles include the iab-2Kuhn gypsy insertion and the iab-2671 breakpoint (Karch et al.,

1990). Breaks or deletions farther distal impinge on the abd-A transcription unit, so

that it is not easy to determine how the segmental regulation of abd-A might be

disturbed. This analysis would put the transition between the bxd (PS6) and iab-2

(PS7) regulatory regions within a few kb between Uab5 and iab-2S3. This analysis is

tentative, however, since any individual break may involve some position effect that

affects BX-C sequences distant from the breakpoint.

The definition of the bxd regulatory region is based not only on mutant

transformations of the adult cuticle, but also on changes in the expression pattern of

UBX protein in the embryo. UBX protein is strongly expressed in most nuclei in PS6

of the embryo, and the series of bxd rearrangement breaks make it possible to map

cis-regulatory sequences responsible for that PS6 pattern. UBX antigen patterns for

various bxd rearrangements have been reported (Beachy et al., 1985; White and

Wilcox, 1985; Irvine et al., 1991; Camprodón and Castelli-Gair, 1994), but the results

were confusing, with some breaks giving apparent increases in UBX expression in

PS5. We also saw increased PS5 expression in the case of bxd113, but not for other

bxd breaks examined (not shown). It was more revealing to examine UBX expression

in the absence of the abd-A and Abd-B genes, in part because potential cross

regulatory interactions are removed, and in part because the PS6 pattern is repeated

in PS7-12. It was possible to create synthetic deficiency genotypes for six

rearrangements, each of which has one copy of the Ubx transcription unit, with

various extents of the bxd region intact, as shown by the bars in Figure 1B. Each

genotype lacks BX-C DNA distal to the break (see Materials and Methods).

Embryo pelts from the six genotypes are shown in Figure 1B, all stained for UBX

antigen. All six show UBX expression in PS5 that looks identical to that of wild type

embryos. Embryos with the complex truncated at the Hm break, 3 kb upstream of the

Ubx RNA start site, show UBX staining in PS6-PS11 nearly identical to that of PS5.

There are some additional stained nuclei in PS6 in the ventral-lateral region, including

muscle nuclei, as judged with Nomarski optics. When the complex is truncated at the

bxd100 break, 12 kb upstream of the Ubx start, the embryos look very similar to the Hm

embryo, except that there is more staining in the epidermal cells in the lateral region

around the tracheal pit. With additional sequences to the bxd111 breakpoint, 27 kb

from the Ubx start, there are many additional stained nuclei in the ventral nerve chord

and the lateral epidermis. Additional sequences to the bxd1068 breakpoint, 35 kb from

the Ubx start, give additional nuclei staining the ventral nerve chord. Embryos with

DNA up to the Uab5 breakpoints (50 kb from the Ubx start) show more intense staining

in the nuclei of the ventral nerve chord; the pattern and intensity resembles the

staining in PS6 of the wild type. Additional DNA up to the P10 breakpoint (within the

ABD-A coding region), does not noticeably alter the UBX expression pattern. The P10

pattern was previously reported by Struhl and White (1985).

The analysis of UBX expression patterns shows that the PS6 regulatory region

extends beyond the bxd1068 break, but not necessarily beyond the Uab5 breakpoint.

Both the antigen patterns and the adult phenotypes suggest that the cis-regulatory

region controlling UBX expression in PS6 extends at least 35 kb upstream of the Ubx

promoter, and that it contains a succession of elements, each controlling a part of the

UBX pattern. There is no single site (such as the major Polycomb Response Element

(Chan et al., 1994; Chiang et al., 1995; Sipos et al., 2007)) necessary or sufficient for

PS6 expression and maintenance.

Mapping by Enhancer traps

The regulatory domains of the bithorax complex can also be defined by the

expression patterns of enhancer trap insertions. Many P element insertions carrying

marker genes such as LacZ, Gal4, or GFP have been recovered in the bithorax

complex; in nearly every case, the marker gene is repressed in head segments. More

specifically, the anterior-most parasegment showing marker expression corresponds

to the anterior-most parasegment affected by mutations in the neighborhood of the

enhancer trap insertion (Galloni et al, 1993; McCall et al., 1994; Casares et al., 1997;

Barges et al., 2000; Bender and Hudson, 2000; Fitzgerald and Bender, 2001; Herranz

and Morata, 2001; Estrada et al., 2002). Enhancer traps are particularly informative in

regions where the mutant lesions give only subtle or ambiguous segmental

transformations, such as the iab-3 and iab-4 domains. In the distal extent of the bxd

domain and in the proximal part of the iab-2 domain, the phenotypes of mutant lesions

are subtle, as discussed above. There are several enhancer traps in this region, all

of which were “trimmed down”, so that the P element contained only the lacZ reporter

(Bender and Hudson, 2000). These minimal enhancer traps divide clearly into two

groups, with anterior expression limits in PS6 or PS7 (Figure 1). This assay delimits

the bxd/iab-2 border to a 12 kb interval; the most distal PS6 enhancer trap (HC184B)

is at the same position as the most distal rearrangement breakpoint with a bxd

phenotype (Uab5).

D. virilis sequence comparison

The extent of the bxd regulatory region might also be inferred from a DNA

sequence comparison with the comparable region in Drosophila virilis. The D. virilis

homeotic genes lie in two clusters, as do those of D. melanogaster, but the split in

virilis lies between Ubx and abd-A, instead of between Antp and Ubx (Von Allmen et

al., 1996)(Figure 2A). Assuming that the virilis Ubx and abd-A genes have intact PS6

and PS7 regulatory regions, respectively, then the limits of those regions should be

revealed by the position of the split in the ancestral sequence. Recombinant

bacteriophage were recovered from D. virilis genomic libraries using D. melanogaster

probes from the distal bxd region or from the proximal end of the abd-A transcription

unit. These hybridized to the 24E or 26D regions of the virilis chromosome 2,

respectively (Von Allmen et al., 1996). The initial D. virilis phage clones were used to

recover additional overlapping phage clones in both locations. Primer walking was

used to sequence16,660 bp from the 24E region and 19,267 bp from the 26D region.

The virilis sequences could be easily aligned with the corresponding sequences

from melanogaster (Martin et al., 1995). Figure 2B diagrams the alignment in a dot-

matrix format. Throughout most of the sequence, there were blocks of 20-100 bp with

high homology (~80%), spaced by regions of low homology, often A/T rich, and often

different in length between the two species. The homology blocks are uniformly

collinear, except for three segments of the 24E virilis sequence that appear to be

inverted relative to the melanogaster sequence (Figure 2B). The virilis 24E homology

to the melanogaster bxd region abruptly ends at about 185,200 on the melanogaster

sequence, just beyond the position of the Uab5 breakpoint. Coming from the other

direction, the virilis 26D homology to the melanogaster iab-2 region stops abruptly at

about 183,400, close to the iab-2S3 breakpoint. The intervening ~1.8 kb of

melanogaster sequence has no clear homology anywhere in the virilis genomic

scaffold.

Sugar transporter sequence

The distal bxd domain includes the coding region of the sugar transporter homolog,

Glut3, which was first identified by examination of the BX-C sequence (Martin et al.,

1995). Glut3 is the only “foreign” gene in the bithorax complex, but the Antennapedia

complex includes many non-homeobox genes (including Amalgam, cuticle proteins,

and tRNAs). It was not clear if the melanogaster GLUT3 represents a pseudogene,

without function, and so we looked for evidence of protein sequence conservation.

The D. virilis homology to the D. melanogaster Glut3 is nearly exactly delimited by a

~1500 bp inversion (Figure 2B). The dot matrix diagram of Figure 2B also illustrates

that the transporter region shows less DNA homology than adjacent, noncoding

regions. The virilis region contains an open reading frame of 478 amino acids, with

clear homology to the melanogaster transporter homolog over most of that length.

Figure 3 presents an alignment of the virilis and melanogaster predicted amino acid

sequences, along with plant and human sugar transporter proteins, for comparison.

The overall homology between the two fly peptides is only 36% (compared to ~92%

for UBX), but the presence of a full length transporter homolog (without stop codons)

argues for functional conservation. Certain amino acids are tightly conserved among

sugar transporter genes from bacteria, fungi, plants and animals (Baldwin, 1993).

These amino acids are also well conserved in fly evolution; there are 45 positions

where the melanogaster protein matches the most conserved amino acids, and the

virilis sequence matches 37 of them (82% homology) (Figure 3). Thus, the fly

sequences appear to be evolutionarily selected for function as a transporter, but it is

not possible to predict what molecule they might transport (Marger and Saier, 1993).

Sugar transporter function

Our collection of P element insertions into the bithorax complex permitted us to

delete Glut3 fairly precisely. Since the P elements include FRT sites for the yeast

FLP recombinase (Golic and Lindquist,1989), it is simple to create duplications or

deletions between any pair of such insertions, as long as their FRT sites are in the

same orientation (Bender and Hudson, 2000). Two such insertions, HC154A and

HC148A, flank the sugar transporter homolog, less than 1 kb from either end of the

open reading frame (Figure 4A). FLP-induced recombination produced a 3.2 kb

deletion, with one copy of the P element remaining at the site of the recombination.

Since the starting P elements each have two internal FRT sites, the final P element

can be any of three sizes, depending on the FRT sites involved in the recombination

event (Bender and Hudson, 2000). Figure 4B illustrates the smallest final P element,

which contains only a LacZ reporter fused to the P promoter, plus a single FRT site.

Such deletion derivatives are homozygous viable, but they have a strong bxd

phenotype, most obvious in the absence of the first abdominal tergite (Figure 4C).

This phenotype is unexpected, because rearrangement breaks to the left of the

transporter homolog, including bxd266, bxd517, and bxdL69A, all have much weaker

phenotypes, with little or no reduction in the A1 tergite. This implied that the

transporter homolog has a function in specification of the A1 segment, independent of

Ubx, or that the phenotype is due to some action-at-a-distance from the remaining P

element.

The remaining P element could be removed by P transposase (Figure 4D),

accomplished by crossing the original deletion strain to the 99B∆2-3 source

(Robertson et al., 1988). We actually used a deletion derivative carrying a full length

copy of the starting P element, including the rosy+ transformation marker, so that P

excisions could be recognized by the loss of rosy. Nineteen independent rosy-

derivatives were analyzed; two appeared by Southern blots to be clean deletions. For

both lines, the site of the deletion was recovered in a polymerase chain reaction, and

the products were sequenced. One had 31bp remaining at the site of the P element,

derived from the P element terminal repeats; the other had 36bp of P sequence.

Other workers have described similar fragments of P remaining at the sites of P

excisions (Staveley et al., 1995; Beall and Rio, 1997). Figure 4E illustrates an adult

homozygous for one of these deletion lines; the A1 tergite is restored to the full wild-

type size. The small P element in the initial derivative (Figure 4B) must have been the

cause of the bxd phenotype.

Both lines of the final deletion derivative (Figure 4D and E) were healthy and fertile

as homozygotes, with no apparent segmental transformation. Glut3 is expressed

predominantly in the adult male testis (Chintapalli et al., 2007), but 10 out of 10 tested

single males lacking Glut3 were fertile. Thus, the Glut3 transporter homolog has no

obvious function in our culture conditions. We have no rationale for the presence of

Glut3 in the BX-C, but this position should not inhibit expression in the testis. The

testis is derived from the rudimentary 9th abdominal segment (Chen et al., 2005),

where we expect that nearly the entire BX-C is released from Polycomb repression.

Border deletion

The most distal mutant lesion still within the bxd domain is the Uab5 rearrangement

breakpoint, and the most proximal lesion in the iab-2 domain is the iab-2Kuhn gypsy

element insertion (Figure 1). We sought to generate a deletion that would extend

between these two markers, which would unequivocally remove the border between

these two domains.

We initially attempted to generate deletions by imprecise excisions of the enhancer

trap P elements. These efforts yielded a variety of mutant lines showing dominant

gain-of-function “Ultraabdominal” phenotypes (first abdominal tergite transformed to

second or third abdominal tergite), but most of these were associated with

rearrangements of the P elements (Bender and Fitzgerald, 2002). One deletion of

1890 bp was recovered (shown as ∆1.9kb in Figures 5 and 7), which did not span the

entire border region. Flies homozygous for this deletion had no apparent segmental

transformations.

P element-mediated gene conversion can be used to introduce small deletions, but

it seemed unlikely that a conversion interval would be large enough to include the ~4

kb border region. Xie and Golic (2004) developed a DNA cut-and-repair strategy that

can be used in conjunction with homologous recombination to generate large and

precise deletions. We used a similar strategy, combined with P element gene

conversion, as diagramed in Figure 5. The procedure yielded a 4,328 bp

deletion(182,353-186,679 in SEQ89E numbering), spanning the distance between the

most distal bxd lesion and the most proximal iab-2 lesion. Flies heterozygous for this

deletion, called Front-ultraabdominal (Fub), showed a dramatic transformation of the

first abdominal segment to the character of the second. The A1 tergite shows black

pigmentation and large bristles, like those of A2 (Figure 5), and the A1 sternite,

normally lacking bristles, has bristles like those of A2. Homozygotes usually die as

pharate adults, with an apparently complete transformation of A1 to A2, and often

missing one or both halteres and (rarely) one or both third legs. Parasegment 6

includes the posterior compartments of the halteres and metathoracic legs, and so

PS6 to PS7 transformations should also affect these appendages, causing their

failures to emerge. Homozygotes do not have apparent bxd or pbx loss-of-function

phenotypes (anterior transformations in PS6, such as posterior haltere-to-wing

transformation, loss of the first abdominal tergite, or appearance of extra legs from the

first abdominal segment). When embryos from heterozygous adults were stained for

ABD-A protein, there were three staining patterns (Figure 6). Most of the embryos

showed ectopic ABD-A in PS6, some with half the intensity of the PS7 level, and

some (the presumed Fub homozygotes) with PS6 and PS7 equal in pattern and

intensity. The appearance of ABD-A in PS6 is not obviously delayed relative to that in

PS7; ABD-A is equally intense in both parasegments in homozygous embryos at

stage 10 (~5 h old).

Discussion

Dissection of the bxd domain

The deletion series shown in Figure 1 looks strictly cumulative, in that additional

DNA upstream of the Ubx promoter gives additional expression of UBX protein. But

the details are surprising in several respects. The DNA segments ending at the Hm

and the bxd100 breakpoints show UBX expression in PS6-12, above that seen in PS5.

Yet these DNA segments lack all of the mapped embryonic enhancers in the bxd

region that drive PS6 expression in transgene assays (designated as bxd, S1, S2, and

pbx in Figure 1; Poux et al., 1996). They also lack the prominent Polycomb Response

Element, but the UBX expression pattern does not spread to PS5 or more anterior

parasegments in late embryos. It is likely that there are additional PS6-specific

embryonic enhancers, not yet mapped, and perhaps cryptic PREs. It is also possible

that enhancers and/or PREs within the Ubx transcription unit contribute to this pattern.

The DNA segments extending up to the bxd111 breakpoint, ~28 kb from the Ubx start,

also lack the promoter for the major noncoding RNA, which spans much of the bxd

domain (Lipshitz et al., 1987). It has been proposed that transcription of noncoding

RNAs across a domain (or across a PRE) is required for that region to be functionally

active (Schmitt et al., 2005); such a function cannot be assigned to the major

embryonic bxd noncoding RNA.

In the embryos of Figure 1B, there are distinct posterior limits to the UBX

expression driven by portions of the bxd domain. The embryonic enhancers included

in the bxd100 DNA segment drive expression in PS6-12, while the more distal

enhancers work in PS6-13. Thus, the lack of UBX expression in PS13 and PS14 is

not solely a function of repression by ABD-B.

The Fub border

The border between the bxd and iab-2 regulatory domains is now positioned by 1)

enhancer trap patterns, 2) mutant lesions, and 3) homology to D. virilis. Figure 7

presents the limits on the position (or extent) of the border from each of these criteria.

The tightest limit is provided by the edges of homology to D. virilis, and this 1.8 kb

interval is contained within the limits of the two phenotypic assays. The deletion of

this border interval gives a homeotic protein expression pattern (spread through the

anterior adjacent segment) and an adult phenotype (dominant, one-segment posterior

transformation) that are both analogous to those of Mcp, Fab-6, Fab-7, and Fab-8.

Thus, the original assumption that these latter four deletion mutations remove barriers

to the spread of activation seems validated.

The Fub border interval does not include a PRE, in that it lacks binding sites for

known components of the Polycomb Group repression machinery. Specifically,

genome wide chromatin immunoprecipitation profiles from several cultured cell lines

show reduced levels of POLYCOMB at this border, relative to adjacent regions, and

little or no binding for other proteins of PRC1 (POLYHOMEOTIC, POSTERIOR SEX

COMBS), of PRC2 (ENHANCER OF ZESTE), or PhoRC (PLEIOHOMEOTIC,

SFMBT) (Schwartz et al., 2006; Schwartz and Pirrotta, 2007; Schuettengruber et al.,

2009; The modENCODE Consortium, 2010; Enderle et al., 2011). Likewise,

chromatin IP from 4-12 h old embryos shows reduced POLYCOMB levels at this

border, and little or no binding of POLYHOMEOTIC or PLEIOHOMEOTIC

(Schuettengruber et al., 2009). The Mcp, Fab-6, Fab-7, and Fab-8 borders are

associated with prominent peaks of POLYHOMEOTIC and PLEIOHOMEOTIC

(Schuettengruber et al., 2009). The position of the iab-3/iab-4 border can be guessed

from the positions of enhancer traps marking PS8(HCJ200, Bender and Hudson,

2000) and PS9(HF608B, Fitzgerald and Bender, 2001); this interval (125,800 to

127,370) also corresponds to peaks of PH and PHO. Although the coincidence

between borders and Polycomb Group binding sites is striking, the Fub border

indicates that PRE function is not essential for border function. There are no apparent

loss-of-function phenotypes caused by the Fub deletions, as there were with the Fab-

6 deletions and the Fab-7 deletions retaining the PRE (Iampietro et al., 2010; Mihaly

et al., 1997). Perhaps the spread of repression from a PRE is short-range, and there

is no PRE in the iab-2 domain sufficiently close to the border for repression to spread

across in the Fub deletion mutants.

The Fub border region includes a prominent binding site for the CCCTC-binding

factor (CTCF) (Figure 7), as assayed in early embryos and in cultured cells by

chromatin immunoprecipitation (Holohan et al., 2007; Nègre et al., 2010). CTCF is a

zinc finger DNA-binding protein proposed to be involved with intrachromosomal

looping and with locus boundaries (Herold et al., 2012). The Mcp, Fab-6, and Fab-8

borders are also sites for CTCF binding, and there are additional sites that may mark

the iab-2/iab-3, and iab-3/iab-4 borders (Negre et al., 2010). The Fab-7 border has

only a very weak association with CTCF, and lacks consensus CTCF binding sites

(Holohan et al., 2007). There are also CTCF sites within the bxd region and within the

Ubx transcription unit that do not correspond to suspected border regions. The

correspondence between borders and CTCF sites is striking, although evidence for

CTCF function at borders is limited. Mohan et al. (2007) examined zygotic null

mutants for CTCF, and reported partial posterior transformations of the fourth

abdominal (A4) and fifth abdominal (A5) segments in pharate adults. The A4 to A5

transformation appeared less severe than that seen in Mcp/+ animals, and there were

no apparent Fab-7 (A6 to A7) or Fub (A1 to A2) transformations. It should be

informative to remove maternal as well as zygotic CTCF, and to mutate the CTCF

sites in the BX-C, to learn if CTCF is essential for blocking the spread of activation at

borders.

Homing

The Fub border lies within a 7.5 kb SalI fragment (Figure 7) shown to confer

homing of P elements to the BX-C (Bender and Hudson, 2000). In that study, LacZ

transgenes positioned proximal or distal to this “homing fragment” showed expression

with anterior limits in PS6 and PS7, respectively, while a LacZ reporter placed

between two copies of the homing fragment showed no segmental limit to LacZ

expression. It was argued that this fragment included a boundary to the domain of

Polycomb-mediated repression (Bender and Hudson, 2000). The best-characterized

sequence with analogous homing properties has been mapped at the edge of the

even skipped (eve) locus. Fujioka et al. (2009) have defined a ~600 bp fragment

called “Homie” that directs P element insertions into or near the eve locus; it also

includes a prominent binding site for CTCF (Nègre et al., 2010). P element homing

has also been well documented for small fragments near the promoters of engrailed

(Kassis et al., 1992; Cheng et al., 2012) and linotte/derailed (Taillebourg and Dura,

1999). In both of these cases, the minimal homing fragment coincides with a CTCF

binding site in embryos or cultured cells (Nègre et al., 2010; modENCODE ID 2638

and 2639). The association of CTCF with P element homing seems clear, but there

must be distinctive properties to each of these CTCF regions, since each homing

fragment targets its own locus.

Possible border functions

Mapping the borders is merely a first step in the larger investigation of how they

function. In the cells of PS6, the Fub border lies between an active bxd domain, and a

silenced iab-2 domain. When the border is deleted, activation spreads through the

iab-2 domain. The deeper question, then, is how activation spreads. An appealing

model is that noncoding RNAs might extend across the bxd domain, leaving activating

chromatin marks as they go, until they are blocked or terminated at the border.

However, no such transcripts approaching the Fub border from the proximal side have

been detected in embryos (B. Pease and W. B., unpublished results). Moreover,

borders between the iab-2 and iab-8 domains (including Mcp, Fab-6, Fab-7, and Fab-

8) are not barriers to transcripts in the distal to proximal direction, since the iab-8

noncoding RNA proceeds through them all (Gummalla et al., 2012). However, all

these domains are in the active mode in PS13, where the iab-8 RNA is made.

Spreading activation need not involve transcription; perhaps nucleosome modification

or remodeling could be propagated from the early enhancers that respond to gap and

pair rule genes. The PS6 misexpression of ABD-A in very early Fub embryos

suggests that the spread of activation is fast, although it is not clear how much of the

iab-2 domain must be activated before Abd-A transcription begins.

The border’s blockage to spreading activation could be entirely passive; each

domain could be activated or repressed, regardless of the state of adjacent domains.

By this model, the structure of the border need not change from one parasegment to

another. Alternatively, the borders could be active attachment points for segregating

DNA domains into repressive structures or nuclear compartments. The Fub border

might be attached in PS1-6, but released in PS7-13. This model would require that a

border is modified according to its segmental position. The positional sensor is not

likely to be intrinsic to the border, since swapping experiments, switching the Fab-7

and Fab-8 borders, suggest that borders are largely interchangeable (Iampietro et al.,

2008). To distinguish between the passive and active models, it would be instructive

to assay the proteins bound at a border, and to see if the composition changes from

one parasegment to another.

Acknowledgments

We are indebted to the late E. B. Lewis for providing his collection of bxd

rearrangement breaks and for designing the synthetic deficiencies. We are grateful to

François Karch and Barbara Weiffenbach for supplying recombinant phage carrying

D. virilis sequences. Xiao-qiang Qin helped in the mapping of several bxd

rearrangement breaks, Barbara Weiffenbach cloned the breakpoint fragments of

Uab5, and Julia Buratowski isolated and mapped the HCJ61A enhancer trap. Helpful

suggestions for the manuscript were provided by Kami Ahmad, Guillermo Orsi,

François Karch, László Sipos, and anonymous reviewers. This work was supported

by a grant from the National Institutes of Health (RO1-GM28630).

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Figure legends

1. The extent of the bxd regulatory domain.

A. The long horizontal line indicates the DNA map with the upper coordinates

according to Seq89E (Martin et al., 1995) and lower coordinates from D.

melanogaster Genome Release 5.37. Splicing patterns are shown for the abd-A

transcription unit and the major embryonic bxd noncoding RNA, and the start site of

the Ubx transcription is shown at the left. Colored triangles above the DNA map show

insertion positions of enhancer traps that have anterior expression limits in PS6

(green) or PS7 (blue). Four mapped embryonic enhancers are indicated by the pink

boxes on the DNA line, and the red box shows the site of the bxd Polycomb

Response Element. Mutant lesions are shown below the line; rearrangement

breakpoints are shown with vertical arrows (dashed bars show mapping

uncertainties), the pbx1 and pbx2 deletions are indicated by horizontal dashed lines,

and the iab-2Kuhn gypsy insertion is shown by the lower triangle. The Glut3 coding

region is shown in orange. B. The series of horizontal black lines diagram the BX-C

DNA remaining in synthetic deficiencies which end at the indicated breakpoints. The

pictures below show pelts of stage 14 embryos stained for UBX protein, which has an

anterior limit in PS5. The UBX staining in PS6-13 increases in pattern and intensity

with additional DNA sequences from the bxd region. The maximal expression is

reached in the Uab5 embryo; additional sequences up to the P10 breakpoint do not

add to the pattern.

2. Homology matrix comparison of D. virilis and D. melanogaster sequences.

A. A diagram of breakup of the homeotic gene complex in Drosophila evolution

(adapted from Lewis et al., 2003). In melanogaster, the ancestral complex was split

between Antennapedia and Ubx; in virilis, the split occurred between Ubx and abd-A.

The cytological positions of the resulting clusters are shown for chromosome 3R

(melanogaster) and chromosome 2 (virilis). The left/right orientation of the two virilis

clusters is not yet established.

B. The horizontal line in the middle of the figure is a map of the melanogaster

sequence. The Glut3 open reading frame is shown below the map on the left, and the

final two exons of the abd-A gene are shown above the map on the right. The grid

above the map shows a homology comparison with the ~16.7 kb of virilis sequence

from 24E on chromosome 2. The grid below the sequence line shows the

comparison with ~19.3 kb of virilis sequence from 26D. The vertical axes are virilis

sequence coordinates, the horizontal axes are melanogaster sequence coordinates,

aligned with the map. The sequences of both virilis DNA strands are included in the

comparison, so that sequence inversions appear as diagonals from bottom left to top

right. Note the gap in homology, indicated by the brackets near the middle of the

melanogaster map. The matrices were constructed by the MacVector program, with

window size = 30, minimum % score = 42, and a hash value = 5.

3. Sugar transporter alignment.

The predicted amino acid sequence for the Glut3 sugar transporter homologs from D.

virilis and D. melanogaster are aligned with each other and with glucose transporters

from Arabidopsis thaliana (STP1; Sauer et al., 1990) and human erythrocytes

(GLUT1; Mueckler et al, 1985). Below these sequences are shown the residues most

conserved in a comparison of many sugar transporters from diverse species (Baldwin,

1993). Some positions in the conserved line indicate groups of amino acids: + =

positively charged, R or K; - = negatively charged, D or E; º = hydroxyl-bearing, S or

T; Ø = aromatic, F, W, or Y (after BALDWIN, 1993). The shading indicates agreement

with one of the conserved amino acids; many other sequence homologies are not

marked. Note that most of the conserved positions that are shaded in the

melanogaster sequence are also shaded in virilis, and vice versa.

4. Deletion of the Glut3 sugar transporter homolog.

A. Diagram of the two chromosomes bearing P elements flanking the Glut3 coding

region. The P element insertions, indicated by the large triangles, are drawn to scale,

showing their internal maps. The segment marked “homing” is the 7.5 kb fragment

from the BX-C used to target P insertions into the BX-C (Bender and Hudson, 2000).

The two FRT sites in each P element are sites for FLP, the yeast site-specific

recombinase. B. Deletion recombination product. Recombination between the left

FRT site of the HC154B P element and the right FRT site of the HC148B element

produces a deletion of ~3 kb of BX-C DNA, and leaves a small P element at the site of

the deletion. C. Dorsal view of an adult fly homozygous for the deletion diagramed in

B. Note the severely reduced tergite on the first abdominal segment (labeled A1). D.

Elimination of the remaining P element. A deletion chromosome with a P element

remaining was crossed to a source of P transposase. From the offspring of the

dysgenic fly, chromosomes were recovered with the P sequences excised. E. Dorsal

view of a fly homozygous for the deletion diagramed in D. Note that the first

abdominal tergite (labeled A1) appears normal in size.

5. Generation of bxd/iab-2 border deletion.

The HC184B P element was mobilized by P recombinase, in embryos injected with a

plasmid with homology to genomic sequences on both sides of the P element

insertion site (red and orange segments). Between these two segments, the

conversion donor plasmid contained a short DNA segment homologous to the distal

edge of the desired deletion (blue segment), followed by a marker for successful

integration, the GAL4-VP16 transcriptional activator (purple triangle). The GAL4-

VP16 marker was flanked by restriction sites for the rare-cutting restriction enzyme I-

SceI. The injected animals were crossed to flies homozygous for a UAS-GFP

reporter, and the progeny were screened for fluorescence. Animals with the

conversion chromosome were crossed to a heat-inducible source of the I-SceI

restriction enzyme, and progeny carrying the conversion chromosome were screened

for loss of GAL4-VP16 driven GFP. The structure of the final deletion chromosome

was verified by PCR. The pictured fly is heterozygous for the 4.3 kb Fub deletion.

The arrow marks the first abdominal tergite, transformed to the character of the

second abdominal tergite.

6. ABD-A expression in embryos with the bxd/iab-2 border deletion.

Embryos were collected from adults heterozygous for the Fub deletion and stained for

ABD-A. Stage 15 embryos (~12 h old) are illustrated; three classes were apparent.

The left embryo shows the wild type ABD-A pattern. The middle embryo, presumed to

be a heterozygote, shows ectopic ABD-A expression in PS6, at ~1/2 the intensity of

PS7. The embryo on the right is the presumed deletion homozygote; it shows ABD-A

misexpression in PS6 equivalent to the normal expression in PS7. Brackets show the

extent of PS6 in the epidermis ( ] ) and in the CNS ( [ ).

7. Summary map of bxd/iab-2 border region.

The thick black line gives DNA coordinates according to Seq89E (above the line) or D.

melanogaster Genome Release 5.37 (below). The small triangle at ~184.6 shows the

site of a 278 bp insertion of the Jockey element present in the background strain for

the enhancer trap insertions and their derivatives. Above the DNA line are shown the

mutant lesions closest to the border, the regions of homology to the split complex in

D. virilis, and the closest enhancer traps. Green coloration indicates inclusion in the

bxd domain (by phenotype, homology, or expression pattern); blue indicates the iab-2

domain. All three criteria confine the bxd/iab-2 border to a 2 kb interval which

includes a prominent binding site for the CTCF factor. The ∆1.9kb deletion, shown in

black, retains the CTCF binding site and had no phenotype. The Fub deletion, shown

in red, removes the CTCF site, and causes a dominant PS6 to PS7 transformation.

The yellow double-headed arrow marks the the 7.5 kb SalI fragment that confers P

element homing to the bithorax complex.

Figure 1

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