Download Homeotic selector genes

Bio 108 - 3/17/2000
Molecular Genetics of Pattern Formation III
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Contact information
office hours W/F 3-4
phone 824-8573
[email protected] (preferred contact mode)
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Lectures posted at
http://blumberg-serv.bio.uci.edu/bio108-w2000/index.htm
http://blumberg.bio.uci.edu/labtemp/bio108-w2000/index.htm
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Exam update
– Dr. Cho and I will write the exam.
– Questions will be approximately equally distributed
between the sections each of us taught
– The examination will not be identical to any given in
previous years
BioSci 108 lecture 28 (Blumberg) page 1
©copyright
Bruce Blumberg 2000. All rights reserved
Homeotic selector genes specify segment identity
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Hierarchy
– maternal egg polarity genes divide the embryo into
broad regions anterior/posterior, dorsal/ventral
– gap genes respond to this information and divide the
embryo into smaller domains along the A/P axis
– pair-rule genes respond to the gap genes by being
expressed in 7 stripes along the A/P axis
– segment-polarity genes respond to the pair-rule
genes by subdividing the embryo into 14
parasegments, each of which contains 3
compartments.
– Homeotic selector genes interpret the pattern
created by the actions and interactions of the egg
polarity, gap, pair-rule and segment-polarity genes to
create unique anteroposterior positional codes for
each compartment of the embryo
Drosophila has two clusters of homeotic selector genes
– antennapedia and bithorax complexes
– most other invertebrates and insects have a single
complex that contains both antennapedia and
bithorax complexes
• can think of antp and bx complexes as the two
halves of HOM-C
– The invertebrate complex is collectively referred to
as HOM-C. The correxponding complexes in
vertebrates are called the HOX-C
BioSci 108 lecture 28 (Blumberg) page 2
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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Homeotic selector genes have precise domains of action
– like the pair-rule genes, the domain of action is the
parasegment (Fig 21-50)
– homeotic genes have precise expression boundaries,
but these are typically only at either the anterior or
posterior
– mutations are dramatic -> antp (Fig 21-67)
homeotic selector genes are recessive lethal
– embryos typically do not survive beyond hatching of
the egg into a first instar larva
– practically speaking, this means that one must
evaluate such mutations at ~24 hours or so (just
when the larva would ordinarily hatch
– clear view of what is happening (Fig 21-68)
– larvae deficient in the entire bithorax complex are
particularly interesting.
• All of the parasegments posterior to P5 take on
the character of P5
• P5 is T2/3
• these flies consist of a head,T1 and then 11
segments which look more or less like T2
• T2 has a pair of wings and a pair of legs
– ancestral “ground state”
– essential role of homeotic selector genes is to define
the differences among parasegments
• loss of gene function = loss of differences
BioSci 108 lecture 28 (Blumberg) page 3
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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Homeotic selector genes are molecular address labels
– first activated at cellular blastoderm
– all of HOM-C genes are cloned and expression
patterns have been analyzed
– to a first approximation, the anterior border of each
gene coincides with the regions that develop
abnormally in loss-of-function mutations
– this implies that these genes encode molecular
address labels for each cell
• if the address labels are changed, the cells
behave as if they are somewhere else
– expression patterns of HOM-C genes coincides with
parasegmental boundaries established by
segmentation genes
• combination of HOM-C and segmentation gene
products defines a unique address for cells in
one subdivision of one segment
Homeotic selector genes are the “keepers” of positional
information
– all homeotic selector genes are transcription factors
– all contain a highly conserved DNA sequence called
the “homeobox”
– the homeobox encodes a segment of the protein
called the “homeodomain”
• homeoboxes were first identified in homeotic
selector genes, hence the name
BioSci 108 lecture 28 (Blumberg) page 4
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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Homeotic selector genes and positional information
(contd)
– together the antennapedia and bithorax complexes
contain 8 genes (the HOM-C)
• these are very large transcription units (more
than 300 kilobases each)
• these large transcription units contain a large
number of regulatory elements that control the
temporal and spatial expression of the genes
• these regulatory elements contain binding sites
for the products of egg polarity and
segmentation genes
– this is the molecular mechanism underlying
the combinatorial regulation elicited by
these genes
– these binding sites are the interpreters of
positional information
BioSci 108 lecture 28 (Blumberg) page 5
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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Position of genes within the complex corresponds to the
regions of expression along the A/P axis (Fig 21-69)
– order of genes is invariant across species
– all genes are transcribed in the same direction
– most proximal genes are expressed in the anterior,
more distal genes are expressed in the posterior
– appears that the genes are serially activated by an
unknown process that spreads along the chromosome
– most of the genes have unique 5’ borders
• but the expression domains can overlap
posteriorly
• it turns out that the proteins are expresses in a
more restricted pattern than the mRNAs
– overlapping expression patterns means more genes
are expressed in the posterior
– this leads to predictions about the effects of
mutations
• loss-of-function -> anterior transformations
• gain-of-function -> posterior transformations
– questions remaining:
• why is direction of transcription the same?
• why is order conserved?
– accident or design?
• why are inversions and rearrangements not
tolerated?
BioSci 108 lecture 28 (Blumberg) page 6
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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There are not enough HOM-C genes for all parasegments
– only 8 HOM-C genes but 14 parasegments
– bithorax complex contains only 3 genes but is
responsible for the differences among 10
parasegments
– many of Bx-C mutations affect only a single segment
or part of a segment
• map along the chromosome in the order of
expression
• most map to noncoding regions of DNA,
putative regulatory sequences
– suggests that differences between body regions are
defined not only by the presence of homeotic gene
products but by persistent differences in states of the
control regions
• implies that control regions are not simple on-off
switches but integrate the signals received in a
complex way
BioSci 108 lecture 28 (Blumberg) page 7
©copyright
Bruce Blumberg 2000. All rights reserved
HOM-C (contd)
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What is the mechanism that retains positional memory?
– one good mechanism is positive feedback
• once a gene product is expressed, it stimulates its
own expression
• many HOM-C genes have autoregulatory
binding sites in their promoters
– but positive feedback, in itself, is insufficient to
maintain memory without other factors
– another group of genes, the Polycomb group, are
required to repress homeotic selector genes that
should not be expressed in a particular region
• loss-of-function mutations result in
indiscriminate upregulation of HOM-C genes all
over the embryo
• polycomb is bound to the chromatin of the genes
it controls
– genes related to polycomb appear to be involved in
the control of chromatin structure
• this suggests that persistent modifications in
chromatin structure can also have an important
role in positional memory
BioSci 108 lecture 28 (Blumberg) page 8
©copyright
Bruce Blumberg 2000. All rights reserved
HOX-C
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Vertebrates have homologous developmental control
genes to invertebrates
– homologous means derived from a common ancestor
– when Drosophila homeobox genes were identified,
researchers screened for homologs in vertebrates
– an important point to remember is that although not
all developmental mechanisms are conserved, the
genes employed to control development are the same
across species.
• e.g. bicoid and goosecoid
• dpp and BMP-4
– the vertebrate homologs of the HOM-C are called
HOX-C
Genes homologous to HOM-C are found in all organisms
that have been examined
– C. elegans
– Hydra
– they are invariably grouped into complexes that
maintain the order and direction of transcription
HOX-C and HOM-C complexes contain very similar
genes (Fig 21-80)
– similar (paralogous) genes occupy the same position
in each complex!
– this suggests that the HOM-C(HOX-C) complex was
invented very early in evolution retained
• retained and used with only few changes
BioSci 108 lecture 28 (Blumberg) page 9
©copyright
Bruce Blumberg 2000. All rights reserved
HOX-C (contd)
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Expression of HOX-C genes is highly ordered along the
A/P axis (Fig 21-81)
– most clearly seen in the developing neural tube
– A/P position mirrors position in the complex
Gene expression domains draws parallels between the
body parts of insects and vertebrates (fig 21-82)
– stop and think about this for a minute - the genes that
specify head in Drosophila are the same genes that
pattern your head
• e.g. labial and HOX-A,B,D-1 genes
– as in Drosophila compartments, the regions specified
by HOX-C genes do not cross compartment
boundaries
– clearest example is in the vertebrate hindbrain
• segments are called rhombomeres
• lateral to rhombomeres are the branchial arches
– one branchial arch/two rhombomeres
Vertebrates have four HOX-C complexes
– two genome duplications in the vertebrate lineage
• four complexes are organized like HOM-C
– some genes may be lost in one complex
– additional internal duplications have
occurred
» paralog 3 genes and dfd
» paralog 10-13 and AbdB
BioSci 108 lecture 28 (Blumberg) page 10
©copyright
Bruce Blumberg 2000. All rights reserved
HOX-C (contd)
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HOX-C genes specify a discrete combinatorial code that
uniquely identified each cell in the body
– called the HOX code
– alterations in the HOX code cause predictable
changes in patterning
• loss-of-function cause anterior transformations
• gain-of-function cause posterior transformations
– since there are multiple copies of each HOM-C gene,
it is difficult to obtain perfect homeotic
transformations
• important concept: functional redundancy
• this means that the if one gene is knocked out,
the remaining paralogous genes can partially
compensate
– HOX-C and HOM-C genes bind to the same target
DNA sequence
• suggests that differences in affinity may be an
important factor in regulation
• also suggests that the genes may be functionally
redundant
• vertebrate HOX genes can rescue Drosophila
homeotic mutations
– best proof of conserved function
– this is also a good justification for studying
simpler model organisms that only have a
single gene at each position in the complex
BioSci 108 lecture 28 (Blumberg) page 11
©copyright
Bruce Blumberg 2000. All rights reserved
Final comments
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You may have noticed that prices at the UCI bookstore
are not especially good.
– in fact, the bookstore marks items up by a fixed
amount (26%) over cost
– the very frequent result is that books cost MORE
than the publisher’s list price
– what can you do?
• buy your books direct from the publisher online
• buy your books from an online discount
bookstore
• but be careful about edition numbers
– a good resource is http://www.bestbookbuys.com/
• this site has a search engine that compares prices
and availability of a book among many
booksellers.
some students are not happy with the selection of upper
division satellite courses required
– one solution is to complain to the Dean, Susan
Bryant
– another possibility is to take graduate courses. Most
of these are open to undergraduates who have
completed the core and a few other satellites.
• feel free to ask the instructor
BioSci 108 lecture 28 (Blumberg) page 12
©copyright
Bruce Blumberg 2000. All rights reserved