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Eukaryotic Gene Regulation
Gene regulation in eukaryotic cells may occur before or during transcription or
translation or after protein synthesis.
The nucleosome.
Digital model of a nucleosome, the fundamental structural unit of chromosomes in the eukaryotic cell nucleus,
derived from X-ray crystallography data. Each nucleosome consists of a core group of histone proteins (orange)
wrapped in chromosomal DNA (green). The nucleosome is a structure responsible for regulating genes and
condensing DNA strands to fit into the cell's nucleus. Researchers once thought that nucleosomes regulated gene
activity through their histone tails, but a 2010 study revealed that the structures' core also plays a role. The finding
sheds light on how gene expression is regulated and how abnormal gene regulation can lead to cancer.
Kenneth Eward/Science Source.
Topics Covered in this Module
Mechanisms of Gene Regulation in Eukaryotic Cells
Major Objectives of this Module
Describe the role of chromatin in gene regulation.
Explain how transcription offers multiple opportunities for gene regulation.
Describe mechanisms of gene regulation that occur during or after translation.
Describe the variety of mechanisms for gene regulation in eukaryotic cells.
page 264 of 989
3 pages left in this module
Principles of Biology
52 Eukaryotic Gene Regulation
Mechanisms of Gene Regulation in Eukaryotic Cells
Most multicellular organisms develop from a single-celled zygote into a
number of different cell types by the process of differentiation, the
acquisition of cell-specific differences. An animal nerve cell looks very
different from a muscle cell, and a muscle cell has little structurally in
common with a lymphocyte in the blood. What do all these cells of a
particular organism have in common? They all have a nucleus with identical
DNA sequences, cytoplasm, and cytoplasmic organelles like the Golgi
apparatus and mitochondria. Thinking back to the zygote, what drives the
differentiation process? If all the cells have the same DNA, the same
"genetic blueprint," why do they become so different?
The answer lies in the process of gene expression. All cellular structures are
built from structural proteins or are constructed from raw materials that are
synthesized using enzymes. Tracing back to the DNA in the genome, it all
starts with the transcription of mRNA specific for the polypeptide chains the
cell uses to build its components. Building a nerve cell and want to make
some neurotransmitter? Need some actin or myosin to build a muscle cell?
Or perhaps a lymphocyte needs to produce a cytokine. In all of these cases,
the cell needs to express particular genes and coordinate the expression of
multiple genes. How does it go about orchestrating this complex process?
Regulation of gene expression involves many different mechanisms.
In prokaryotes, regulatory mechanisms are generally simpler than those
found in eukaryotes. Prokaryotic regulation is often dependent on the type
and quantity of nutrients that surround the cell as well as a few other
environmental factors, such as temperature and pH. A combination of
activators, repressors and occasionally enhancers control transcription.
Prokaryotic gene expression also happens in the same space as translation,
reducing the opportunities for compartmentalization of regulation.
Multicellular organisms have more complex genomes and the presence of a
nucleus and separate cytoplasm provide a more compartmentalized
structure. There are a number of different stages at which gene expression
may be regulated in eukaryotes (Figure 1).
contents
Figure 1: Regulation of gene expression in eukaryotes may take
place at several different stages.
In the nucleus, the process of chromatin remodeling regulates the
availability of a gene for transcription. Once transcribed, the primary
transcript of mRNA, or pre-mRNA, undergoes RNA processing, which
involves splicing and the addition of a 5′ cap and a 3′ poly(A) tail to
produce a mature mRNA in the nucleus. The mature mRNA is then
exported from the nucleus to the cytoplasm, where its life span varies.
Once outside the nucleus, localization factors may target mature mRNAs
to specific regions of the cytoplasm where they are translated into
polypeptides. The resulting polypeptides can undergo post-translational
modifications, which can regulate protein folding, glycosylation,
intracellular transport, protein activation, and protein degradation.
© 2014 Nature Education All rights reserved.
Figure Detail
Several gene expression mechanisms involve chromatin structure.
When eukaryotic cells aren't dividing, chromosomes exist in an uncondensed
state called chromatin. Chromatin consists of DNA wrapped around a
histone protein core. The wrapped DNA isn't as available for transcription
as the DNA of prokaryotes, and as we'll discuss, mechanisms exist to relieve
this repression. Also in eukaryotes, the RNA polymerase doesn't bind directly
to the DNA, but instead binds via a set of proteins: the transcription initiation
complex.
Two different types of chromatin can be seen during interphase: euchromatin
and heterochromatin. Euchromatin, which is a lightly packed form, contains
areas of DNA that are undergoing active gene transcription. Not all of the
chromatin is undergoing gene transcription, however. Heterochromatin, in
contrast, is mostly inactive DNA that is being actively inhibited or repressed
in a region-specific manner. The chromatin state can change in response to
cellular signals and gene activity. This is facilitated by enzymes that modify
histones by adding methyl and acetyl groups to their N-terminal tails.
Acetylation reduces the net positive charge of the histones, loosening their
affinity for DNA, and increasing transcription factor binding. Methylation, in
contrast, leads to increased binding of histones to DNA, and decreases the
availability of DNA for transcription. Figure 2 shows an example of how
acetylation and methylation of histones may affect transcriptional activity in a
normal cell compared to a cancer cell with inappropriate gene expression.
Figure 2: Modifications of methyl and acetyl groups in histones
affect transcriptional activity.
The grey cylinders represent histone octamers. Acetylation (blue circles)
and methylation (green circles) of histone subunits are shown. In normal
cells, the promoters of tumor-suppressor genes show acetylation of
histone subunits, associated with active transcription. In contrast, in
cancer cells, the promoters of tumor-suppressor genes are not acetylated,
and the genes are not actively transcribed. In normal cells, the
heterochromatic regions at the ends of the chromosomes do not show
acetylation, and the genes are not actively transcribed. In cancer cells, the
heterochromatic regions at chromosome ends are acetylated and
transcriptionally active.
© 2007 Nature Publishing Group Esteller, M. Cancer epigenomics:
DNA methylomes and histone-modification maps. Nature Reviews
Genetics 8, 286-298 (2007) doi:10.1038/nrg2005. Used with permission.
Besides the acetylation and methylation of histones, methylation of the DNA
itself is also used to transcriptionally inactivate DNA. Some transcriptionally
inactive DNA, such as that in inactivated mammalian X chromosomes,
shows more methylation than transcriptionally active chromosomal regions.
Among individual genes, those that are transcriptionally inactive usually
show more methylation than genes that are active, and removal of methyl
groups can "turn on" genes. Methylation seems to be important for genes
that are to remain inactive for a number of cell divisions. The methylation
pattern is preserved during DNA replication, so the daughter cells have the
same methylation pattern as the parent cell. Methylation may therefore be an
important component in the differentiation process in eukaryotes.
If a methylation pattern, and hence the pattern of gene expression, may be
inherited in a cell line, is it possible that these kinds of patterns may be
inherited through generations? This phenomenon is called "epigenetic
inheritance" because it is inheritance "outside of the genes," and it has been
observed in a large number of circumstances. The key to the process is the
inheritance of epigenetic tags, typically methylation of DNA or methylation or
acetylation of histone proteins, instead of the inheritance of mutated or
variant sequences of DNA. In eukaryotes, these tags can be passed through
the gametes to the next generation.
Transcription is an important stage for gene regulation.
Test Yourself
What is necessary before transcription may occur in eukaryotes?
Submit
In eukaryotes, the RNA immediately transcribed from a DNA template, the
pre-mRNA, undergoes a number of processing events before it becomes a
mature mRNA (Figure 3). The RNA polymerase needs transcription factors
to initiate transcription. Some general transcription factors are required for all
genes. Some bind to specific sequences of DNA such as the TATA box.
Others bind to proteins such as RNA polymerase II. These general
transcription factors don't usually produce high rates of transcription, and for
that reason, gene-specific transcription factors called activators or repressors
are also required. These factors bind to proximal or distal control elements,
which are specific DNA sequences that are usually four to eight base pairs
long. The rate of gene expression may be greatly affected by binding of
specific transcription factors to control elements. Proximal control elements
are close to the promoter. Distal control elements may be grouped as
enhancers, and may be thousands of nucleotides removed from the gene.
Although one gene may have more than one enhancer, a given enhancer is
usually associated with only one gene.
Figure 3: The structure of a eukaryotic gene and its transcript.
Each gene has a promoter, the DNA sequence where RNA polymerase,
along with transcription factors, binds and begins transcription. RNA
processing removes introns and splices the exons together using
structures called spliceosomes, and a 5′ cap and poly(A) 3′ tail are added
to the mRNA transcript. The mRNA is then translated into a polypeptide.
© 2013 Nature Education All rights reserved.
How does the binding of transcription factors to control elements regulate
transcription? There seem to be two structural components in transcription
factors: a region that binds to DNA and an activation domain that attaches to
other proteins or components of the transcription apparatus itself. There are
only a few different kinds of binding regions in control elements: these are
called DNA sequence motifs. The binding of transcription factors that
function as activators to control elements in an enhancer may cause the
DNA to bend. This bending brings the enhancer complex into contact with
the protein complex at the proximal promoter, creating a large complex that
promotes RNA polymerase binding. RNA polymerase II is then recruited and
transcription can begin (Figure 4). Some transcription factors function as
repressors that bind to control elements, effectively blocking the binding of
activators.
Figure 4: The eukaryotic transcription initiation complex.
When activator proteins bind to distal control elements called enhancers,
the bound activators are brought closer to the promoter by a DNA-bending
protein. The activators bind to the Mediator protein complex, which forms
an active transcription initiation complex on the promoter together with
RNA polymerase and the general transcription factors.
© 2014 Nature Education All rights reserved.
Figure Detail
The number of different DNA sequence motifs found in control elements is
quite small and is thought to be around ten. It is believed that the
combination of control elements in an enhancer provides the specificity for
gene regulation. The availability of ten different sequences gives a very large
set of available combinations — much like the lock on a bicycle, only the
correct combination will "unlock" and allow activation of an enhancer.
How do eukaryotic cells coordinate gene expression?
Eukaryotic cells frequently need to activate combinations of genes, but unlike
prokaryotes, genes involved in the same metabolic pathway or another set of
coordinated events may be scattered across different chromosomes. How is
their expression coordinated? The answer lies in the combination of control
elements for each gene. If all the genes that need to work together have the
same set of control elements, the same activators will work on all the control
elements, and transcription will be simultaneous for all the genes with the
same set of control elements. Similar to the induction of gene activity in a
bacterial operon in response to nutrient levels in the surrounding medium,
coordinated gene activity in a eukaryote tissue is often in response to
chemical or mechanical signals from outside the cell.
Future perspectives.
By using the FISH (fluorescence in situ hybridization) technique with probes
that bind to RNA, we now know that nascent transcription and active RNA
polymerase II are often concentrated at foci in the nucleus. These foci have
been named transcription factories. The fascinating thing about
transcription factories is that it looks as if genes on different chromosomes
are brought together into proximity to coordinate transcription. For example,
globin genes in developing erythrocytes have been shown to consistently
associate with transcription factories that are sites of active transcription of a
number of coexpressed genes. Transcription factories can only exist in
interphase, as the chromosomes have to condense to undergo mitosis
during prophase.
Additional mechanisms of gene expression occur after transcription.
So far we have concentrated on gene expression up until the stage of mRNA
transcription, but what happens after that? Are there other mechanisms for
controlling gene expression? And if so, why do they exist?
One post-transcriptional control mechanism is alternative RNA splicing,
which produces different mRNA molecules from the same primary transcript.
The primary mRNA transcript is composed of both non-coding introns and
protein-coding exons. Regulatory proteins remove the introns and control the
exon choices by binding to regulatory sequences within the primary
transcript. Alternative RNA splicing may be a major reason for the diversity of
proteins in higher animals over those found in simpler organisms. For
example, the number of genes in a human is remarkably similar to those in a
nematode or sea urchin. However, there are many more genes with multiple
exons in higher animals, so alternative RNA splicing may provide a way of
making more types of proteins from the same amount of genomic DNA
(Figure 5).
Figure 5: Alternative splicing of RNA.
Different splicing patterns result in the production of two different mRNAs
and translation of two different proteins from the same gene. In this
example, a gene gives rise to a primary transcript, or pre-mRNA, that is
spliced differently in two different tissues, A and B. In both tissues, the
three blue exons are present in the mature mRNA, but in tissue A (left),
the orange exon is spliced out, leaving the purple exon, and in tissue B
(right), the purple exon is spliced out, leaving the orange exon. Translation
of the respective mature mRNAs results in two structurally and functionally
distinct proteins derived from the same gene.
© 2014 Nature Education All rights reserved.
Eukaryotic mRNA molecules are longer-lasting than prokaryotic mRNAs, and
mRNA life span is a key parameter in protein synthesis in a cell. Rapid
mRNA degradation is a useful feature of prokaryotes because they may
need to change their protein synthesis rapidly in response to environmental
changes. In eukaryotes, some mRNAs may exist for periods ranging from
days to weeks, and they may be repeatedly translated, such as the mRNAs
that produce hemoglobin molecules in red blood cells. mRNA stability seems
to be associated with changes in the poly(A) tail length. If the tail is
shortened, enzymes may be triggered that remove the 5′ cap of the RNA.
Once the cap is removed, nuclease enzymes degrade the mRNA.
Before a polypeptide is produced, translation has to occur. Therefore,
another stage where control of gene expression can occur is by blocking the
initiation of translation. One place where this is often seen is in unfertilized
eggs. Eggs have many mRNA molecules that are not translated until
fertilization occurs. These mRNAs will produce many proteins that are
important in development, but they are not needed while the egg waits to be
fertilized. Translation of the mRNAs may be blocked by the binding of
regulatory proteins to sequences in the leader region at the 5′ end of the
mRNA, preventing the attachment of ribosomes.
Finally, regulation may occur post-translationally. In eukaryotes, polypeptides
must often be processed to create functional proteins. For example, proteins
may need to be folded, modified by adding carbohydrate groups, or activated
by phosphorylation. Regulation may occur by modifying any of these steps.
Protein degradation also occurs in the cell, facilitated by a protein called
ubiquitin, so named because it is ubiquitous in cells. Once a protein is
"tagged" by adding ubiquitin to it, a protein-degrading enzyme complex
called a proteasome cuts the protein up, effectively destroying it and making
the amino acids available for synthesis of new polypeptides.
Future perspectives.
Post-translational modifications to proteins may result in specific functions.
For example, histone polypeptides, which are intimately associated with DNA
in chromatin, are subject to many post-translational modifications. It has
been suggested that there may be a "histone code" in which histone tails are
"read" by effector molecules and that this coding system may provide a way
that epigenetic processes are coded.
BIOSKILL
Control Regions of Genes Specify Developmental Patterns
In the fruit fly Drosophila melanogaster, a group of mutations was analyzed by
Walther Gehring's laboratory in Switzerland in the 1970s and 1980s.
Gehring's group, together with a group at Indiana University Bloomington,
studied fruit fly mutations like Antennapedia and Ultrabithorax. Antennapedia is a
mutation in which legs grow where the antennae should be, and Ultrabithorax
flies have a second set of wings on the third thoracic segment. Normal flies
have a single set of wings on the second thoracic segment.
Test Yourself
What effects are these two genes having on the fly's development? How might the genes be
working?
Submit
and Ultrabithorax are actually members of a group of related genes
that control anterior-posterior organization in an animal. These are called the
Hox genes. Hox genes are found in organisms from insects to humans and are
characterized by having a 180-base-pair DNA sequence known as the
Antennapedia
homeobox that encodes a transcriptional activator. The Hox genes are
arranged in a cluster along a chromosome, and they show an expression
pattern where the linear order of the genes along the chromosome
corresponds to the anterior-posterior region of their expression in the
developing embryo (Figure 6).
Figure 6: Drosophila melanogaster embryo that has been colored to
indicate the approximate domains of transcriptional expression for
Hox genes.
Here, the expression domain of Antennapedia is colored light brown and that
of Ultrabithorax is colored red. The segments are labeled (Md, mandibular;
Mx, maxillary; Lb, labial; T1-T3, thoracic segments 1-3; A1-A9, abdominal
segments 1-9).
© 2011 Nature Education All rights reserved.
Each of the proteins encoded by the Hox genes binds to specific DNA binding
sites that regulate the expression of other transcription factors, turning on the
hundreds of genes that determine the characteristics of that region of the
embryo. It is thought that the Hox genes regulate whole series of other genes
— for example, the gene pathway that produces the proteins needed to
make an appendage.
BIOSKILL
IN THIS MODULE
Mechanisms of Gene Regulation in
Eukaryotic Cells
Summary
Test Your Knowledge
WHY DOES THIS TOPIC MATTER?
Stem Cells
Stem cells are powerful tools in
biology and medicine. What can
scientists do with these cells and their
incredible potential?
Synthetic Biology: Making Life from
Bits and Pieces
Scientists are combining biology and
engineering to change the world.
Cancer: What's Old Is New Again
Is cancer ancient, or is it largely a
product of modern times? Can
cutting-edge research lead to prevention
and treatment strategies that could make
cancer obsolete?
PRIMARY LITERATURE
Using sterile mates and
engineered toxins to beat bugs
Suppressing resistance to Bt cotton with
sterile insect releases.
View | Download
Growing new heart cells to treat
damaged hearts
Conversion of mouse fibroblasts into
cardiomyocytes using a direct
reprogramming strategy.
View | Download
Interfering with microRNAs to
control gene expression
Silencing of microRNA families by
seed-targeting tiny LNAs.
View | Download
Classic paper: How scientists
cloned the first mammal (1997)
Viable offspring derived from fetal and adult
mammalian cells.
View | Download
Inhibitors may block entry of
hepatitis C into cells
EGFR and EphA2 are host factors for
hepatitis C virus entry and possible targets
for antiviral therapy.
View | Download
page 265 of 989
2 pages left in this module
Principles of Biology
52 Eukaryotic Gene Regulation
Summary
Describe the variety of mechanisms for gene regulation in
eukaryotic cells.
Eukaryotic cells have several mechanisms for gene regulation, involving
regulation of transcription, post-transcriptional modifications, control of
translation, control of mRNA degradation and post-translational controls.
OBJECTIVE
Describe the role of chromatin in gene regulation.
Chromatin plays an important role in gene expression by controlling the
availability of genes and their regulatory sequences for transcription.
OBJECTIVE
Explain how transcription offers multiple opportunities for
gene regulation.
Transcription offers multiple opportunities for gene regulation using general
and specific transcription factors. Transcription factories may allow
simultaneous regulation of genes on different chromosomes.
OBJECTIVE
Describe mechanisms of gene regulation that occur during or
after translation.
Gene regulation that occurs during or after translation includes controlling the
initiation of translation and post-translational modifications, which include
protein folding, glycosylation, intracellular transport, proteolytic activation,
and degradation.
OBJECTIVE
Key Terms
acetylation
The modification of a histone by the addition of an acetyl (–COCH3) functional
group, which reduces the net positive charge of the histone, loosens its binding to
DNA, and improves access and binding of transcription factors and RNA
polymerase to the DNA.
alternative RNA splicing
An RNA processing event that produces different mRNA molecules from the same
primary mRNA transcript.
control element
A DNA sequence, such as an enhancer, insulator, or repressor binding site, that
controls the rate of gene expression.
differentiation
The acquisition of cell-specific differences during a multicellular organism's
embryonic development or adult life.
enhancer
A DNA sequence that is used by a transcriptional activator to increase the
expression of a particular gene; this sequence is not necessarily located close to
the gene in question and may even be very far from the gene or on a different
chromosome altogether.
euchromatin
A lightly compacted form of chromatin that is usually under active gene
transcription.
heterochromatin
A densely compacted form of chromatin that is usually being actively repressed
from gene expression.
histone protein
One of eight proteins that form the histone, a protein structure around which DNA
contents
is compacted to form chromatin.
methylation
The addition of a methyl (–CH3) functional group; methylation of histones
increases the compaction between histones and DNA, decreasing the availability
of DNA for transcription; methylation of DNA bases can permanently and heritably
alter gene expression without changing the DNA sequence.
mRNA degradation
The destruction of an mRNA molecule; exists as a normal mechanism to regulate
gene expression; additionally, in eukaryotes, can be caused by the removal of the
3′ poly(A) tail and/or the 5′ cap of the mRNA.
primary transcript
The mRNA molecule immediately transcribed from a DNA transcript in eukaryotes;
subject to post-transcriptional modification, such as splicing, 5′ capping and 3′
polyadenylation, after its synthesis.
protein degradation
The decomposition of unneeded polypeptides into their constituent amino acids,
freeing the amino acids for use in synthesizing new polypeptides.
transcription factor
A protein that regulates the transcription of specific genes.
transcription factory
Sites of active transcription in eukaryotic cells where multiple genes are
simultaneously transcribed to maximize efficiency; often involves genes that
perform related functions.
IN THIS MODULE
Mechanisms of Gene Regulation in
Eukaryotic Cells
Summary
Test Your Knowledge
WHY DOES THIS TOPIC MATTER?
Stem Cells
Stem cells are powerful tools in
biology and medicine. What can
scientists do with these cells and their
incredible potential?
Synthetic Biology: Making Life from
Bits and Pieces
Scientists are combining biology and
engineering to change the world.
Cancer: What's Old Is New Again
Is cancer ancient, or is it largely a
product of modern times? Can
cutting-edge research lead to prevention
and treatment strategies that could make
cancer obsolete?
PRIMARY LITERATURE
Using sterile mates and
engineered toxins to beat bugs
Suppressing resistance to Bt cotton with
sterile insect releases.
View | Download
Growing new heart cells to treat
damaged hearts
Conversion of mouse fibroblasts into
cardiomyocytes using a direct
reprogramming strategy.
View | Download
Interfering with microRNAs to
control gene expression
Silencing of microRNA families by
seed-targeting tiny LNAs.
View | Download
Classic paper: How scientists
cloned the first mammal (1997)
Viable offspring derived from fetal and adult
mammalian cells.
View | Download
Inhibitors may block entry of
hepatitis C into cells
EGFR and EphA2 are host factors for
hepatitis C virus entry and possible targets
for antiviral therapy.
View | Download
page 266 of 989
1 pages left in this module
Principles of Biology
52 Eukaryotic Gene Regulation
Test Your Knowledge
1. How do eukaryotes and prokaryotes differ?
Eukaryotes contain RNA, while prokaryotes do not.
Prokaryotes contain DNA, while eukaryotes do not.
Eukaryotes contain a nucleus, while prokaryotes do not.
Prokaryotes contain ribosomes, while eukaryotes do not.
Eukaryotes contain proteins, while prokaryotes do not.
2. Which of the following reduces the net positive charge of a histone?
binding to a promoter
RNA polymerase
lactose binding
acetylation
methylation
3. Which of the following statements is true of an enhancer?
Enhancers are downstream of the promoter.
Enhancers are usually specific for many genes.
Enhancers may be thousands of nucleotides from the gene they are associated
with.
One gene cannot have more than one enhancer.
None of the answers are correct.
4. Which of these is NOT a process that may be involved in post-transcriptional
regulation?
methylation
blocking translation
phosphorylation
protein degradation
protein folding
5. What is a transcription factory?
a supergene that transcribes many different mRNA molecules
a physical grouping of genes on different chromosomes that come together to
coordinate transcription
mitochondrial genes
a repeated sequence of genes
a group of genes clustered together on the same chromosome
6. What is the function of the proteasome?
mRNA degradation
ubiquitin production
protein degradation
stitching exons together
modifying the folding structure of proteins
contents
Submit
IN THIS MODULE
Mechanisms of Gene Regulation in
Eukaryotic Cells
Summary
Test Your Knowledge
WHY DOES THIS TOPIC MATTER?
Stem Cells
Stem cells are powerful tools in
biology and medicine. What can
scientists do with these cells and their
incredible potential?
Synthetic Biology: Making Life from
Bits and Pieces
Scientists are combining biology and
engineering to change the world.
Cancer: What's Old Is New Again
Is cancer ancient, or is it largely a
product of modern times? Can
cutting-edge research lead to prevention
and treatment strategies that could make
cancer obsolete?
PRIMARY LITERATURE
Using sterile mates and
engineered toxins to beat bugs
Suppressing resistance to Bt cotton with
sterile insect releases.
View | Download
Growing new heart cells to treat
damaged hearts
Conversion of mouse fibroblasts into
cardiomyocytes using a direct
reprogramming strategy.
View | Download
Interfering with microRNAs to
control gene expression
Silencing of microRNA families by
seed-targeting tiny LNAs.
View | Download
Classic paper: How scientists
cloned the first mammal (1997)
Viable offspring derived from fetal and adult
mammalian cells.
View | Download
Inhibitors may block entry of
hepatitis C into cells
EGFR and EphA2 are host factors for
hepatitis C virus entry and possible targets
for antiviral therapy.
View | Download
page 267 of 989