HMB265H1 Lecture Notes - Gene Expression, Expressed Sequence Tag, Encode
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Tuesday, January 13, 2009
-Today’s class is on genes and gene expression.
-There’s three main components:
-1) Talking about what a gene is over time and how it has evolved.
-2) Talking about regulation of genes and how genes are expressed.
-3) Talking about how genes are identified.
-These are the challenges faced with genes in 2001.
-When they sequenced the genome, they started to try and figure out
where the genes were. They didn’t know all of the genes, they knew
about 50% of the genes, but they didn’t know all of them and this was
one of the key things: to identify where the genes were and what they
-Why do we care so much about genes? Over the last 100 years, people
realized that genes are absolutely critical for understanding the
phenotype of an organism.
-Let’s take a look at how the definition of genes has evolved over the
last 100 years.
-In the 1900s, the term gene was only known as a theoretical thing. It
was known that there were these traits, they called them genes but they
didn’t have any idea what they were. All they knew was you could have
a change in the gene and it would cause a different phenotype. So the
idea of the gene was in place b/c you could examine what a plant looked
like & see that it was short or tall & you could transmit that info to
offspring so they knew that there was a physical gene but they didn’t
have any sense of what it really was.
-In 1950-1960’s, with the info from Oswald Avery’s experiments, the
scientists realized that the genes were DNA. Initially, they just thought
that the idea was that there was DNA and it coded for RNA so that
knowledge came about with experiments done in the 50s and 60s.
-In the pictures, each triangle is supposed to represent a change. So it
was known that if there was a mutation or a change in the DNA
sequence then you could have a change in the phenotype. For example,
blue flowers or red flowers; a bacterium that is virulent and one that is
not; a change in the gene here that could cause the death of a mouse.
-Within the 1970s and up to the 2000s, people realized that the protein
coding info of a gene is not continuous but is split up by these intron
sequences. So there are both intron sequences and protein coding
regions. And that the initial transcript of RNA is spliced to form a
mature messenger RNA and that’s what allows us to have different
isoforms of proteins. This is probably the definition of a gene that most
of us are familiar with: the idea of the DNA being transcribed and RNA
being processed and translated.
-Early on, in the 1970s and 1980s and even to the 1990s, the rest of the
DNA was considered to be spacing – it was considered to be junk & not
really carrying any info. The idea was that the protein coding regions
(only about 3% of the genome) & the rest just happened to be repetitive
DNA or not useful info. This idea has changed & now we know that this
-If you’re looking for genes in the entire genome sequence, then the
knowledge of how genes are organized & regulated will help you to
identify genes when you have all of these thousands & millions of base
-Genes are so important because through the expression of a gene,
through transcribing it and, in most cases, translating it, we determine
the phenotype of us as individuals and of all the cells in the body.
-The genes we know are critical for determining the phenotype.
-Cells are different so in each cell, not all of the genes are expressed at
the same time even though each cell has a complete copy of the
-Genes that are in your genome of all cells have a differential expression
so brain cells will express a certain subset of genes & liver cells will
express a different subset of genes. You can analyze that at the protein
level which is what we see in the picture, that there are differences in
the proteome of both cell types. That kind of regulation happens at 2
-In the long term, when certain genes in the brain will be shut down,
liver genes for example, and will never be expressed again.
-Or, in the short term, when, for example, in the liver when you’ve
eaten a meal & you need to make the enzymes to store glucose into
-So there will be times when you’ll need short term regulation and, on
top of that, long term regulation is imposed. So short term, genes are
quickly turned on and off whereas in long term, it allows for a cell to
take on a certain phenotype which is the identity of it.
-So what proteins you end up with in the cell can be influenced by all
these steps but one of the main ones is at the level of transcription, is the
gene transcribed or not?
-Review the next two slides by yourself since we (Campbell and
French) assume you’ve already learned this stuff in other courses.
-How does transcription happen? For transcription to happen, there are
going to be general transcription factors that are going to bind to the
promoter regions of genes. In this textbook, they take the minimal
promoter region that you’ve heard about and talk about promoter-
proximal elements and the TATA box and this would be the minimal
promoter region that you’ve heard about previously. Those are for sort-
of basal level transcription.
-And then there could be other control elements that could be found in
other places which can be either enhancers or silencers that bind to other
transcription factors and will regulate transcription either up or down.
So these are some of the elements (whenever you say elements you’re
talking about DNA) that regulate transcription in eukaryotic genes.
-So you have the RNA polymerase coming along and then the
transcription factors will bind and the RNA polymerase will make a
primary transcript that is then spliced to make a mature messenger RNA
and then that mature mRNA is translated to proteins. That’s how the
gene expression will work.
-In terms of regulatory regions for genes, there’s the promoter region
and the enhancers that are relatively close to where the protein-coding
gene is. At least they’re on the same chromosome as the protein-coding
gene in this case. So there’s the promoter and the promoter-proximal
elements that are going to recruit the general transcription factors and
then RNA polymerase to allow for a base-line of transcription.
-Enhancers and silencers can be found either upstream (5’) or
downstream (3’) of the protein-coding region and those bind to the
transcription factors that will tweak the expression either upwards or
-Enhancers are bound by activators that activate transcription and
silencers are bound by repressors that repress transcription.
-These elements are called cis-acting elements. You need to have them
on the same piece of DNA at some point in order for transcription to
Today"s class is on genes and gene expression. 1) talking about what a gene is over time and how it has evolved. 2) talking about regulation of genes and how genes are expressed. These are the challenges faced with genes in 2001. When they sequenced the genome, they started to try and figure out where the genes were. They didn"t know all of the genes, they knew about 50% of the genes, but they didn"t know all of them and this was one of the key things: to identify where the genes were and what they were. Over the last 100 years, people realized that genes are absolutely critical for understanding the phenotype of an organism. Let"s take a look at how the definition of genes has evolved over the last 100 years. In the 1900s, the term gene was only known as a theoretical thing.