ONE TYPE OF uses THREE RNA

12.10 Transcription in Eukaryotes POLYMERASE

-Bacterial RNA
polymerases

polymerase
Differs from Bacterial Transcription in

Several Ways RNA polymerases are enzymes —

meaning they’re biological molecules
(usually proteins) that speed up chemical
reactions in the cell.

Specifically, RNA polymerases are

DIFFERENCES responsible for making RNA from a
DNA template — this process is called
BACTERIA EUKARYOTES transcription.

everything happens TRANSCRIPTION Eukaryotes are more complex

in the occurs in the organisms with compartmentalized
CYTOPLASM NUCLEUS cells . Thus, three specialized RNA
polymerases to handle specific type of
Reasoning: In bacteria, everything RNA
happens in the cytoplasm because they
don’t have a nucleus. So as soon as RNA Bacteria/ Prokaryote - simpler with no
is being made, ribosomes can already nucleus and less compartmentalization -
start translating it into proteins. That’s one RNA to transcribe all types of RNA
called coupled transcription and
translation. No chromatin, CHROMATIN must
No Histones be
But in eukaryotes, transcription happens REMODELED/UNC
inside the nucleus, which is a protected OILED for
compartment. Because of the nuclear TRANSCRIPTION
membrane, RNA can’t immediately meet to OCCUR
ribosomes, which are located outside in
the cytoplasm. Reasoning:

So the RNA has to be completely made, Eukaryotic DNA is tightly wrapped

processed, and then exported to the around HISTONE PROTEINS forming
cytoplasm before translation can NUCLEOSOMES which pack into
begin. CHROMATIN

Why? Because this separation allows -> Coiling PROTECTS DNA but makes
more control and regulation. The RNA it INACCESSIBLE to enzymes like RNA
must first be fully made, capped, spliced, polymerase
and polyadenylated before it can exit the
nucleus. The cell can check the RNA first Prokaryotic DNA is NAKED —->
— fix it, modify it — before it ever gets Accessible to RNA polymerase
used to make protein.
simpler genomes-> less need for complex
packaging
only ONE SIGMA Transcription dissociation of
factor to help RNA REQUIRES many RNA
polymerase find the TRANSCRIPTION POLYMERASE
promoter FACTORS (GTF’s) from the DNA
template
prokaryotes have only a sigma factor to
bind the promoter and initiate transcription
whereas in eukaryotes, SEVERAL
general transcription factors are required ​ •In bacteria, a simple hairpin loop
to bind the promoters, recruit RNA in the RNA can cause RNA polymerase to
polymerase and initiate transcription. fall off.

EUKARYOTES HAVE ENHANCERS AND In eukaryotes, termination involves:

SILENCERS
​ •A specific sequence (AAUAAA)
ENABLES cell-type specific and called the polyadenylation signal.
context-specific gene expression
Function:
Cell-type-specific gene expression:
Different cell types within an organism Cleavage and Polyadenylation: The
have distinct functions, and this is PAS signals the RNA cleavage
achieved through the expression of complex to cleave the pre-mRNA at a
specific genes. This means that certain specific site, releasing the mRNA
genes are turned "on" (expressed) in transcript.
one cell type but not in another.
Poly(A) Tail Addition: After cleavage,
polyadenylation polymerase (PAP) adds a
Context-specific gene expression: poly(A) tail (a string of adenine
The environment or circumstances nucleotides) to the 3' end of the newly
surrounding a cell can also influence formed mRNA.
which genes are expressed. This
means that even within the same cell mRNA Stability and Translation: The
type, genes can be expressed differently poly(A) tail plays a critical role in mRNA
depending on the signals or conditions it's stability, protecting it from
exposed to. degradation, and facilitating
translation by aiding ribosome
binding.
TRANSCRIPTION TRANSCRIPTION
TERMINATION is TERMINATION is ​ •Then the RNA is cleaved 10–35
DEPENDENT upon more COMPLEX bases downstream.
the format of a
hairpin structure transcriptional ​ •Finally, RNA polymerase
in the transcript termination for dissociates, ending transcription.
(intrisic) protein-coding
genes involves
SEQUENCE-SPEC
Why is it complex?
IFIC CLEAVAGE of
the transcript,
​ •​ It ties directly into RNA
which then leads to
processing (see next point).
eventual
​ •​ The cleavage also triggers and rRNAs) go through simple trimming
poly-A tail addition, essential for or chemical modifications, but:
stability and export. ​ •mRNA in bacteria = mostly used
as-is right after being made.
​ •It’s short-lived and doesn’t need
all the fancy stuff.

(protein coding
DOES NOT mRNAS)
UNDERGO pre-mRNAs, INITIATION, ELONGATION, AND
PROCESSING undergo complex TERMINATION OF TRANSCRIPTION IN
alterations, EUKARYOTES
generally referred
to as “processing,”
●​ Each eukaryotic RNA polymerase is
LARGER and MORE COMPLEX than the
single form of RNA polymerase found in
In Eukaryotes (like you and me):
bacteria

The RNA made during transcription is not

ready yet.
It needs to be processed —
​ •Capping (5’ cap)
​ •Splicing (cutting out introns)
​ •Tailing (Poly-A tail at 3’ end)

Then, the mature mRNA can leave the

nucleus and go to the cytoplasm to be
translated.

In Bacteria:
TERMS
​ •They have no nucleus, so
transcription and translation happen at Promoter
the same time (this is called coupled
transcription-translation). This is like the “start here” signal in DNA.
​ •Their genes don’t have introns ​ •It’s a specific DNA sequence where RNA
polymerase and transcription factors bind to start
(usually). transcription.
​ -So there’s no need for splicing. ​ •In eukaryotes, a common part of the
​ •And they don’t add a 5′ cap or a promoter is the TATA box.
poly-A tail in the same way eukaryotes ​ •It’s always close to the gene it regulates.
do.
Think of the promoter as the front door of the gene
— if RNA polymerase can’t find it, it can’t get in and
BUT… start working.

Do they have any kind of RNA ⸻

processing? General Transcription Factors (GTFs)

Yes, some bacterial RNAs (like tRNAs These are protein helpers that guide RNA
Polymerase II to the promoter.
​ •Silencers: DNA sequences that
-Specifically, RNA polymerases are responsible decrease transcription when repressor proteins
for making RNA from a DNA template — this bind.
process is called transcription
They can be far from the gene (even thousands
of bases away!), but DNA looping helps bring
​ •Examples: TFIID, TFIIB, TFIIH, etc. them close.
​ •They help assemble the pre-initiation
complex so transcription can begin. ⸻
​ •TFIID, for example, contains a subunit
that binds to the TATA box. Enhancer + Promoter = Hype Team
​ •Enhancers are like cheerleaders for the
They’re like the crew that sets the stage before the promoter.
main show (RNA Pol II) can start. ​ •They are cis-acting DNA elements that
can be far from the gene (upstream, downstream,
⸻ or even in an intron).
​ •​ When activator proteins bind to
Cis-acting elements (cis = “on the same DNA enhancers, DNA loops to bring the enhancer close
strand”) to the promoter.

These are DNA sequences that regulate Result?

transcription, but only affect the gene they’re ​ •Increased transcription
physically attached to. ​ •Promoter gets a boost: RNA polymerase
​ •Examples: Promoters, enhancers, binds more efficiently → more RNA is made.
silencers
​ •“Cis” means “on the same side”—they’re Analogy:
part of the DNA near or far from the gene they The promoter is the stage.
influence. The enhancer is the hype squad screaming “Let’s
​ •They don’t move; they just sit there and go!” from the back — but thanks to DNA looping,
wait for proteins to bind them. they’re heard loud and clear.

Like a signpost next to a house telling visitors ⸻

where to go.
Silencer + Promoter = Block Button
⸻ ​ •Silencers are like the opposite of
enhancers.
Trans-acting factors (trans = “from elsewhere”) ​ •​ When repressor proteins bind to
silencers, they also loop to the promoter — but
These are proteins (like transcription factors) that instead of helping, they block or suppress
bind to cis-acting DNA sequences. transcription.
​ •They are coded by different genes—so
they’re not on the same DNA strand they act Result?
on. ​ •Decreased transcription
​ •The promoter can’t do its job well — RNA
​ •They can float around the nucleus and polymerase may not bind, or may bind less often.
bind wherever needed.
Analogy:
Think of them like delivery guys from somewhere Silencer = that person who whispers to the event
else, showing up to read the signpost (the organizer, “Don’t start the show, it’s not worth it.”
cis-acting element) and do the job.

Enhancers and Silencers Polymerases I and III:

These are cis-acting DNA elements that regulate
gene expression from a distance. ●​ Transcribe transfer RNAs and Ribosomal
​ •Enhancers: DNA sequences that RNAs (needed at all time for basic processes of protein synthesis)
increase transcription when activator proteins
bind.
Polymerases II:
 ●​ Transcribe protein- coding genes (highly
regulated- expressed at different times, in response to different signals and in
different cell types , gene-to-gene basis)

●​ Activity is dependent on both the

cis-acting regulatory elements of the
gene and a number of trans-acting
transcription factors

At Least 4 TYPES OF CIS-ACTING

DNA ELEMENTS regulate the initiation
of transcription by RNAP II.
PROXIMAL- -​ located
PROMOTER upstream of
ELEMENT the start site
1st CORE PROMOTER -​
includes the -​ helps modulate
transcription the level of
start site transcription
-​ Determines
where RNAP ENHANCERS -DNA sequences that
II binds to the increase transcription
DNA when activator
In some eukaryotes: proteins bind.

SILENCERS -DNA sequences that

Goldberg-Hogness decrease transcription
Box or TATA box when repressor
proteins bind.
cis acting element
within the core
promoter

A common sequence
within the core trans-acting transcription factors
promoter is the TATA
box, also known as
the
Goldberg–Hogness complementing the cis-acting regulatory sequences
box. It’s usually
located about 30 2 BROAD CATEGORIES
base pairs upstream
of the transcription
start site. Its
GENERAL TRANSCRIPTIONAL
consensus sequence
TRANSCRIPTION ACTIVATORS AND
is TATAA/TAA(R),
(GTF) TRANSCRIPTIONAL
where R is a purine
REPRESSORS
— either A or G. The
TATA box in
absolutely required influence the efficiency
eukaryotes serves a
for all RNAP II and rate of RNAP II
similar function to the
transcription TRANSCRIPTION
–10 region in
INITIATION
bacterial promoters,
but RNAP II doesn’t
bind directly to it like essential because -bind to the
bacterial RNA RNAP II cannot bind enhancer and
polymerase does. directly to the silencer elements
eukaryotic and regulate
 core-promoter sites transcription
and initiate initiation by aiding
transcription without or preventing
them assembly of pre
initiation complexes
Well characterized and and the release of
designated RNAP II from
TFIIA,TFIIB and so on. pre-initiation into full
transcription
TFIIB binds directly to elongation
the TATA BOX —>
TFFIB initial binding
allow other general
transcription factors
along with RNAP II to
bind sequentially to
TFIID = form
pre-initation complex

NO SPECIFIC SEQUENCE THAT SIGNALS FOR

TERMINATION OF TRANSCRIPTION (unlike
bacteria)

●​ RNAP II continues transcription well

beyond the 3’ end of the mature mRNA
●​ Once transcription has incorporated a
specific sequence AAUAA
(Polyadenylation signal sequence)

-transcript enzymatically cleaved roughly 10-30

bases further downstream in the 3’ direction
- Destabilizes RNAP II = Both DNA AND RNA are
released from the enzyme as transcription is
terminated
 mRNAS at their 3’ end , a stretch of as many as
250 adenylic acid residues

CLEAVED ROUGHLY 10-35 RIBONUCLEOTIDES -

and enzyme known as poly-A polymerase then
catalyzes the addition of a POLY-A tail to the free
3’ -OH group at the end of the transcript
-important for the expor of mRNA from nucleus to
cytplasm(Xrn2 or exonuclease)

-POLY A TAILS ARE ALSO FOUND ON MRNAS IN

BACTERIA AND ARCHAEA - much shorter and
found only a small fraction of mRNA molecules

PROCESSING -degradation in bacteria ; protective in eukaryotes

EUKARYOTIC RNA:
Caps and Tails AAUAAA SEQUENCE IS NOT FOUND ON ALL
EUKARYOTIC mRNAS but is essential to those
who have it : mutation —-> lack of Poly A —-
degraded by nucleases
Base Sequence of DNA in bacteria is transcribed into
an mRNA that is immediately and directly translated
into the amino acid sequence as dictated by the
genetic code

EUKARYOTIC mRNAS require significant

alteration before transported to the cytoplasm and
translated

1970= evidence shows that eukaryotic mrna is

transcribed initially as a precursor molecule much
larger than that which is translated into protein

IMPORTANT POST TRANSCRIPTIONAL

MODIFICATION of EUKARYOTIC RNA
TRANSCRIPTS destined to become mRNA occurs at
the end —> at the 5’ end of these molecules

●​ 7-methylguanosine (m7G) cap is added

●​ Stabilizes the mRNA by PROTECTING the
5’end of the molecule from nuclease
attack
●​ Facilitates the TRANSPORT of mature
mRNAs from the nucleus into the
cytoplasm (required for the initiation of
translation of the mRNA into protein)
●​ Chemicaly, THe cap is a GUANOSINE
RESIDUE with a METHYL GROUP (CH3)
at a position 7 of the base