DNA replication

Transcription
Translation
Maria Cristina Gambetta
Center for Integrative Genomics (CIG)
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3 major classes of biopolymers

• Nucleic acids
• Proteins
• Polysaccharides
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid

base
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid

pentose
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid

phosphate
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid

nucleotide
Nucleic acids = chains of nucleotides
deoxyribonucleic acid ribonucleic acid

Nucleic acids are synthesized from 5’ —> 3’

Nucleic acids = chains of nucleotides
Nucleic acids = chains of nucleotides

deoxyribose ribose
Nucleic acids = chains of nucleotides

uracil

thymine
Proteins = chains of amino acids

N (amino)- C (carboxyl)-
terminus terminus

Direction of protein chain growth: N à C

Proteins = chains of amino acids

structures of all 20 amino acids commonly found in proteins

 DNA
RNA
protein
 DNA
RNA
protein
“The central dogma of molecular biology deals with the detailed residue-by-residue transfer of
sequential information.”
-Francis Crick, 1970 Nature
replication DNA
transcription

RNA
translation

protein
replication DNA
transcription

RNA
translation

protein
Challenges of DNA replication
In our bone marrow, every
minute : ~500 Mio new blood
cells with a total length of 1
Mio km of DNA (25x equator
of the earth).
DNA is not naked in the eukaryotic cell
Nucleosome = structural unit of chromatin

Luger..Richmond, 1997 (Nature)

DNA replication

O’Donnell et al., 2013 (CSHPB)

DNA replication in eukaryotes

Timing domain =
large chromosomal regions that
replicate at similar times (early or
late in S phase).

Replication domain =
cluster of 5-10 adjacent origins
that fire almost simultaneously.

Replicon =
stretch of DNA replicated bi-
directionally from a single origin.
DNA replication in the eukaryotic cell cycle
DNA replication in the eukaryotic cell cycle
DNA replication
DNA replication
Breaks hydrogen bonds between complementary base pairs
DNA replication
Stabilize the separated strands and prevent them from
rejoining
DNA replication
Reduces torsional strain caused by unwinding of the DNA
double helix
DNA replication
Synthesizes an RNA primer.
DNA replication
Adds DNA nucleotides to primers in 5’ -> 3’ direction
DNA replication
Adds DNA nucleotides to primers in 5’ -> 3’ direction
DNA replication
The leading strand is continuously synthesized
DNA replication
The lagging strand is discontinuously synthesized
DNA replication
Removal of RNA primer, replacing it with DNA nucleotides
DNA replication
Adds DNA nucleotides to primers in 5’ -> 3’ direction
DNA replication

Drew Barry
Histone recycling
replication DNA
transcription

RNA
translation

protein
replication DNA
transcription

RNA
translation

protein
Transcription

Electron micrograph of chromatin spreads from yeast

Different eukaryotic polymerases
transcribe different RNAs
Different eukaryotic polymerases
transcribe different RNAs

RNA polymerase

RNA Pol I

RNA Pol II

RNA Pol III

RNA Pol II
Different eukaryotic polymerases
transcribe different RNAs

RNA polymerase

RNA Pol I

RNA Pol II

RNA Pol III

RNA Pol II
messenger RNAs (mRNAs) code
for proteins

Prokaryotic mRNA

Eukaryotic mRNA
messenger RNAs (mRNAs) code
for proteins

Prokaryotic mRNA

Eukaryotic mRNA
messenger RNAs (mRNAs) code
for proteins

Prokaryotic mRNA

Eukaryotic mRNA
Prokaryotic gene structure
Eukaryotic gene structure
Different eukaryotic polymerases
transcribe different RNAs

RNA polymerase

RNA Pol I

RNA Pol II

RNA Pol III

RNA Pol II
Eukaryotic gene structure
Eukaryotic gene structure

Y = T or C
R = A or G
Eukaryotic gene structure
Eukaryotic gene structure
Eukaryotic transcription cycle

Adelman & Lis, 2012

Transcription occurs in bursts

Fukaya et al., 2016 (Cell)

Transcription

Drew Barry
Eukaryotic gene structure
Genes are expressed in specific patterns

ON

RNA in situ hybridizations of Drosophila embryos

Regulatory elements
TFs bind to ‘open’ determine
chromatin regions expression
patterns
Epigenetic control of gene expression
Epigenetic regulation

Drew Barry
Coloring chromatin
Heterochromatin

Housekeeping genes

Specific genes

Heterochromatin

Silent, gene-poor

Drosophila chromatin states, determined by chromatin proteins

Filion..van Steensel, 2010 (Cell)
Transcription is not limited to promoters

Ren, 2010 (Nature)

• Enhancer RNAs (eRNAs) are transcribed by the same machinery as gene promoters.
• eRNAs are less stable than protein-coding mRNAs.
(Therefore only recently detected by nascent transcript sequencing or upon
inactivating RNA degradation machinery in cells).
• Levels of eRNAs correlate with enhancer strength.
replication DNA
transcription

RNA
translation

protein
In prokaryotes
In eukaryotes

Nucleus
Cytoplasm
 60S subunit
46 proteins
+ 3 rRNAs (25S, 5.8S, 5S)

40S subunit
33 proteins
+ 1 rRNA (18S)

Crystal structure of the yeast ribosome (Shem et al., 2010 Science)

RNA polymerase

RNA Pol I

RNA Pol II

RNA Pol III

RNA polymerase

RNA Pol I

RNA Pol II

RNA Pol III

The central dogma
coding strand 5’ ATG AAG CCG AGT GTA GAT 3’
template strand 3’ 5’
codon
5’ 3’
‘wobble’ position
anti-codon

5’

3’
The central dogma
coding strand 5’ ATG AAG CCG AGT GTA GAT 3’
template strand 3’ 5’
codon
5’ 3’
‘wobble’ position
anti-codon

5’

3’
The genetic code

The genetic code:

amino acids specified by each mRNA codon
Translation cycle
Translation cycle

A: amino acid
P: polypeptide
E: exit
Translation cycle
Translation cycle
Translation cycle
Translation cycle
Translation cycle
First amino acids in proteins

Table 1: N-Terminal Sequences of Proteins

Percent of Prokaryotic Proteins with Percent of Eukaryotic Proteins with
N-Terminal Sequence
This Sequence This Sequence

MA* 28.24% 19.17%

MK** 10.59% 2.50%

MS* 9.41% 11.67%

MT* 7.65% 6.67%

* Methionine was removed in all of these proteins

** Methionine was not removed from any of these proteins

Translation

Drew Barry
Questions