Download Chromosomes

Chromosome and genome
11-16-2015
Genome: whole set of DNA to
store all genetic information
Circular versus
linear chromsome
Human Genome
• How many chromosomes does each human cell have?
– 22 pairs of autosomal chromosome and 1 pair of sex
chromosomes
• What is the size of the human genome?
– The human genome is made up of 3 billion base pairs
• How many genes does the Human Genome code for?
– Define the meaning of gene first!
Chromosomes
p
Centromere
q
Chromosome 5
Chromosomes as seen at metaphase during
cell division
Telomere
DNA and protein cap
Ensures replication to tip
Tether to nuclear
membrane
Light bands
Replicate early in S phase
Less condensed chromatin
Transcriptionally active
Gene and GC rich
Short arm
p (petit)
Centromere
Joins sister chromatids
Long arm q
Essential for chromosome segregation at cell division
100s of kilobases of repetitive DNA: some nonspecific, some chromosome specific
Dark (G) bands
Telomere
Replicate late
Contain condensed chromatin
AT rich
Total Genes On Chromosome 17: 723
373 genes in region marked red, 20 are shown
FZD2
AKAP10
ITGB4
KRTHA8
WD1
SOST
Genes are arranged in linear order on
chromosomes
MPP3
MLLT6
STAT3
BRCA1
GFAP
NRXN4
NSF
NGFR
Chromosome 17
source: Human Genome Project
CACNB1
HOXB9
HTLVR
ABCA5
CDC6
ITGB3
breast cancer 1, early onset
Genome Comparison
Organism
# of Genes
Genome Size (bp)
E.coli
4,200
4,600,200
S. cervisiae (yeast)
6,000
12,000,000
C. elgans (nematode)
14,000
100,000,000
D. melanogaster (fruit fly)
14,000
140,000,000
A. thaliana (mustard plant)
24,000
120,000,000
Human
19,000
3,000,000,000
Human Genome
• What is a gene?
– A gene is segment of a genome that encodes a
single specific end product (a protein or RNA) or a
functional unit or information
• How much of the genome are “genes”?
– ~1.5% of the genome for protein coding
• What accounts for the rest of the DNA in the
genome?
Human Genome
• Other items in genome
– Introns
– Repeated sequences (telomeres, centromeres)
– Non-coding RNAs
•
•
•
•
tRNA, rRNA, snRNA.
miRNA
Long non-coding RNA
Functional or noise????
– Transposons (SINES and LINES)
– Psuedogenes (genes that no longer produce
functional products)
Transposons: Mobile DNA
• Class II transposons: DNA (transposons) that
moves directly from place to place.
• Class I transposons: retrotransposons
– That first transcribe the DNA into RNA and then
– use reverse transcriptase to make a DNA copy of
the RNA to insert in a new location
Discovery of transposons
Barbara McClintock (1902-1992)
Nobel prize in Physiology and Medicine 1983
Mobile genetic elements in maize 1940-1950
Discovery of TE
- study
of chromosomal breakage
- increased frequency in certain site
(= marker „dissociation“ Ds)
- location of Ds (dissociator) was unstable
after crossing with some lines with
Ac (activator)
(= line carrying „activator“ Ac)
Discovery of TE
- in one location – Ds insertion was
connected with loss of purple pigment
of endosperm
- after crossing with activator line
pigment synthesis was recovered in
some cells
Three of the many types of mobile genetic elements found in bacteria
Transposase gene: encoding enzymes for DNA breakage and joining
Red segments: DNA sequences as recognition sites for enzymes
Yellow segments: antibiotic genes
Transposition: Cut and Paste (command/control-X and
command/control-V in your computer)
DNA-only
What is wrong about class I element?
How to handle such problem?
The transposable element content of the human genome
What we should know about Alu element!
• All Alus are approximately 300 bp in length.
• A single recognition site for the restriction enzyme AluI
located near the middle of the Alu element.
• Alu elements are found only in primates.
• Human chromosomes contain about
1,000,000 Alu copies (10% of the total genome).
• Alu is a "jumping gene" – a transposable DNA
sequence that "reproduces" by copying itself and
inserting into new chromosome locations.
What we should know about Alu element!
• No evidence that it is ever excised or lost from a
chromosome locus. Each Alu insertion is the "fossil"
of a unique transposition event that occurred only
once in primate evolution.
• Each Alu element has an internal promoter for RNA
polymerase III.
• However, Alu lacks the enzyme functions to produce
a DNA copy of itself and to integrate into a new
chromosome position
Alu transposition
via an RNA
intermediate:
L1 provides RT for
reverse
transcription and a
nick on the host
chromosome!
Alu is a parasite of
L1, which, in turn,
is a relic of a
retrovirus ancestor.
What we should know about Alu element!
• The rate of Alu transposition is about one in every 200
newborns today.
• The vast majority of Alu insertions occur in noncoding regions and are thought to be neutral.
• An Alu insertion in the NF-1 gene is responsible for
neurofibromatosis I.
• Alu insertions in introns of genes for tissue
plasminogen activator (TPA) and angiotensin
converter enzyme (ACE) are associated with heart
disease.
PV92, a human-specific Alu insertion on chromosome 16
How Alu jump!
http://labcenter.dnalc.org/labs/dnafinge
rprintalu/dnafingerprintalu_d.html
DNA
Nucleosome
細胞所有的遺傳資訊都完全登
錄在DNA上的ATGC序列嗎？
Epigenetics: the study of mitotically and/or
meiotically heritable changes in gene function
that cannot be explained by changes in DNA
sequence (Riggs et al. 1996)
Epigenetic chromatin regulation
A. Modification at the DNA level
1. cytosine methylation
B. Histone modification - the histone code
1. Histone acetylation
2. Histone methylation
3. Histone phosphorylation
4. Histone ubiquitilation
5. Different types of histones
The five nucleotides that make up the DNA
Maintenance of methylation
Brand eis, M., Ariel, M. & Cedar, H. ( 1 99 3 ) Bioessays 1 5 , 70 9-71 3.
Genomic imprinting
Some genes are expressed only from the
maternal genome and some only from the
paternal genome
It is estimated that about 40 genes are
imprinted and they can be found on several
different chromosomes
Imprinting is maintained by DNA methylation
Why gene imprinting?
Parent Offspring Conflict Hypothesis (Haig hypothesis)
Conflict between male and female over allocation of maternal
resources to offspring
Paternally expressed genes would promote growth, maternally
expressed genes should slow it down.
For example:
IGF2 (growth factor) / IGF2 receptor (make IGF2 inactive)
IGF2 gene is paternal or maternal imprinted?
How about IFG2 receptor?
Epigenetic chromatin regulation
A. Modification at the DNA level
1. cytosine methylation
B. Histone modification - the histone code
1. Histone acetylation
2. Histone methylation
3. Histone phosphorylation
4. Histone ubiquitilation
5. Different types of histones
Features of Histone Modifications
•
Covalently attached groups (usually to histone tails)
Methyl
Acetyl
Phospho
•
Reversible and Dynamic
– Enzymes that add/remove modification
– Signals
•
Have diverse biological functions
Ubiquitin
SUMO
Cell, 111:285-91, Nov. 1, 2002
Features of Histone Modifications
•
•
Small vs. Large groups
One or up to three groups per residue
Ub = ~8.5 kDa
H4 = 14 kDa
Jason L J M et al. J. Biol. Chem. 2005
Types of Histone Modifications
Bhaumik, Smith, and Shilatifard, 2007.
Histone Modifications and Modifers
•
Writers: enzymes that add a mark
•
Readers: proteins that bind to and “interpret” the mark
•
Erasers: enzymes that remove a mark
Tarakhovsky, A., Nature Immunology, 2010.
Dynamic of chromosome structure
• Copy Number Variation (CNV) in human genome
• Total 1,447 CNV were identified across the 270
samples
• Established average length of CNV regions per
genome was over 20 million base pairs
Nature 444:445 (2006)
Copy number variation of amylase gene among different people with different diet!
EXPANDING THE GENE CONCEPT
BEYOND THE PROTEIN ENCODING
SEQUENCESES of DNA:
TRANSCRIPTION OF SOME GENES
PRODUCES NONCODING RNAs
Non-Coding RNA: Formerly known as “JUNK”
A Key to Eukaryotic Complexity?
Types of RNA
CODING
In translation (mRNA)
NON-CODING
In translation (tRNAs and rRNAs)
In RNA processing: ribozymes
Regulatory RNAs: Riboswitch; microRNA and
lincRNA
Capping by Branching: A New Ribozyme Makes Tiny Lariats
Science 309: 1350-1; 2005
A decade of riboswitch Cell 152: 17-24; 2013
What is miRNA?
51
Characteristics of miRNAs
•
•
•
•
•
•
Small non-coding double stranded RNAs
Approximately 19-22 nt long
Repress activity of complementary mRNAs
Regulate 30% of mammalian gene products
1 miRNA = hundreds of mRNAs
Many are conserved between vertebrates and
invertebrates
Genomic Organization
miRNA processing
Microprocessor
Complex
Differences in miRNA Mode of Action
CORRELATION OF MIR EXPRESSION WITH PROGRESSION AND
PROGNOSIS OF GASTRIC CANCER*
PATIENTS: 181 patients from 2 cohorts (Japan)
CLASSIFICATION: Stages I-IV
Diffuse vs. Intestinal type
ANALYSIS:
• Custom miR microarray chip (Ohio State Univ.)
• miR expression in 160 paired samples
(tumor vs. non-tumor)
• Correlations of miR expression vs. stage,
type and prognosis (survival)
* Lancet Oncol. 11,136, 2010
MiRs AS PROGNOSTIC FACTORS: GASTRIC
CANCER SURVIVAL*
Intestinal-Type Gastric Cancer
miR-495
HAZARD RATIO
(disease free survival)
5
4
3.2
3
2
1
0
Stages
I-II
Stages
III-IV
HAZARD RATIO
(disease free survival)
10
9
8
7
6
5
4
3
2
1
0
miR-199
Let-7g
high
low
high
low
low
high
I-II
III-IV
I-II
III-IV
I-II
III-IV
ANTIMETASTATIC ACTIVITY OF AHR AGONISTS IN ER
BREAST CANCER (Mol Cancer Therap. 11, 108-118, 2012).
Ligand
activated
Ahr
AhR
arnt
miR-335
Normal cells
Preneoplastic
miR-335cells
Cancer cells
(Invasive carcinoma)
Metastasis
SOX4
SOX4 and other miR-335
regulated metastatic
mRNAs
SOX4
SOX4 and other miR-335
regulated proteins
What is lincRNAs?
Large intergenic noncoding RNAs (lincRNAs)
are emerging as key regulators of diverse cellular
processes.
Determining the function of individual lincRNAs
remains a challenge.
Recent advances in RNA sequencing (RNA-seq)
and computational methods allow for an
unprecedented analysis of such transcripts.
Cell July 3, 2013. Page 26
Cell nucleus is a highly organized structure just like a Rome city!
Long Noncoding RNAs May Alter Chromosome’s 3D Structure
24 MAY 2013 VOL 340 SCIENCE page 910
RNA world
• Carry information (DNA)
• Catalyze chemical reaction (protein enzyme)
• Nutrient sensor to control gene expression
(protein receptor)
• Broadly control gene expression through
mRNA stability, translational efficiency etc.
(protein activator or repressor)
• Global control nuclear and chromosome
structure.(Histone code)