Human Genome Structure in 2011
Peter Wilson
18th June 2011
Overview
™Chromosome Structure
™Chromosome Abnormalities
Genome Structure Overview
DNA methylation
Histone modifications
DNA
Insertions
Deletions
Inversions
Translocations
CNVs
nucleosome
euchromatin
RNA
pol II
chromosome
heterochromatin
SNPs
Micro-insertions
Micro-deletions
mRNA, miRNA,
ncRNA
Aberrant expression
Alternative splicing
RNA editing
Fusion genes
Truncations
Chromosome Banding
Human chromosome 12: low resolution.
Giemsa staining at a fairly low resolution
produces about 400 total bands in a
karyotype
The Human Genome project has provided
a single nucleotide resolution picture of
each chromosome and the ultimate
chromosome map
Chromosome constituents
Telomeres - A telomere is a region of repetitive, DNA
sequence, TTAGGG in the case of humans and it is found at
the end of all chromosomes. The sequence protects the end of
the chromosome from deterioration or from fusing with
neighbouring chromosomes.
The Nucleosome - The Unit of
Chromatin
30-nm chromatin fibre
Chromatin spread at a moderate ionic
strength to maintain the 30-nm higherorder fibre. Size marker: 50 nm
Euchromatin
Euchromatin is found in parts of the chromosome that contain many genes it
is loosely-packed in 30-nm fibre loops.
The loops are separated from adjacent heterochromatin by insulators.
Heterochromatin
Found in parts of the chromosome where there are few or no genes, such as centromeres
and telomeres it is densely packed
•It is greatly enriched with transposons and other so called "junk" DNA
•It is replicated late in S phase of the cell cycle and has reduced cross over in meiosis
•genes present in heterochromatin are generally not transcribed and show increased
methylation at CpG islands associated with gene promoters
Centromeres
The centromere is critical for mitosis.
It holds the chromatids together and it is where the kinetochore is
formed.
It serves as the point of attachment for spindle fibres when the spindle
fibres are pulling the chromosomes toward the centrioles prior to
cytokinesis.
When the centromere is not functioning properly, the chromatids do not
align and separate properly this results in the wrong number of
chromosomes in the daughter cells leading to conditions such as Down
Syndrome.
Centromeres
Centromeres & Kinetochores
At the heart of the kinetochore is a
specialized nucleosome that contains
centromere protein (CENP)-A, a
histone H3 homologue. Several inner
kinetochore components (cyan and
purple
ovals)
associate
with
kinetochores throughout the cell
cycle. Most proteins indicated in this
drawing are present at kinetochores
in all metazoans.
Chromosome Territories
The Arrangement of Chromosomes in the Nucleus
Chromosome territories by
fluorescence in situ
hybridization
A) Chromosome territories (green) in liver cell nuclei (blue). B) Visualization of multiple chromosomes reveals spatial patterns of organization. Chromosomes 12 (red), 14 (blue), and 15 (green) form a cluster in mouse lymphocytes. Copyright 2004 BioMed Central Ltd.
Chromosome Abnormalities
Two primary mechanisms involved
in chromosome structure
alteration
1. The total amount of genetic information in the
chromosome can change by
Deletion, Duplication or Insertions
2. The genetic material may remain the same,
but is rearranged by
Inversions or Translocations
Copy Number Variation and
Human Disease
The schematic summarizes the distribution of insertions, deletions and inversions on
each human chromosome. A total of 297 clusters were identified: 139 insertions, 102
deletions and 56 inversions breakpoints. Across the genome, 163 of the structural
variants map to regions of segmental duplication.
Aneuploidies
Incidence of aneuploidy during
development
CNV detection by SNP array
Chr12 data for a pancreatic tumour with matched normal DNA
Tumour
Normal
Chromosome Duplications &
Deletions
Chromosome Inversion
Chromosome Translocations
a) An ideogram of a reciprocal translocation between chromosomes 12 and 17.
b) An ideogram of a Robertsonian translocation between chromosomes 14 and 21
Detection of Structural Variations by NGS
Interpretation
Mapping to reference
Interpretation
Mapping to reference
Deletion
Correct orientation (longer)
Inversion
Different strand
Tandem duplication
Incorrect orientation
Intra‐chr. insertion
Correct + incorrect orientation
Different chromosome
Inter‐chr. Insertion
Different chromosome
translocation
Integrated Cancer
Genome Analysis
Circos Plot
Chromosomes
Differential Methylation
Copy number variation
Germline SNVs
Germline SNVs (novel)
Somatic mutations (WGS)
Somatic mutations (Exome)
Translocations
Patient Report Card
Acknowledgements
QCMG
Sean Grimmond
Genome Biology
Peter Wilson
Deborah Gwynne
Life Technologies
Bioinformatics
Sequencing
Evgeny Glazov
Nic Waddell
Hilary Martin
John Pearson
David Miller
John Sheppard
Nicole Cloonan
Jason Steen
Lynn Fink
Ehsan Nourbakhsh
Emma Campbell
Karin Kassahn
Nick Matigian
Darrin Taylor
Craig Nourse
John Davis
Katia Nones
Mellissa Brown
Scott Wood
Suzanne Manning
Shivangi Wani
Ana Foster
Conrad Leonard
Ivon Harliwong
Keerthana Krishnan
Alan Robertson
Oliver Holmes
Senel Idrisoglu
Anita Steptoe
William Waterson
Rathi Thiagarajan
Christina Xu
David Wood
Matt Anderson
Muhammad Fudlullah
Sarah Song
Silicon Graphics
HPC (UQ)
Nick Comono
Lutz Poss
Todd Churchwood
Ziping Fang
Gerald Hofer
David Green