A consortium of 440 scientists from 32 laboratories characterized functional elements in the human genome as part of the ENCyclopedia Of DNA Elements (ENCODE) project. They found that 80% of the genome is biochemically active, with millions of regulatory elements such as promoters, enhancers, and insulators. Many of these elements interact with genes over long distances to control gene expression. This study significantly changes understanding of how the genome works.
6. NHGRI
Solicited RFAs were
First
pilot sought for
Publicat
proposal full
ion in
for ENCODE ENCODE
2000
In October GWAS -
1990 Human Finished 90% lies First Report
ENCODE
Genome paper in outside on Encode
published
project 2003 coding Published
2005 2012
started in 2007
8. Treasure Hunt?
It is like google map says Eric Lander : Map of earth
from outer space
9. 95% of the genome is “junk”.
◦ 2.94% of the genome is coding
cis regulatory elements occur within a
limited genome distance.
Most of the genome is transposable
elements that are of obscure origin are
dying.
Transcribed elements are most often
translated than not.
10. 80% of the human genome is active!!
◦ 70,000 promoters and 400,000 enhancers
75% of the genome transcribed in some
tissue or other during life time.
Environment plays great role in switching on
or off of a lot many genes. [Epigenetics]
Most of the diseases don‟t lie with the genes
but the switches!!
Dark matters controlling the genes are
physically close to the genes they control.
11. Genes and the switches don‟t hold one to one
relationship!
4 million switches controlling 21,000 genes!!
Identical twins are NOT identical – greatly
influenced by environments.
Astronomy and genetic Biology looks
similar(95% of the Universe is called as dark
matter – we don‟t understand)
12. “This explains why 6.5 billion people on earth
don‟t look alike”..
Intelligent Design (Creationism) believers are
excited that it is handiwork of God.
Natural selectionists (Darwinists) excited that
natural selection at its best.
◦ This has raged a war between democrats and
republicans as usual.
Junk DNA is an “Oxymoron”.
Some are still wondering about the remaining
20%.
13. „I hope this information stirs the mind of
those researchers that have ignored "trace
minerals" in food as part of the nutritional
package‟.
The more we think we are close to finding an
answer – the far we find ourselves. Reminds
me of Aristotle Who once said “The more you
know, the more you know you don't know”
14. Most part of DNA was considered “Garbage”
but later upgraded to “junk”.
Most people are actually happy because it is
happening during their “life time”.
Switches are software and genes are
hardware.
Ancient Egyptians considered “torso” has a
divine role and discarded grey matter in head
as “junk”.
15. Sean Eddy “At least 40% of the human genome is
composed of the decaying DNA remains of transposable
elements (TEs), different species of which have
replicated in great waves during the evolution of our
genome.”
“I sure wish I‟d gotten the memo, because this week a
collaboration of labs led by myself, Arian Smit, and
Jerzy Jurka just released a new data resource that
annotates nearly 50% of the human genome as
transposable element-derived, and transposon-derived
repetitive sequence is the poster child for what we
colloquially call “junk DNA”.”
http://cryptogenomicon.org/
19. The Cell Types
Cell Type Tier Description Source
GM12878 1 B-Lymphoblastoid cell line Coriell GM12878
Chronic
K562 1 Myelogenous/Erythroleukemia ATCC CCL-243
cell line
Human Embryonic Stem Cells, Cellular Dynamics
H1-hESC 1
line H1 International
HepG2 2 Hepatoblastoma cell line ATCC HB-8065
HeLa-S3 2 Cervical carcinoma cell line ATCC CCL-2.2
Human Umbilical Vein
HUVEC 2 Lonza CC-2517
Endothelial Cells
PLoS Biol.
Various (Tier 3) 3
Various cell lines, cultured
primary cells, and primary Various
2011
tissues April; 9(4):
e1001046
.
20. DNAseI -> Transcription factor binding sites
(2.9 million sites, 1/3 rd in one cell type and
remaining in others)
Chip-seq -> sequence transcription factor
and histone binding sites (HeLA and
GM12878 – qualified to be called as new
species)
5C technology -> Finding proximity between
regulatory and regulated regions
High density 5 bp tiling DNA micro arrays
21. Cap Analysis of Gene Expression
Paired-End diTag (PET)
Reduced Representation Bisulphite
Sequencing (RRBS)
22. 33.45% exon and 66.55% intron.
62% of the genome is transcribed
reproducibly.
231 MB of genome has protein binding sites.
◦ 80% of which are low affinity sites
(http://www.factorbook.org/)
◦ Many are highly conserved cell selective type
96% of the CpG exhibited differential
methylation pattern.
GWAS SNPs had overlaps with ENCODE
elements.
23. Chromosome confirmation capture carbon
copy(5C)
◦ 1% of the genome is distally regulated (>1000 bp)
◦ On an average 3.9 distal elements interacted with
TSS.
◦ Distance could be several KBs to MBs
24. cis-regulatory elements - Enhancers,
promoters, insulators, silencers.
2.9 million DHS encompassing 125 diverse
cell and tissue types.
20-50 bp length DHS mapped uniquely to
86.9% of genome
◦ 580,000 distal DHS with target promoters
◦ 3% lie in TSS
◦ 5% lie within 2.5 KB of TSS
◦ 95% lie distally (introns and intergenic regions)
◦ Strongly enriched in LTRs
25. 3/4th of genome is capable of transcription –
redefine concept of gene?
◦ 62.1% AND 74.7% are processed or primary
transcripts.
◦ 10-12 expressed isoforms per gene per cell.
◦ Coding and non-coding transcripts are localized in
cytoplasm and nucleus respectively.
◦ 6% of the coding and non-coding transcripts
overlap with small RNAs – precursors?
◦ Most of the novel transcripts lacked protein coding
ability.
26. Mapping job is only half done.
Characterizing everything a genome does is
10% done.
Finding Network of switches for genes.
A number of correlations…..
27. Where does gene therapy go from here?
Our fundamental understanding of genes as
the functional units are flawed??
Epigenetics becomes the key player…
Gives impetus to holistic approach in treating
a disease.
Do we still believe that human genome is
most efficient?
