HUMAN GENOME PROJECTHUMAN GENOME PROJECT101101

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001

Human Genome Project

Begun in 1990, the U.S. Human Genome Project is a 13-year effort coordinated by the U.S. Department of Energy and the National Institutes of Health. The project originally was planned to last 15 years, but effective resource and technological advances have accelerated the expected completion date to 2003.

HGP goals are to:  ■ identify all the approximately 35,000* genes in human DNA,

■ determine the sequences of the 3 billion chemical base pairs that make up human DNA,

■ store this information in databases, ■ improve tools for data analysis, ■ transfer related technologies to the private sector, and ■ address the ethical, legal, and social issues (ELSI) that may

arise from the project.  

Human Genome DataHuman Genome Data

• Derived from the Human Genome Project

• sequence freeze date in anticipation of data release: 22 July 2000

• Release of First Draft Sequence of Human Genome :

Nature 409 (6822), 15 February 2001

Science 291 (5507), 16 February 2001

• Release of “Complete” Draft Sequence of Human Genome: April 2003

GENE GENEIntragenic region

exons intronsinterspersed

repeatstandemrepeats

Fine Structure of Human Genomic DNA

ACGTTGTGTCGCTGATTAGCTAGACCAAGATAGTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATATATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTAGATG

3.2 billion nucleotides

The

Human

Genome

How many genes?

>100,000 < 40,000

But think of allall our traits, Jim-

bo!

Ours?! Are you of my species?

Get lost, punk!

Ouch!

The

Human

GenomeACGTTGTGTCGCTGATTAGCTAGACCAAGATAGTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATACGCWHENISAGENEAGENETATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGC

Comparative Genomics (Alignment)

Gene Prediction

Experimental Discovery (Genetics)

Alignment

CTCGCTGACTCAATCGGATTATGCTAGTCG

GCCCCCCCCCCCCTGAGTCAGGGGGGCTCGCTGCTGTGCTG

TGACTCAATCGGATTATGCTAGTCG

ATAGCCTAATAGCTGACTCAATCGGATTATGCTAGTCG

ATTTTTTTGACTCAATCGGATTA

CGGGGTGACTCAATCGGA

AAAAATATATTGACTCAATCGGATTATGCTAGTCG

GTCGTAGCTTGACTCAATCGGATTATGCTAGTCG

TCATATGACTCAATCGGATTATGCTAGTCG

CTCGCTGACTCAATCGGATTATGCTAGTCG

GCCCCCCCCCCCCTGAGTCAGGGGGGCTCGCTGCTGTGCTG

TGACTCAATCGGATTATGCTAGTCG

ATAGCCTAATAGCTGACTCAATCGGATTATGCTAGTCG

ATTTTTTTGACTCAATCGGATTA

CGGGGTGACTCAATCGGA

AAAAATATATTGACTCAATCGGATTATGCTAGTCG

GTCGTAGCTTGACGGAATCGGATTATGCTAGTCG

TCATATGACTCAATCGGATTATGCTAGTCG

CTCGCTGACTCAATCGGATTATGCTAGTCG

GCCCCCCCCCCCCTGAGTCAGGGGGGCTCGCTGCTGTGCTG

TGACTCAATCGGATTATGCTAGTCG

ATAGCCTAATAGCTGACTCAATCGGATTATGCTAGTCG

ATTTTTTTGACTCAATCGGATTA

CGGGGTGACTCAATCGGA

AAAAATATATTGACTCAATCGGATTATGCTAGTCG

GTCGTAGCTTGACGGAATCGGATTATGCTAGTCG

TCATATGACTCAATCGGATTATGCTAGTCG

Gene Prediction

TTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGAATATAAAGGATAGATTACATGTGATATATGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTATGGATTGCGCTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATAGCGATATGACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATATGATATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAAATAATATAAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGC

TTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGAATATAAAGGATAGATTACATGTGATATATGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTATGGATTGCGCTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATGCGATATAACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATAGCGATATGACCCAGGGGGGATACGCTATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAATATATAAGAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGCTTCGCTATAGGCTATAGCGATATAACCCAGGGGGGATATGATATTAGGAGGAGAGATATAGGATAGATTACATGTGATATATAGGAGAGAGAAATAATATAAGAGAGAGAGATTTTTTCTCCTGGTAAAAAGCTCGCTTAGGATTGCGC

GENE GENEIntragenic region

exons intronsinterspersed

repeatstandemrepeats

Gene Prediction Algorithmsbased on consensus nucleotide sequences of

•tata boxes and start codons

•stop codons

•splice junctions

•CpG islands

Comparative Gross Results from Model Genome

Projects

Humans have about 35,000 genes!

You were right.

So what’s new!

Human Genes

Surprising Findings = !!

• !! Only 35,000 genes• most genes in euchromatin• GC/AT patchiness• !! Gene density higher & intron

size smaller in GC-rich patches• !! 1.4% translated, 28%

transcribed• !! Origins of genes

Some Origins of Human Genes

• Most from distant evolutionary past(basic metabolism, transcription, translation,repli-cation fixed since appearance of bacteria and yeast)

• Only 94/1278 families vertebrate-specific• 740 are nonprotein-encoding RNA genes• many derive from partial genomes of viruses and

virus-like elements—genomic fossils• some acquired directly from bacteria

(rather than by evolution from bacteria)

Genomic Fossils

Genomic Fossils(also known as Molecular Fossils)

• interspersed repeats

• generated by integration of transposable elements or retrotransposable RNAs

• active contemporary modifier of some vertebrate genomes (mouse)

• formerly active modifier of human genome

• some as prevalent as 1.5 million copies

Alu ElementsType of Short Interspersed Nuclear Element (SINE)

• transcribed by RNA polymerase III • 3’ oligo dA-rich tail• found only in primates• 1,500,000 copies • derived from 7SL RNA gene• dimer-like structure• most retroposition occurred 40 mya

A/T-richregion and3’-UTR

direct repeats

5’ 3’

A-rich regionRNA polymerase

III Promoter

AAAnA B

31 bp

50-300 bpAlu

Reverse TranscriptionEssential for Retroposition and Proliferation of Retroelements

• Converts primed RNAs into cDNAs• catalyzed by RNA-dependent DNA pol

» (reverse transcriptase)

• pol encoded by retroviruses and active LINEs

Retroviral genomic RNA

Alu RNA

LINE RNA

Alu Subfamily Structure (millions of years)

Oldest [J]

Intermediate [S]

Youngest [Y]

Jo Jb (65)

S (50) Sq

Sp Sx

Sc Sg

Y (25)

Yb8 Ya5 Ya8

450,000 copies

50,000 copies

Alu Elements as Genomic Fossils

Alu Subfamily Structure

PS [J]: Primate-Specific. Abundant in all primates.65-70 mya: Early Prosimian (strepsirhini)

AS [S]: Anthropoid-Specific (haplorhini) 50-60 mya One mutation difference than PS.

Alu Subfamily Structure

CS[S]: Catarrhine-specific. Nine mutations arising30-40 mya: Platyrrhines (FN) (Marmoset)Catarrhine (DFN) (Macaque)

macaque

Alu Subfamily Structure

HS [Y]: Human-specific. Five or more additional20-25 mya: Almost exclusively Hominids

Alu Subfamily Structure

Master Gene Model of RetropositionP. Deininger, M. Batzer, Trends in Genetics 8:307, 1992

2. Master mutation

1. Amplification

TIME (m.y.)CO

PY

N

UM

BER

3’5’

3’5’

Alu Subfamily Structure (millions of years)

Oldest [J]

Intermediate [S]

Youngest [Y]

Jo Jb (65)

S (50) Sq

Sp Sx

Sc Sg

Y (25)

Yb8 Ya5 Ya8

450,000 copies

50,000 copies

Alus as Genomic Fossils

ALU INSERTIONS AND DISEASE

LOCUS DISTRIBUTION SUBFAMILY DISEASE REFERENCE

BRCA2 de novo Y Breast cancer Miki et al, 1996Mlvi-2 de novo (somatic?) Ya5 Associated with

leukemiaEconomou-Pachnis andTsichlis, 1985

NF1 de novo Ya5 Neurofibromatosis Wallace et al, 1991APC Familial Yb8 Hereditary desmoid

diseaseHalling et al, 1997

PROGINS about 50% Ya5 Linked with ovariancarcinoma

Rowe et al, 1995

Btk Familial Y X-linkedagammaglobulinaemia

Lester et al, 1997

IL2RG Familial Ya5 XSCID Lester et al, 1997Cholinesterase one Japanese family Yb8 Cholinesterase

deficiencyMuratani et al, 1991

CaR familial Ya4 Hypocalciurichypercalcemia and

neonatal severehyperparathyroidism

Janicic et al, 1995

C1 inhibitor de novo Y Complement deficiency Stoppa Lyonnet et al, 1990ACE about 50% Ya5 Linked with protection

from heart diseaseCambien et al, 1992

Factor IX a grandparent Ya5 Hemophilia Vidaud et al, 19932 x FGFR2 De novo Ya5 Apert’s Syndrome Oldridge et al, 1997GK ? Sx Glycerol kinase

deficiencyMcCabe et al, (personalcomm.)

What’s New About Old Fossils?In the Human Genome

• Comprise nearly 50% of genome• 50% more Alu elements than were predicted by

molecular biology• scarce in highly-regulated regions (detrimental?)• enriched in GC regions (beneficial?)• little activity, but little scouring• occur frequently within exons• contribute to formation of genes encoding novel

proteins

3.2 billion bases

28% transcribed

<1.4% encodes protein

50% repeats

Only ~35,000 genes!

FEATURESFEATURESThe

Human

Genome

not many modern protein families

Humans have about 35,000 genes!

Well, then…How can you

explain human complexity?