Junk DNA Most human genome does not encode for proteins.

Junk DNA

Most human genome does not encode for proteins

Transposable elements in the human genome

Transposable elements

Barbara McClintock1902-1992

Nobel Prize in Physiology orMedicine (1983)

DNA transposons and retroelements

DNA transposonsRetroelements

Worm

Fruit fly

Oikopleura

Fugu

Chicken

Mouse

Human

Genes

19.000

14.000

15.000

31.000

23.000

30.000

30.000

DNA transposons

3.000

400

100

8.000

13.000

112.000

294.000

Retroelements

600

1200

600

22.000

230.000

2.800.000

2.900.000

Transposable elements vs. genes in animal genomes

Transposable elements can be lost without altering host fitness

pl a

tyf i

sh

mo

ll y

kill i

f ish

med

aka

t il a

pia

t ro

ut

pi k

e

car p

zeb

rafi

sh

eel

stu

rgeo

n

C

Rex3

Orgel LE, Crick FH (1980)

Selfish DNA: the ultimate parasite.

Nature 284: 604-607.

Transposable elements can negatively affect host genes

Element Organism Disease Gene Mechanism

L1 Human Haemophilia A Factor VIII InsertionL1 Human DMD Dystrophin InsertionL1 Human Colon carcinoma APC InsertionAlu Human Breast cancer BRCA2 InsertionAlu Human Haemophilia B Factor IX InsertionAlu Human Dent's disease CLCN5 InsertionSVA Human Various Various InsertionL1 Mouse Myoclonus Glrb InsertionIAP Mouse Various Various Insertion

L1 Human Glycogen storage dis. PHKB Ectopic recombination (del)Alu Human Hunter disease IDS Ectopic recombination (del)Alu Human Wiskott-Aldrich sdr WASP Ectopic recombination (del)Alu Human Lesch-Nyhan sdr HPRT1 Ectopic recombination (del)Alu Human Lesch-Nyhan sdr HPRT Ectopic recombination (dupl)L1 Mouse Beige-like coat color Lystbg Ectopic recombination (del)

Alu Human Ornithine AT def. OAT ExonisationAlu Human Sly syndrome GUSB ExonisationAlu Human Alport syndrome COL4A3 Exonisation

Transposable elements can cause disease

Only ?

Xmrk

Txi-1

Anticancer mutagenic insertion in the platyfish

Gene regulation

X chromosome inactivation

Telomere maintenance (Drosophila)

Gene and genome evolution / Genetic diversity

…

Proposed and demonstrated functions

of transposable elements

About 25% of human promoter regions contain sequences

derived from transposable elements

(Jordan et al. 2003)

Transposable elements are drivers of gene evolution

About 4% of human genes contain sequences derived from

transposable elements in their coding region

(Nekrutenko and Li 2003)

Comparative genomics of transposable elements in vertebrates

Many transposable elements have been lost from the mammalian lineage

Ty3/Gypsy retrotransposons

Fly

Ciona

nematodeCiona

sea urchin

Fly

Trematode

Ty3 Yeast

Maggy Fungus

Nematode

Sea urchin

Ciona

0.1 changes

Osvaldo

Atlanticcod

Gmr1

Gmr1L

Rex8

silkworm

Jule

SURL-like

SURL

Ciona

GypsyFly

CsRn1

Sushi

Barthez

Diversity of Gypsy/Ty3 LTR retrotransposons in fish genomes

Pufferfish

Takifugu rubripes

Clades

SURL

SURL-like

Jule

CsRn1

Sushi

Barthez

Gmr1(-like)

Rex8

Osvaldo

Total

8

20

10

10

140

290

25

55

10

0

560

5

fossils

fossils

8

25

120

45

15

fossils

0

213

9

20

20

10

8

700

85

510

12

25

1390

0: not detected

Pufferfish

Tetraodon nigroviridis

Zebrafish

Danio rerio

Gypsy/Ty3 retrotransposons in the vertebrate lineage

0

0

0

0

0

fossils

0

0

0

0

0 (fossils)

Homo sapiens

Sequences related to gag of Sushi in mammalian genomes

Sushi-ichi retrotransposons from fish

CCHC

gag

Pro RT/RNaseH Int

pol

LTRLTR

Poulter et al. 1998

gag

?

Sushi-ichi pufferfish

CCHCgag

Pro RT/RNaseH Int

pol1 kb

LTRLTR

5’ UTR 3’ UTR

Human

Mouse

Human

Human

Mouse

Human

Mouse

Human

Mouse

Human

Mouse

Human (A-C)

Mouse (1-2A/B)1.5 kb

Mart1

Mart2 Mouse

Mart3

Mart4Human

Mouse

Mart5

Mart6

Mart7

Mart8 (x3)

Human

MouseMart9

The Mart gene family

Introns

200 aa

Mart1

CCHCGag

Pro RT/RNaseH Int

PolSushi

Chr

Mart2

Mart3

Mart4

Mart5

Mart6

Mart7

Mart8

Mart9

The Mart family

Gene KA KS KA /KS

Mart1 0.18 0.55 0.33

Mart2 0.13 0.65 0.20

Mart3 0.22 0.45 0.49

Mart4 0.23 0.47 0.49

Mart5 0.06 0.46 0.13

Mart6 0.03 1.0 0.03

Mart7 0.18 0.43 0.42

Mart8 0.21 0.59 0.36

Mart9 0.06 0.20 0.30

Mart genes evolve under purifying (negative) selection

Comparisons mouse/human

(Molecular) domestication

“wild”“domesticated”

TE proteins can - bind nucleic acids

- copy nucleic acids

- break nucleic acids

- join nucleic acids

- degrade nucleic acids

- process proteins

- interact with proteins

- …

Why are transposable element proteins interesting

for the host?

Tetrapods vs. ray-finned fish450 myr

Mart

Mart

Mart

Mart

Mart

Sushi-like

Sushi-like

Domestication(s)Retrotransposon loss

-

Loss?

Duplication(s)?

Amniotes vs. amphibians360 myr

Mammals vs. birds310 myr

Marsupials vs. placental mammals170 myr

Evolution of Mart genes and Sushi retrotransposons in

the vertebrate lineage

Dog

ChimpanzeeHuman

GorillaCow

RatMouse

ChimpanzeeMacaque

Human A-CPigDog-1-4 Cow

Mouse-1

Mouse-2a/b Rat

Opossum

BaboonChimpanzeeHumanMarmoset

CatDogBatPigShrew

Cow

MouseRat

OrangutanHuman Chimpanzee

Mouse RatDog

HumanChimpanzee

Macaque

MouseRat Dog

ChimpanzeeHumanRat

MouseDog

HumanChimpanzee

Rat

Mouse

MouseRat

DogHuman

ChimpanzeeGalago

SheepCow

ChimpanzeeHuman

RatMouse

Dog

Trout

SalamanderFugu

Frog

Sushi-like(Gag)

Frog

Dog

Fugu

Mart9

Mart1

Mart7

Mart8s

Mart2

Mart6

Mart3

Mart4

Mart5

100100

100

100

83

100

69

96

100

87

100

100

XX

X

autosomalimprinted

autosomal

autosomalimprinted

X X X

X

X

Two autosomal Mart genes, PEG10 (Mart2) and PEG11/Rtl1 (Mart1) are

subject to parental imprinting and paternally expressed.

Imprinting of both genes is controlled by differentially methylated regions.

Two miRNA genes are located in Rtl1, are transcribed in an antisense

orientation to Rtl1 and expressed exclusively from the maternal

chromosome (reciprocal imprinting). RNA interference.

Since RNA interference and methylation are considered as defence

mechanism against mobile DNA, genome imprinting of gag-related genes

might be related to retrotransposon silencing.

Expression of Mart genes in mouse adult tissues

Expression of Mart genes during mouse embryogenesis

E14.5, RT-PCR

Function(s) of Mart proteins in mammals?

Immunity against retrotransposons?

Transcription factors?

Control of cell proliferation and apoptosis?

Cell adhesion and migration?

Paper function mart

Other Gypsy/Ty3 gag-derived genes in the human genome

Campillos et al. 2006

The Ma family of gag-derived neogenes in mammals

Wills et al. 2006

HsaX

HsaX

HsaX

Hsa14

Hsa14

Hsa8

Functions: Apoptosis (Ma4), ???

SCAN transcription factors

59 and 40 genes in human and mouse, respectively

Regulation of core body temperature, feeding behaviour and obesity (PW1/Peg3)

Control of lipid metabolism (ZNF202)

Regulation of hippocampal neuronal cholesterol biosynthesis (NRIF)

Muscle stem cell behaviour and muscle atrophy (PW1/Peg3)

Regulation of pluripotency of embryonic stem cells (ZNF206)

Hematopoiesis (MZF1)

Negative regulator of the hypoxia-inducible factor-1alpha (ZnF197)

Roles in apoptosis, cell proliferation (several genes)

Subject to parental imprinting: Peg3/Pw1 (paternally expressed)

Campillos et al. 2006

Interactome of Gag-derived proteins in mammals

CCHC

gag

Pro RT/RNaseH Int

pol

LTRLTR

Gypsy/Ty3 LTR retrotransposons

Domesticated integrase gene: GIN-1

* *Mammals, birds and reptiles

On the Z chromosome in birds

- Conserved HHCC motif

- Conserved DDE motif

Domesticated integrase gene: MGC80999

Birds, reptiles, amphibians and fish

- Conserved HHCC motif

- Non-conserved DDE motif

MGC 80999

Fish

Amphibians

Reptiles

Birds

Mammals

GIN-1

Molecular domestication

event

Duplication event

Fish

Amphibians

Reptiles

Birds

Mammals

Ancient domestication of an integrase gene in vertebrates

Domestication/fusion of a retrovirus integrase domain in mammals

KIAA1305 KIAA0323CBLN3NFATC4

Similar to C-terminus of KIAA0323

Retrovirus integrase- derived domain

N-ter C-ter

KIAA1305

Domesticated transposable element genes in human genome

Gene (family) Protein properties and functions Ancestral gene Ancestral TE Organisms

Rag1 nuclease, V(D)J recombination, adaptive immune system transposase Transib DNA transposon vertebratesDaysleeper DNA binding protein, gene regulation, plant development transposase hAT DNA transposon ArabidopsisGary unknown transposase hAT DNA transposon cereal grassesTram unknown transposase hAT DNA transposon mammalsZbed4 unknown transposase hAT DNA transposon mammalsKIAA0543 unknown transposase hAT DNA transposon mammalsP52rIPK binding to inhibitor of interferon-induced protein kinase PKR transposase hAT DNA transposon mammalsBuster1-3 unknown transposase hAT DNA transposon mammalsDref transcription factor, regulation of DNA replication transposase hAT DNA transposon DrosophilaLin-15B regulator of vulval development transposase hAT DNA transposon CaenorhabditisCenp-b DNA binding protein, centromere function transposase Pogo DNA transposon eukaryotesPdc2/Rag3 transcription factor, regulation of pyruvate utilization transposase Pogo DNA transposon yeastJerky neuron mRNA-binding protein, mutated in epilepsy syndromes transposase Tigger/pogo DNA transposon mammalsJerky-like unknown transposase Tigger/pogo DNA transposon mammalsKIAA0461 unknown transposase Tigger/pogo DNA transposon mammalsTigger-derived unknown transposase Tigger/pogo DNA transposon mammalsMetnase DNA integration, radiation resistance, DNA break repair transposase Mariner DNA transposon humanP-derived DNA binding protein transposase P DNA transposon DrosophilaPhsa/Pgga unknown transposase P DNA transposon mammals, birdsPiggyMac Elimination of germ-line sequences from macronucleus transposase PiggyBac DNA transposon ParameciumPgbd1-4 unknown transposase PiggyBac DNA transposon humanPgbd5 unknown transposase PiggyBac DNA transposon bony vertebratesHarbI1 unknown transposase Harbinger DNA transposon bony vertebratesFhy3, Far1 transcription factors, sensitivity to far-red light transposase Mutator DNA transposon ArabidopsisMustang unknown transposase Mutator DNA transposon flowering plantsGin-1 unknown integrase Ty3/gypsy LTR retrotransposon mammalsc-integrase unknown integrase/tpase Maverick transposon mammalsFob1p replication terminator protein, rDNA metabolism integrase/tpase Maverick/LTR element? baker's yeastTelomerase ribonucleoprotein, reverse transcriptase, telomere replication RT retroelement eukaryotesPeg10/Mart2 cell proliferation, transcription factor?, placenta formation gag Ty3/gypsy LTR retrotransposon mammalsLdoc1/Mart7 inhibition of NF-kappaB activation, induction of apoptosis gag Ty3/gypsy LTR retrotransposon mammalsOther Mart’s unknown gag Ty3/gypsy LTR retrotransposon mammalsMap-1/Ma1 Bax-associating protein, induction of apoptosis gag LTR retrotransposon/retrovirus mammalsOther Ma genes neuronal autoantigens in paraneoplastic neurological diseases gag LTR retrotransposon/retrovirus mammalsFv1 murine leukemia virus restriction gag vertebrate retrovirus mouseSyncytin-1 membrane glycoprotein, cell fusion, placenta formation envelope vertebrate retrovirus humanSyncytin-2 membrane glycoprotein, cell fusion, placenta formation envelope vertebrate retrovirus humanSyncytin-A/B membrane glycoprotein, cell fusion, placenta formation envelope vertebrate retrovirus mouseOther env’s unknown envelope vertebrate retrovirus mammalsIris defence against viruses? envelope Kanga BEL-like retrovirus DrosophilaIris-like defence against viruses? envelope Kanga BEL-like retrovirus mosquito

PPutative and confirmed examples of protein-coding neogenes derived from TEs

Gene Protein properties and functions Ancestral TE Organisms

Transposase-derived genes

Rag1 nuclease, V(D)J recombination, adaptive immune system Transib DNA transposon vertebrates

Daysleeper DNA binding protein, gene regulation, plant development hAT DNA transposon Arabidopsis

Cenp-b DNA binding protein, centromere, transposon restriction Pogo DNA transposon eukaryotes

PiggyMac Elimination of germ-line sequences from macronucleus PiggyBac transposon Paramecium

Reverse transcriptase-derived genes (?)

Telomerase ribonucleoprotein, RT, telomere replication Retroelement eukaryotes

Gag-derived genes

Fv1 murine leukemia virus restriction vertebrate retrovirus mouse

Envelope-derived genes

Syncytin-1 membrane glycoprotein, cell fusion, placenta formation vertebrate retrovirus human


Syncytin-A/B membrane glycoprotein, cell fusion, placenta formation vertebrate retrovirus mouse

Iris defence against viruses? Kanga BEL-like retrovirus Drosophila

P

Best-studied examples of protein-coding neogenes derived from TEs

Somatic V(D)J recombination in immunoglobulin genes

L: Leader

V: Variable

C: Constant

J: Joint

D: Diversity

RSSs recombination signal sequences

V(D)J recombination

Transposition

Triangles: recombination signal sequences (RSSs)

Reactions catalyzed by the Rag1/2 recombinase

Similarities between Rag1 and RSS with Transib transposons

Kapitonov and Jurka 2005









Gag-derived genes







P


The telomerase is a reverse transcriptase

The telomerase is related to retroelement reverse transcriptases

Eickbush 1997









Gag-derived genes







P


Molecular domestication and disease

- Syncytin-1: Oligodendrocytes death and demyelination in multiple

sclerosis

- Rag1: DNA translocations in lymphatic tumors

- Ma‘s: Targets of auto-immune response in paraneoplastic

neurological disorders

- Peg10: Cancer

Domesticated TE-derived genes are found in major eukaryotic lineages

- Animals, Fungi, Plants

Domesticated genes can be derived from different types of retroelements,

DNA transposons and viruses

Domesticated genes can be derived from different types of genes

- Transposase, RT, Gag, integrase, Env, …

RNA genes have been also domesticated from TEs

- neural gene BC200 (Alu-derived)

Conclusions

Co-domesticated features?

- Epigenetic regulation (imprinting of Mart genes)

- Binding sites (Rag1 recombination signal sequences)

Timing of domestication

Domestication Minimal date (years ago)

Dog 17.000Pig / Sheep / Cow 10.000Horse 4.000Rabbit 500Hamster 80

Iris (Env, insects) 25.000.000Mart (Gag, mammals) 180.000.000P-derived (transposase, tetrapods) 300.000.000Rag1 (transposase, vertebrates) 500.000.000Telomerase (RT, eukaryotes) 1.000.000.000

Transposable elements are a major source of regulatory

and coding sequences for genetic innovation

Equipe “Génomique Evolutive des Vertébrés“

Institut de Génomique Fonctionnelle de Lyon

CNRS/INRA/UCBL/ENSL

Domitille Chalopin

Astrid Böhne

Frédéric Brunet

Christina Schultheis

Marta.Tomaszkiewicz

Amandine Darras

Delphine Galiana-Arnoux

Jean-Nicolas Volff

http://igfl.ens-lyon.fr/les-equipes/equipe-9

Collaborations

Manfred Schartl (University of Würzburg, Germany)

Manfred Gessler (University of Würzburg, Germany)

Indrajit Nanda, Michael Schmid (University of Würzburg, Germany)

Cécile Fischer, Laurence Bouneau, Sylvie Samain, Jean Weissenbach

(Genoscope, Evry, France)

Catherine Ozouf-Costaz, Agnés Dettai (Muséum National d’Histoire Naturelle,

Paris, France)

Daniel Chourrout (SARS Centre, Bergen, Norway)

Christoph Winkler (University of Singapore)

Yann Guigen (INRA Rennes)

Carine Genet (INRA Jouy)

Christophe Terzian (Lyon)

Possible evolutionary scenarios leading to molecular

domestication

Junk DNA Most human genome does not encode for proteins.

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