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Table 5C-1. Mobile Elements Found to be Exapted
as cis-Regulatory
Control Sites in Animals
|
|
Organism
|
Locus or system
|
Mobile Element
|
References
|
|
Drosophila simulans
|
Cyp6g1 (encoding a cytochrome
P450) – insecticide resistance
|
Doc DNA transposon
|
(Schlenke
and Begun 2004)
|
|
Drosophila
melanogaster
|
Tissue-specific
expression of the insecticide resistance gene Cyp6g1.
|
Cis-regulatory elements in the Accord
retrotransposon
|
(Daborn,
Yen et al. 2002; Chung,
Bogwitz et al. 2007)
|
|
Deuterostomes
|
105 highly conserved sequences from
amphioxus through humans not associated with
protein coding sequences.
|
Ancient SINE family AmnSINE1,
(Amniota SINE1)
present in mammals and birds; AmnSINE1 chimeric
structure of 5S rRNA and a tRNA-derived SINE,
related to five tRNA-derived SINE families in the
coelacanth, dogfish shark, hagfish, and amphioxus
genomes. We collectively name DeuSINE (Deuterostomia
SINE) superfamily.
|
(Nishihara,
Smit et al. 2006)
|
|
Indonesian coelacanth, Latimeria
menadoensis
|
Previously unknown SINE
retroposon family active in Sarcopterygii
(lobe-finned fishes and terrestrial vertebrates) in
Silurian period >410 million years ago
|
Mouse enhancer assay
recapitulates multiple aspects of Isl1 expression
patterns. A >200-base-pair ultraconserved region,
100% identical in mammals, and 80% identical to the
coelacanth SINE, contains a 31-amino-acid-residue
alternatively spliced exon of the messenger RNA
processing gene PCBP2.
|
(Bejerano,
Lowe et al. 2006)
|
|
Mammals (placentals,
marsupials, monotremes), but not other vertebrates
|
Proopiomelanocortin (POMC)
locus
|
Ancient exaptation of a CORE-SINE
into highly conserved neuronal enhancer nPE2.
|
(Santangelo,
de Souza et al. 2007)
|
|
Rodent
|
16 Pax6 binding sites (eye
and CNS development factor)
|
B1 SINE elements
|
(Zhou,
Zheng et al. 2000)
|
|
Homo sapiens
|
Novel PAX6 binding sites
|
Alu SINE repeats at 3 loci
|
(Zhou,
Zheng et al. 2002)
|
|
Mouse
|
Lama3 transcript, stimulated by
transcription factor USF (upstream stimulatory
factor)
|
B2 SINE elements provide RNA
polymerase II promoter
|
(Ferrigno,
Virolle et al. 2001)
|
|
Mammals
|
CTCF (11-zinc
finger protein or CCCTC-binding transcription
factor) networks; transcriptional regulation,
insulator activity, V(D)J joining and chromatin
formatting
|
Fossilized repeat elements flank
conserved CTCF-binding regions,
indicating retrotransposon
expansions hundreds MYA; repeat-driven dispersal of
CTCF binding is ancient and
still highly active
|
(Schmidt,
Schwalie et al. 2012)
|
|
Mouse
|
FGF8 (fibroblast growth
factor 8)
|
AmnSINE1 (AS071) enhancer
recapitulates FGF8 expression in developing
forebrain, diencephalon and hypothalamus
|
(Sasaki,
Nishihara et al. 2008)
|
|
Mouse
|
SINE 390 kbp upstream of
Satb2
|
AmnSINE1
(AS021) SINE displays specific enhancer activity in
developing cerebral cortex
|
(Tashiro,
Teissier et al. 2011)
|
|
Rodents, humans
|
Anti-apoptotic locus NAIP (BIRC1)
|
Repeated recruitment of LTR
retrotransposons as promoters during mammalian
evolution; 5' flanking regions of IAP
family as group, in both human and mouse, enriched
for LTR insertions
|
(Romanish,
Lock et al. 2007)
|
|
Homo sapiens
|
Novel NAIP isoform
|
Alu SINE element start site
|
(Romanish,
Nakamura et al. 2009)
|
|
Primates (baboon, human)
|
Primate beta3GAL-T5
colon expression
|
ERV1 LTR
promoter
|
(Dunn,
Medstrand et al. 2003; Dunn,
van de Lagemaat et al. 2005)
|
|
Homo sapiens
|
enhancer in last intron of human CD8
alpha locus
|
Alu SINE-containing, T-cell-specific enhancer
|
(Hambor,
Mennone et al. 1993)
|
|
Homo sapiens
|
Down syndrome critical
region 4 (DSCR4) and DSCR8 loci
|
ERV1 LTR acts as a
bidirectional promoter
|
(Dunn,
Romanish et al. 2006)
|
|
Mouse, human
|
REST (RE1-Silencing
Transcription Factor) targets many neural genes in
preimplantation embryo and CNS by cognate DNA motif,
RE1 (Repressor Element 1).
|
1301 and 997 RE1s in human
and mouse genomes, respectively, >40% are novel
(many LINE1,
LINE2, Alu SINE
in human genome); weak RE1 elements in hERV.
|
(Johnson,
Gamblin et al. 2006; Johnson,
Samuel et al. 2009)
|
|
Mouse
|
Estrogen Receptor α (ERα) response
loci
|
MIR (mammalian interspersed repeat)
SINEs 15-25% of TEs conserved between human and
mouse; include targets
ERα, such as GREB1, RARα. TAP/SEC14L2, GLUT1/SLC2A1
(ERα mediated response to hypoxia), Anxa6,
Fyn, CA12, CYP1B1, KRT13
and PRKACA
|
(Testori,
Caizzi et al. 2012)
|
|
zebrafish (Danio rerio)
|
180 p53 responsive loci; human
orthologs contribute neuronal morphogenesis,
axonogenesis, synaptic transmission and regulation
of programmed cell death
|
EnSpmN6_DR non-autonomous DNA
transposon
|
(Micale,
Loviglio et al. 2012)
|
|
Homo sapiens
|
p53 regulon
|
1,509 of ~ 319,000 human
ERV LTR regions have a near-perfect p53 DNA binding
site; LTR10 and MER61 families particularly
enriched; primate-specific
|
(Wang,
Zeng et al. 2007)
|
|
Homo sapiens and mouse
|
c-Myc regulatory subnetwork
|
Thousands TEs bound by
c-Myc; 816-4564 contain canonical c-Myc binding
motifs; c-Myc binding sites over-represented among
ancient families LINE2 and MIR; loci
with TE-derived c-Myc binding sites co-expressed
with each other and with c-Myc. Conserved fragments of MIR and LINE2
transposable elements in intergenic regions within
the mouse and human genomes
|
(Wang,
Bowen et al. 2009) (Silva,
Shabalina et al. 2003)
|
|
Eutherian mammals
|
Endometrial expression in
placental mammals
|
13% of 1,532
endometrial-expressed loci are within 200 kb of a
Eutherian-specific MER20 transposable element; these
elements have epigenetic signatures of enhancers,
insulators and repressors and directly bind
transcription factors essential for pregnancy to
regulate expression in response to progesterone and
cAMP.
|
(Lynch,
Leclerc et al. 2011)
|