Retroposition and chromosome structure/function

There is grow ing evidence that retrotransposed sequences cannot only be exapted as genes or regulatory control elements, b u t m ay also play an im portant p art in chrom osom e structure. Tliey can act as carriers of high density CpG

dim ers in regional DNA methylation242, 243^ and (conversely) specific Alu-

binding proteins have been show n to prevent DNA m éth y latio n ^ ^ . For this reason, the m éthylation state of such repetitive elements m ay be im portant in gene regulation, including genomic imprinting. M oreover, SINEs can provide binding sites for n u d ear proteins, and in this w ay can m odulate chrom atin organisation245-247^ which in tu rn m ay play a role in the determ ination of differentiation s ta te ^ ^ . These repetitive elements can act indirectly, inducing recom bination betw een otherw ise unrelated DNA fragm ents, leading to new combinations within genes and consequently to genetic d i v e r s i t y H o w e v e r ,

the discovery of the direct involvem ent of retroelem ents such as Het-A and

TART in the maintenance of telom eres in Drosophila offers the first direct

evidence of transposable elements w ith a clear role in chrom osom e structuredly, d49. This role, which is perform ed by the cellular reverse transcriptase enzym e

telom erase in m am m alian cells, m ay represent the first of m any bona fide cellular

roles of retroposons, not just in Drosophila b u t other organism s also.

In condusion, retroposition is a mechanism, alongside the m ore conventional gene duplication by recom bination process, which m ay constitute an extrem ely im portant evolutionary process in the generation of genetic diversity. Even

pseudogenes can be recruited as functional genes, and parts of pseudogenes o r SINEs can be integrated into coding regions as functional dom ains o r novel regulatory elements. The vehicle of retroposition, reverse transcriptase, m ay still exert, as it did m ore than 3 billion years ago, a huge influence on genom ic plasticity by n o t only creating novel genes b u t by allowing the mixing of existing genes w ith novel regulatory elements. Altering w hen, w here and w hat am ount of a gene is expressed can have a p rofound evolutionary impact, b o th positive and negative. The price paid for long-term evolutionary benefit this plasticity provides for the population is frequently paid by the individual, w h en a deleterious genetic combination produces genetic disease.

1.7 Evolution of the M us genus

One of the objectives of this w ork is to offer an explanation of how and w hy the

Fvl gene has evolved the phenotypes of the m ajor alleles we see today. In o rd er

to do this, a basic knowledge of the evolution of the genus M us is necessary. For

this reason, the Introduction wiU finish w ith a brief account of the radiation and

spéciation of M us genus.

1.7.1 Phylogeny of M us

Despite the fact that the house m ouse has been vital for so m any aspects of

fundam ental science for m any years, its wild populations (of the subgenus Mus)

have been relatively poorly studied. Due to the few m orphological

characteristics that differentiate the wild mice, even the taxonom y of this

subgenus as determ ined by classical approaches has been unclear. In older

literature, this resulted in either m inute descriptions of m any species and subspecies or the oversimplification of a single polytypic ta x o n ^ ^ . W ithin the last 2 decades, the advent of biochemical, karyological, molecular, and biom etric

approaches to study evolution has done m uch to shed light on the origin of Mus.

The phylogenetic tree of the genus M us in Figure 1.8 w as obtained from

aUozymic data^51, 252^ RFLP polym orphism data of various genes^^^, mtDNA254 and D N A /D N A hybridisation of single-copy nuclear DNA (scnDNA) data255. It jg also consistent w ith the limited m urid fossil re c o rd ^ ^ . There are various levels of quasi-synchronous spedation events. The first corresponds to

the separation of the subgenus M us from the other subgenera. The second level

is not indicated on the tree. This level refers to the separation of the Indian

pigm y mice. Mus dunni and M us booduga (also called Leggada), which also

corresponds to the appearance of a 40 acrocentric chrom osom e karyotype that is

characteristic of the whole Mus subgenus. These spedes cannot be placed

accurately due to the lack of molecular data to predsely calibrate the split of this

all-Indian offshoot of Mus, and therefore are not represented in the Figure. The

third level corresponds to the radiation of the Asian spedes (Mus caroli, Mus

cookii, M us cervicolor) in India around 2 million years ago. The fourth level corresponds to the radiation of the W est Palearctic spedes around 1 million years ago which have m igrated as far as eastern and southern Europe and n o rth ern

Africa. A lthough Mus spicilegus and Mus macedonicus have separated very

Figure 1.8 Phylogenetic map of the genus Mms311

Mus musculus complex

— domesticus — musculus — molisslnus - castaneous — bactrianus - M. spretus ■ M. spicilegus - M. macedonicus - M. caroli . M. cookii - M. cervicolor • Pyromys - Coeiomys ■ Nannomys ■ Apodemus - Rattus — I--- 1 r 6 4 million yea rs 12 10

recently, the ancestor of these 2 species diverged quasi-simultaneously from M us musculus and M us spretus. The last level of radiation corresponds to the

individualisation of the m ain subspecies of M us musculus within the last 0.5

million years following its m igration from the Indian subcontinent. The genus

M us therefore represents the classical image of a taxon that has actively radiated

th ro u g h geographical spedation, form ing new spedes w herever m igration is possible.

1.7.2 Partitioning in M us musculus

There is considerable scope for confusion w hen analysing genetic characteristics

in the Mus musculus complex. Studies of several types of genetic m arkers have

been carried out in peripheral house m ouse populations: analysis of chrom osom al C-band p a t t e m s 2 5 7 , 2 5 8 ^ n u d e a r autosom al genes studied by

protein electrophoresis^!» ^^» 2 5 9 - 2 6 1 or by DNA RFLP^^2^ rDNA no n ­

transcribed spacers RFLP263^ im m u n o g lo b u lin ^ ^ ^ ^ , satellite DNA, serological studies^^^, som e Y chrom osom e s e q u e n c e s 2 b 8 - 2 7 1 ^ m itochondrial D N A ^ ^ 2 The

proposed scheme of the 4 subspedes of the M us musculus spedes in Figure 1 . 8 is

based largely on the combinations of allele frequendes at m any nuclear encoded protein lod^^!. This dassification is supported by the study of m itochondrial DN A p h y l o g e n y 2 7 2 b , 2 7 2 d (gee Figure 1 . 9A) as 4 m ain lineages could be defined,

corresponding to either M us musculus domesticus^ musculus, castaneous, o r

bactrianus (although Mus musculus bactrianus was found at low frequency in the M us musculus castaneous territory). O ther m arkers studied are compatible w ith this partitioning of the complex, b u t the picture is not clear as the phylogeny of the alleles is not known. Some of the m arkers appear to be diagnostic betw een

pairs of subspedes whilst others are confined to one subspedes (reviewed i n 2 5 1 ,

2 5 7 , 2 7 6 ) There is, how ever substantial variation w ithin the subspedes from

different geographical areas, for example betw een E uropean and Asian M us

musculus musculus 2 5 8 , 2 7 7 or betw een northw estern and southeastern M us

musculus domesticus 2 7 8 There are no single characters in the M us musculus

complex that allows the partition of the peripheral populations, therefore, b u t combinations of characters do perm it the subspedes to be clearly identified.

Figure 1.9 Phylogenetic trees of the Mus musculus complex based on different DNA sequences

A. M ito c h o n d ria l DNA

DOM - DOM DOM