Nuclear Receptor HNF4α Binding Sequences are Widespread in Alu Repeats

<p>Abstract</p> <p>Background</p> <p>Alu repeats, which account for ~10% of the human genome, were originally considered to be junk DNA. Recent studies, however, suggest that they may contain transcription factor binding sites and hence possibly play a role in regulating gene expression.</p> <p>Results</p> <p>Here, we show that binding sites for a highly conserved member of the nuclear receptor superfamily of ligand-dependent transcription factors, hepatocyte nuclear factor 4alpha (HNF4α, NR2A1), are highly prevalent in Alu repeats. We employ high throughput protein binding microarrays (PBMs) to show that HNF4α binds > 66 unique sequences in Alu repeats that are present in ~1.2 million locations in the human genome. We use chromatin immunoprecipitation (ChIP) to demonstrate that HNF4α binds Alu elements in the promoters of target genes (<it>ABCC3, APOA4, APOM, ATPIF1, CANX, FEMT1A, GSTM4, IL32, IP6K2, PRLR, PRODH2, SOCS2, TTR</it>) and luciferase assays to show that at least some of those Alu elements can modulate HNF4α-mediated transactivation <it>in vivo </it>(<it>APOM, PRODH2, TTR, APOA4</it>). HNF4α-Alu elements are enriched in promoters of genes involved in RNA processing and a sizeable fraction are in regions of accessible chromatin. Comparative genomics analysis suggests that there may have been a gain in HNF4α binding sites in Alu elements during evolution and that non Alu repeats, such as Tiggers, also contain HNF4α sites.</p> <p>Conclusions</p> <p>Our findings suggest that HNF4α, in addition to regulating gene expression via high affinity binding sites, may also modulate transcription via low affinity sites in Alu repeats.</p

The role of fertility restoration in the maintenance of the inversion In(2L)t polymorphism in Drosophila melanogaster

In order to explain the worldwide latitudinal distribution and seasonal fluctuations in In(2L)t frequencies in Drosophila melanogaster, fitness differences among In(2L)t and Standard (ST) homo-and heterokaryotypes under high-temperature conditions were determined. Viabilities were measured for high-temperature treatment started at different juvenile stages. The capacity to restore fertility after high-temperature treatment was measured for adults and juveniles. Furthermore, genetic adaptation for increased temperature resistance for these traits was determined for strains which were reared at 33 degrees C for 10 generations. Whereas larva-pupa survival rates were high, highest juvenile mortalities and strongest karyotypic effects were observed during the pupal stage when preceding larval stages were reared at 33 degrees C. ST karyotypes showed lowest viabilities. Although mating rate was hardly influenced, sterility was induced for females and males after high-temperature treatment of adults as well as juveniles. Subsequent transfer to 25 degrees C, however, resulted in restored fertility in some of the individuals, depending on the length of the recovery period. Fertility restoration was significantly higher for heterokaryotype males and females. Heterokaryotype superiority for restored fertility as well as for viability was positively correlated with severity of the treatment. Tell generations of selection at 33 degrees C resulted in significant improvement of juvenile survival and fertility restoration for all karyotypes. These fitness components were positively correlated (r = 0.91; P <0.001), which might suggest pleiotropic effects. It is concluded that the capacity to restore fertility after heat stress is an important fitness component, especially with respect to the In(2L)r polymorphism The observed heterokaryotypic superiority fits with the idea that the latitudinal distribution of In(2L)t frequencies is maintained by balancing selection, with equilibrium values decreasing with latitude