Comparative sequence analysis of the Gdf6 locus reveals a duplicon-mediated chromosomal rearrangement in rodents and rapidly diverging coding and regulatory sequences

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

BACKGROUND

The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.

RESULTS

To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.

CONCLUSION

Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.

Control of BMP gene expression by long-range regulatory elements

Much evidence suggests that "developmental regulator" genes, like those encoding transcription factors and signaling molecules, are typically controlled by many modular, tissue-specific cis-regulatory elements that function during embryogenesis. These elements are often far from gene coding regions and promoters. Bone morphogenetic proteins (BMPs) drive many processes in development relating to organogenesis and differentiation. Four BMP family members, Bmp2, Bmp4, Bmp5, and Gdf6, are now known to be under the control of distant cis-regulatory elements. BMPs are thus firmly placed in the category of genes prone to this phenomenon. The analysis of distant BMP regulatory elements has provided insight into the many pleiotropic effects of BMP genes, and underscores the biological importance of non-coding genomic DNA elements.

Principles of genome evolution in the Drosophila melanogaster species group

That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.

The organization of genes on chromosomes changes over evolutionary time. In some organisms, such as fruit flies and mosquitoes, inversions of chromosome regions are widespread. This has been associated with adaptation to environmental pressures and speciation. However, the mechanisms by which inversions are generated at the molecular level are poorly understood. The prevailing view involves the interactions of sequences that are moderately repeated in the genome. Here, we use molecular and computational methods to study 29 inversions that differentiate the chromosomes of three closely related fruit fly species. We find little support for a causal role of repetitive sequences in the origin of inversions and, instead, detect the presence of inverted duplications of ancestrally unique sequences (generally protein-coding genes) in the breakpoint regions of many inversions. This leads us to propose an alternative model in which the generation of inversions is coupled with the generation of duplications of flanking sequences. Additionally, we find evidence for genomic regions that are prone to breakage, being associated with inversions generated independently during the evolution of the ancestors of existing species.

Chromosomal inversion breakpoints were compared between three closely related Drosophila species. Many are associated with inverted gene duplications, suggesting that the prevalent mechanism for their generation involves staggered breakpoints.

Evidence for an additional locus for split hand/foot malformation in chromosome region 8q21.11–q22.3

We identified a family where five members had nonsyndromic ectrodactyly. There were three known instances of nonpenetrance. Although four individuals had unilateral cleft hand, one individual had more severe, bilateral and asymmetric absence of the digits. None had foot abnormalities. After exclusion of linkage of SHFM in this family to five known loci, a genome wide scan was performed with DNA from 5 affected and 15 unaffected members of this family. Suggestive evidence for linkage of ectrodactyly to 8q was obtained on the basis of a maximum LOD score of 2.54 at theta (max) = 0 with GAAT1A4. Critical recombinants place the ectrodactyly gene in this family in a 16 cM (21 Mb) interval between D8S1143 and D8S556. Mutational analysis of two candidate genes (FZD6, GDF6) did not identify any mutations in affected members of this family. Our data indicate further genetic heterogeneity for ectrodactyly and suggest the presence of an additional SHFM locus in chromosome region 8q21.11-q22.3.

Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes

Background

Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an ~5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS has a transgenic insertion-deletion (TgPWS/TgAS) of chromosome 7B/C subsequent to paternal or maternal inheritance, respectively. In this study, we define the deletion endpoints and examine the impact on expression of flanking genes.

Results

Using molecular and cytological methods we demonstrate that 13 imprinted and 11 non-imprinted genes are included in the TgPWS/TgAS deletion. Normal expression levels were found in TgPWS brain for genes extending 9.1- or 5.6-Mb centromeric or telomeric of the deletion, respectively. Our molecular cytological studies map the proximal deletion breakpoint between the Luzp2 and Siglec-H loci, and we show that overall mRNA levels of Luzp2 in TgPWS and TgAS brain are significantly reduced by 17%. Intriguingly, 5' Chrna7 shows 1.7-fold decreased levels in TgPWS and TgAS brain whereas there is a ≥15-fold increase in expression in neonatal liver and spleen of these mouse models. By isolating a Chrna7-Tg fusion transcript from TgAS mice, we mapped the telomeric deletion breakpoint in Chrna7 intron 4.

Conclusion

Based on the extent of the deletion, TgPWS/TgAS mice are models for PWS/AS class I deletions. Other than for the first gene promoters immediately outside the deletion, since genes extending 5.6–9.1 Mb away from each end of the deletion show normal expression levels in TgPWS brain, this indicates that the transgene array does not induce silencing and there are no additional linked rearrangements. Using gene expression, non-coding conserved sequence (NCCS) and synteny data, we have genetically mapped a putative Luzp2 neuronal enhancer responsible for ~33% of allelic transcriptional activity. The Chrna7 results are explained by hypothesizing loss of an essential neuronal transcriptional enhancer required for ~80% of allelic Chrna7 promoter activity, while the Chrna7 promoter is upregulated in B lymphocytes by the transgene immunoglobulin enhancer. The mapping of a putative Chrna7 neuronal enhancer inside the deletion has significant implications for understanding the transcriptional regulation of this schizophrenia-susceptibility candidate gene.

ICAM-3, a ligand for DC-SIGN, was duplicated from ICAM-1 in mammalian evolution, but was lost in the rodent genome

ICAM-3 is a DC-SIGN ligand that is constitutively expressed on resting leukocytes, and is thus an important molecule for the first immune response. But, ICAM-3 has not been isolated form rodents. Thus, we compare the ICAM gene clusters in human, dog, mouse, and rat. ICAM-1, -4, -5 and -3 are located close to one another on the same chromosome and show genomic synteny in human and dog. Almost the same ICAM gene clusters were found in rodent genome, but only the ICAM-3 was not present. A phylogenetic tree plotting the cDNAs of human, dog, mouse, rat, and bovine suggested that ICAM-3 was made from a duplication of ICAM-1. Thus, ICAM-3 arose from ICAM-1 in the mammalian evolution, but was lost in the rodent's genome. Our study suggests the different immune response in the rodents in comparison with other mammals.