Species-specific organization of CpG island promoters at mammalian homologous genes

De novo assembly, annotation and gene expression profiles of gonads of Cytorace-3, a hybrid lineage of Drosophila nasuta nasuta and D. n. albomicans

Cytorace-3 is a laboratory evolved hybrid lineage of Drosophila nasuta nasuta males and Drosophila nasuta albomicans females currently passing ~850 generations. To assess interracial hybridization effects on gene expression in Cytorace-3 we profiled the transcriptomes of mature ovaries and testes by employing Illumina sequencing technology and de novo transcriptome assembling strategies. We found 26% of the ovarian, and 14% of testis genes to be differentially expressed in Cytorace-3 relative to the expressed genes in the parental gonadal transcriptomes. About 5% of genes exhibited additive gene expression pattern in the ovary and 3% in the testis, while the remaining genes were misexpressed in Cytorace-3. Nearly 772 of these misexpressed genes in the ovary and 413 in the testis were either over- or under-dominant. Genes following D. n. nasuta dominance was twice (270 genes) than D. n. albomicans dominance (133 genes) in the ovary. In contrast, only 105 genes showed D. n. nasuta dominance and 207 showed D. n. albomicans dominance in testis transcriptome. Of the six expression inheritance patterns, conserved inheritance pattern was predominant for both ovary (73%) and testis (85%) in Cytorace-3. This study is the first to provide an overview of the expression divergence and inheritance patterns of the transcriptomes in an independently evolving distinct hybrid lineage of Drosophila. This recorded expression divergence in Cytorace-3 surpasses that between parental lineages illustrating the strong impact of hybridization driving rapid gene expression changes.

Of Men and Mice: Modeling the Fragile X Syndrome

The Fragile X Syndrome (FXS) is one of the most common forms of inherited intellectual disability in all human societies. Caused by the transcriptional silencing of a single gene, the fragile x mental retardation gene FMR1, FXS is characterized by a variety of symptoms, which range from mental disabilities to autism and epilepsy. More than 20 years ago, a first animal model was described, the Fmr1 knock-out mouse. Several other models have been developed since then, including conditional knock-out mice, knock-out rats, a zebrafish and a drosophila model. Using these model systems, various targets for potential pharmaceutical treatments have been identified and many treatments have been shown to be efficient in preclinical studies. However, all attempts to turn these findings into a therapy for patients have failed thus far. In this review, I will discuss underlying difficulties and address potential alternatives for our future research.

CpG Islands: A Historical Perspective

The discovery of CpG islands (CGIs) and the study of their structure and properties run parallel to the development of molecular biology in the last two decades of the twentieth century and to the development of high-throughput genomic technologies at the turn of the millennium. First identified as discrete G + C-rich regions of unmethylated DNA in several vertebrates, CGIs were soon found to display additional distinctive chromatin features from the rest of the genome in terms of accessibility and of the epigenetic modifications of their histones. These features, together with their colocalization with promoters and with origins of DNA replication in mammals, highlighted their relevance in the regulation of genomic processes. Recent approaches have shown with unprecedented detail the dynamics and diversity of the epigenetic landscape of CGIs during normal development and under pathological conditions. Also, comparative analyses across species have started revealing how CGIs evolve and contribute to the evolution of the vertebrate genome.

A cross-study analysis of prenatal exposures to environmental contaminants and the epigenome: support for stress-responsive transcription factor occupancy as a mediator of gene-specific CpG methylation patterning

A biological mechanism by which exposure to environmental contaminants results in gene-specific CpG methylation patterning is currently unknown. We hypothesize that gene-specific CpG methylation is related to environmentally perturbed transcription factor occupancy. To test this hypothesis, a database of 396 genes with altered CpG methylation either in cord blood leukocytes or placental tissue was compiled from 14 studies representing assessments of six environmental contaminants. Subsequently, an in silico approach was used to identify transcription factor binding sites enriched among the genes with altered CpG methylation in relationship to the suite of environmental contaminants. For each study, the sequences of the promoter regions (representing -1000 to +500 bp from the transcription start site) of all genes with altered CpG methylation were analyzed for enrichment of transcription factor binding sites. Binding sites for a total of 56 unique transcription factors were identified to be enriched within the promoter regions of the genes. Binding sites for the Kidney-Enriched Krupple-like Factor 15, a known responder to endogenous stress, were enriched (P < 0.001-0.041) among the genes with altered CpG methylation associated for five of the six environmental contaminants. These data support the transcription factor occupancy theory as a potential mechanism underlying environmentally-induced gene-specific CpG methylation.

A downstream CpG island controls transcript initiation and elongation and the methylation state of the imprinted Airn macro ncRNA promoter

A CpG island (CGI) lies at the 5' end of the Airn macro non-protein-coding (nc) RNA that represses the flanking Igf2r promoter in cis on paternally inherited chromosomes. In addition to being modified on maternally inherited chromosomes by a DNA methylation imprint, the Airn CGI shows two unusual organization features: its position immediately downstream of the Airn promoter and transcription start site and a series of tandem direct repeats (TDRs) occupying its second half. The physical separation of the Airn promoter from the CGI provides a model to investigate if the CGI plays distinct transcriptional and epigenetic roles. We used homologous recombination to generate embryonic stem cells carrying deletions at the endogenous locus of the entire CGI or just the TDRs. The deleted Airn alleles were analyzed by using an ES cell imprinting model that recapitulates the onset of Igf2r imprinted expression in embryonic development or by using knock-out mice. The results show that the CGI is required for efficient Airn initiation and to maintain the unmethylated state of the Airn promoter, which are both necessary for Igf2r repression on the paternal chromosome. The TDRs occupying the second half of the CGI play a minor role in Airn transcriptional elongation or processivity, but are essential for methylation on the maternal Airn promoter that is necessary for Igf2r to be expressed from this chromosome. Together the data indicate the existence of a class of regulatory CGIs in the mammalian genome that act downstream of the promoter and transcription start.

Somatic cytochrome c (CYCS) gene expression and promoter-specific DNA methylation in a porcine model of prenatal exposure to maternal dietary protein excess and restriction

There is growing evidence that maternal nutrition during gestation has an important effect on offspring development as well as on their gene expression with long-term effects on the metabolic state. A potential mechanism forming long-lasting gene expression patterns is DNA methylation of cytosine in CpG dinucleotides within the promoter region of distinct genes. There has been special focus on mitochondrial dysfunction by prenatal malnourishment over the recent years. To this end, we investigated the gene expression of somatic cytochrome c (CYCS), an important member of the respiratory chain, in a porcine model of gestational protein over- and undersupply at 94 d post-conception and 1, 28 and 188 d of age, and analysed the association with the DNA methylation status within the CYCS promoter. Gene expression on day 1 post natum showed a significant increase in the low protein (LP) group (P = 0·0005) and a slight increase in the high protein (HP) group (P = 0·079) compared with the control (CO) group in the liver. The mean of the methylation level over forty-seven CpG sites from nucleotide (nt) − 417 to − 10 was significantly decreased in the LP (P = 0·007) and HP (P = 0·009) groups compared with that in the CO group. Excess and restricted protein supply during pregnancy led to hypomethylation of a number of CpG sites in the CYCS promoter, including those representing putative transcription factor-binding sites, associated with elevated expression levels. However, the impact of the low-protein gestation diet is more pronounced, indicating that the offspring could better adapt to excess rather than restricted protein supply.

CpG islands and the regulation of transcription

Vertebrate CpG islands (CGIs) are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, perhaps all, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters. Shared DNA sequence features adapt CGIs for promoter function by destabilizing nucleosomes and attracting proteins that create a transcriptionally permissive chromatin state. Silencing of CGI promoters is achieved through dense CpG methylation or polycomb recruitment, again using their distinctive DNA sequence composition. CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity.

CpG island chromatin: a platform for gene regulation

The majority of mammalian gene promoters are encompassed within regions of the genome called CpG islands that have an elevated level of non-methylated CpG dinucleotides. Despite over 20 years of study, the precise mechanisms by which CpG islands contribute to regulatory element function remain poorly understood. Recently it has been demonstrated that specific histone modifying enzymes are recruited directly to CpG islands through recognition of non-methylated CpG dinucleotide sequence. These enzymes then impose unique chromatin architecture on CpG islands that distinguish them from the surrounding genome. In the context of this work we discuss how CpG island elements may contribute to the function of gene regulatory elements through the utilization of chromatin and epigenetic processes.

Orphan CpG islands identify numerous conserved promoters in the mammalian genome

CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity Purification plus deep sequencing (CAP-seq). We also asked whether CGIs not associated with annotated transcripts share properties with those at known promoters. We found that, contrary to previous estimates, CGI abundance in humans and mice is very similar and many are at conserved locations relative to genes. In each species CpG density correlates positively with the degree of H3K4 trimethylation, supporting the hypothesis that these two properties are mechanistically interdependent. Approximately half of mammalian CGIs (>10,000) are “orphans” that are not associated with annotated promoters. Many orphan CGIs show evidence of transcriptional initiation and dynamic expression during development. Unlike CGIs at known promoters, orphan CGIs are frequently subject to DNA methylation during development, and this is accompanied by loss of their active promoter features. In colorectal tumors, however, orphan CGIs are not preferentially methylated, suggesting that cancer does not recapitulate a developmental program. Human and mouse genomes have similar numbers of CGIs, over half of which are remote from known promoters. Orphan CGIs nevertheless have the characteristics of functional promoters, though they are much more likely than promoter CGIs to become methylated during development and hence lose these properties. The data indicate that orphan CGIs correspond to previously undetected promoters whose transcriptional activity may play a functional role during development.

In the decade since the sequence of the human genome was announced, efforts have been made to annotate all genes with their regulatory sequences. CpG islands are short regions containing the sequence CG at high density that map to regions controlling the expression of most human genes (known as promoters). Using a biochemical method, we have identified and mapped all CpG islands in the human and mouse genomes and find that over half are remote from known gene promoters—so-called “orphans.” Mice, which were thought to possess far fewer CpG islands than humans, turn out to have a very similar number. Surprisingly, orphan CpG islands in both species often mark hitherto unknown promoters. The activity of these novel promoters is particularly dynamic during normal development, as they are often silenced by DNA methylation. In colorectal cancers, however, aberrant DNA methylation affects all CpG islands equally.

Identifying CpG islands by different computational techniques

CpG islands (CGIs) are generally regarded as important epigenetic regulatory elements due to their association with promoter regions. However, identification of functional CGIs is hampered by repetitive elements and species-specific particularities. Here, we compared the performance of different CGI detection programs on genomic sequences of human and mouse genes. Although mouse CGIs are shorter and G+C poorer than their human counterparts, the different tools tested in our study reliably identify CGIs in promoter regions in both species. Our study confirms that substantially fewer murine than human CGIs coincide with repetitive elements and indicates that such CGIs are subject to accelerated cytosine deamination. In addition, CpG depletion appears to anticorrelate with the epigenetic features of functional regulatory CGIs. Taking into account different deamination rates in unmethylated CGIs versus those in methylated CGIs might support the detection of functional CGIs in other species for which there is little epigenetic information available.

Identification of a promoter for the human C1Q-tumor necrosis factor-related protein-5 gene associated with late-onset retinal degeneration

PURPOSE

The Complement-1q tumor necrosis factor-related protein 5 (C1QTNF5/CTRP5) gene is located in the 3' untranslated region of the Membrane Frizzled Related Protein (MFRP) gene, and these two genes are reported to be dicistronic. The authors examined the 5' upstream sequence of CTRP5 for the presence of a promoter regulating the expression of this gene.

METHODS

The sequence upstream of the translational start site of human CTRP5 (hCTRP5) was analyzed by Promoter Inspector software. A series of plasmids containing segments of hCTRP5 putative promoter sequence (-29 bp to -3.6 kb) upstream of the luciferase gene were generated. Cells were transiently transfected with these plasmids, and luciferase activity was measured. 5' RACE analysis was performed to determine the functional transcription start site. V5 tagged-pig CTRP5 (pCTRP5) gene, cloned downstream of the hCTRP5 putative promoter, was expressed in a human retinal cell line (ARPE-19) and a Chinese hamster ovary cell line (CHO-K1) to study the functionality of the putative promoter.

RESULTS

Bioinformatic analysis identified a putative promoter region between nt -1322 and +1 sequence of hCTRP5. 5' RACE analysis revealed the presence of the transcriptional start site (TSS) at 62 bp upstream of the start codon in the CTRP5. The 1.3-kb sequence of the hCTRP5 predicted promoter produced higher levels of luciferase activity, indicating the strength of the cloned CTRP5 promoter. The promoter sequence between nt -1322 bp to -29 bp upstream of the first ATG of CTRP5 was found to be essential for this promoter activity. The predicted hCTRP5 promoter was found to control the expression of V5-tagged pCTRP5 and nuclear GFP, indicating that the promoter was functional.

CONCLUSIONS

This study revealed the presence of a functional promoter for the CTRP5 gene located 5' of its start site. Understanding the regulation of CTRP5 gene transcription may provide insights into the possible role of CTRP5 in the retina and the pathology underlying late-onset retinal degeneration caused by mutations in this gene. In addition, these studies will determine whether CTRP5 and MFRP are functionally dicistronic.

CpG islands--'a rough guide'

Mammalian genomes are punctuated by DNA sequences containing an atypically high frequency of CpG sites termed CpG islands (CGIs). CGIs generally lack DNA methylation and associate with the majority of annotated gene promoters. Many studies, however, have identified examples of CGI methylation in malignant cells, leading to improper gene silencing. CGI methylation also occurs in normal tissues and is known to function in X-inactivation and genomic imprinting. More recently, differential methylation has been shown between tissues, suggesting a potential role in transcriptional regulation during cell specification. Many of these tissue-specific methylated CGIs localise to regions distal to promoters, the regulatory function of which remains to be determined.

Tollip, a negative regulator of TLR-signalling, is encoded by twin genes in salmonid fish

The factor Tollip is known to dampen TLR2- and TLR4-mediated signalling in mammals. No negative regulator of the piscine TLR-signalling cascade has been described so far, albeit a sizable collection of factors contributing to this ancient pathogen-sensing system are known from fish to date. We identified two closely related Tollip-encoding genes in Atlantic salmon (Salmo salar) and the respective ortholog mRNA molecules in rainbow trout (Oncorhynchus mykiss). The salmonid Tollip genes are segmented into 6 exons, similar to the human orthologous gene. The protein-encoding sequences are homologous to >97% among the twin factors and also between the species. Both encoded proteins contain a C2 domain and an ubiquitin system component, which are also characteristic features of the mammalian Tollip factor. We analysed the expression of these genes in trout. Both Tollip-encoding genes are ubiquitously and also equally expressed, as indicated by similar mRNA concentrations of both factors in any one tissue. Tollip expression was found to be up-regulated by viral infection. Our data suggest that the Tollip genes were duplicated before salmon and trout were evolutionary separated. Moreover, pathways dampening the activity of the TLR-cascade may have been conserved from lower vertebrates to mammals since Tollip, as a respective key factor has been highly conserved from fish to human.

DNA methylation immediately adjacent to active histone marking does not silence transcription

Active promoters generally contain histone H3/H4 hyperacetylation and tri-methylation at H3 lysine 4, whereas repressed promoters are associated with DNA methylation. Here we show that the repressed erythroid-specific carbonic anhydrase II (CAII) promoter has active histone modifications localized around the transcription start, while high levels of CpG methylation are present directly upstream from these active marks. Despite the presence of active histone modifications, the repressed promoter requires hormone-induced activation for efficient preinitiation complex assembly. Transient and positional changes in histone H3/H4 acetylation and local changes in nucleosome density are evident during activation, but the bipartite epigenetic code is stably maintained. Our results suggest that active histone modifications may prevent spreading of CpG methylation towards the promoter and show that repressive DNA methylation immediately adjacent to a promoter does not necessarily repress transcription.

Gene expression divergence and the origin of hybrid dysfunctions

Hybrids between closely related species are often sterile or inviable as a consequence of failed interactions between alleles from the different species. Most genetic studies have focused on localizing the alleles associated with these failed interactions, but the mechanistic/biochemical nature of the failed interactions is poorly understood. This review discusses recent studies that may contribute to our understanding of these failed interactions. We focus on the possible contribution of failures in gene expression as an important contributor to hybrid dysfunctions. Although regulatory pathways that share elements in highly divergent taxa may contribute to hybrid dysfunction, various studies suggest that misexpression may be disproportionately great in regulatory pathways containing rapidly evolving, particularly male-biased, genes. We describe three systems that have been analyzed recently with respect to global patterns of gene expression in hybrids versus pure species, each in Drosophila. These studies reveal that quantitative misexpression of genes is associated with hybrid dysfunction. Misexpression of genes has been documented in sterile hybrids relative to pure species, and variation in upstream factors may sometimes cause the over- or under-expression of genes resulting in hybrid sterility or inviability. Studying patterns of evolution between species in regulatory pathways, such as spermatogenesis, should help in identifying which genes are more likely to be contributors to hybrid dysfunction. Ultimately, we hope more functional genetic studies will complement our understanding of the genetic disruptions leading to hybrid dysfunctions and their role in the origin of species.

New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences

All vertebrates share a similar early embryonic body plan and use the same regulatory genes for their development. The availability of numerous sequenced vertebrate genomes and significant advances in bioinformatics have resulted in the finding that the genomic regions of many of these developmental regulatory genes also contain highly conserved noncoding sequence. In silico discovery of conserved noncoding regions and of transcription factor binding sites as well as the development of methods for high throughput transgenesis in Xenopus and zebrafish are dramatically increasing the speed with which regulatory elements can be discovered, characterized, and tested in the context of whole live embryos. We review here some of the recent technological developments that will likely lead to a surge in research on how vertebrate genomes encode regulation of transcriptional activity, how regulatory sequences constrain genomic architecture, and ultimately how vertebrate form has evolved.

Tandem repeats in the CpG islands of imprinted genes

In contrast to most genes in mammalian genomes, imprinted genes are monoallelically expressed depending on the parental origin of the alleles. Imprinted gene expression is regulated by distinct DNA elements that exhibit allele-specific epigenetic modifications, such as DNA methylation. These so-called differentially methylated regions frequently overlap with CpG islands. Thus, CpG islands of imprinted genes may contain special DNA elements that distinguish them from CpG islands of biallelically expressed genes. Here, we present a detailed study of CpG islands of imprinted genes in mouse and in human. Our study shows that imprinted genes more frequently contain tandem repeat arrays in their CpG islands than randomly selected genes in both species. In addition, mouse imprinted genes more frequently possess intragenic CpG islands that may serve as promoters of allele-specific antisense transcripts. This feature is much less pronounced in human, indicating an interspecies variability in the evolution of imprinting control elements.

The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes

CpG island is a GC-rich motif occurred in gene promoter region, which can play important roles in gene silencing and imprinting. Here, we present a set of discriminant functions that can recognize the structural and compositional features of CpG islands in the putative promoter regions (PPRs) of human and mouse immunoglobulin (Ig) genes. We showed that the PPRs of both human and mouse Ig genes irrespective of gene chromosomal localization are apparently CpG island poor, with a low percentage of the CpG islands overlapped with the transcription start site (TSS). The human Ig genes that have CpG islands in the PPRs show a very narrow range of CpG densities. 47% of the Ig genes fall in the range of 3.5-4 CpGs/100 bp. In contrast, the non-Ig genes examined have a wide range of the density of CpG island, with 10.5% having the density of 8.1-15 CpGs/100 bp. Meantime, five patterns of the CpG distributions within the CpG islands have been classified: Pat A, B, C, D, and E. 21.6% and 10.8% of the Ig genes fall into the Pat B and Pat D groups, respectively, which were significantly higher than the non-Ig genes examined (8.2% and 3.8%). Moreover, the length of CpG islands is shorter in human Ig genes than in non-Ig genes but is much longer than in mouse orthologues. These findings provide a clear picture of non-neutral and nonrandom occurrence of the CpG islands in the PPRs of human and mouse Ig genes, which facilitate rational recommendations regarding their nomenclature.

RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells

RNA interference (RNAi) is a widely used method for analysis of gene function in tissue culture cells. However, to date there has been no reliable method for testing the specificity of any particular RNAi experiment. The ideal experiment is to rescue the phenotype by expression of the target gene in a form refractory to RNAi. The transgene should be expressed at physiological levels and with its different splice variants. Here, we demonstrate that expression of murine bacterial artificial chromosomes in human cells provides a reliable method to create RNAi-resistant transgenes. This strategy should be applicable to all eukaryotes and should therefore be a standard technology for confirming the specificity of RNAi. We show that this technique can be extended to allow the creation of tagged transgenes, expressed at physiological levels, for the further study of gene function.

Inactivation of Imprinted Genes Induced by Cellular Stress and Tumorigenesis

Cellular proliferation under stressful conditions may result in permanent genetic and epigenetic changes. Using primary mouse embryonic fibroblasts, we have completed a screening test to identify gene expression changes triggered when cells proliferate under stress. In this manner, we have discovered a novel phenomenon that consists of the rapid and coordinated silencing of genes subject to imprinting, including Cdkn1c, Igf2, H19, Ndn1, Grb10, and Meg3. This generalized silencing of imprinted genes is independent of the stress-responsive tumor suppressors p53, p19Arf, and p16Ink4a, and it is also independent of the oxidative culture conditions and the stress response known as “mouse embryonic fibroblast senescence”. In the case of Cdkn1c and H19, their silencing is associated with unscheduled de novo methylation of the normally expressed allele at their corresponding CpG island promoters, thus resulting in biallelic methylation. Finally, we provide evidence for frequent de novo methylation of Cdkn1c in a variety of murine cancer types. Altogether, our data support the concept that silencing of imprinted genes, including methylation of Cdkn1c, constitutes an epigenetic signature of cellular stress and tumorigenesis.

Genomic organization and developmental expression of globin genes in the teleost Oryzias latipes

We isolated globin genes from a genomic DNA library of the drR strain of medaka Oryzias latipes, and walked on chromosome. The present study is the first demonstration of the full-length structure of globin gene locus in the teleosts. Two gene clusters were found. One cluster of 36 kbp consisted of nine globin genes and two pseudogenes. Based on structural and phylogenetic similarity of amino acid sequences, the cluster was named embryonic globin gene cluster (E1). The orientation of the genes was in (5')alpha0(3')-(3')beta1(5')-(5')alpha1(3')-(5')beta2(3')-(5')alpha2(3')-(3')alpha3(5')-(5')beta3(3')-(3')beta4(5')-(5')alpha4(3')-(3')psialpha(5')-(5')psibeta(3'). The other cluster of 20 kbp contained three globin genes ((3')ad.alpha1(5')-(5')ad.beta1(3')-(3')ad.alpha2(5')), and was named adult globin gene cluster (A1). Genetic linkage analysis clarified that E1 and A1 were mapped on linkage groups 8 and 19, respectively. The E1 cluster included other genes homologous to human EST clone KIAA0172, Sushi-1 retrotransposon, and protein 14 gene-like gene, while the A1 cluster linked to aquaporin-8 gene-like gene. The expression patterns of the genes were classified into four types: embryo-specific expression (alpha3, beta3, alpha4 and beta4), expression in embryo to young fish (alpha0, beta1, alpha1 and ad.alpha2), expression in young to adult fish (alpha2 and ad.alpha1) and successive expression in embryo to adult (ad.beta1).

Benchmarking tools for the alignment of functional noncoding DNA

BACKGROUND

Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools.

RESULTS

Using rates of noncoding sequence evolution estimated from the genus Drosophila, we simulated alignments over a range of divergence times under varying models incorporating point substitution, insertion/deletion events, and short blocks of constrained sequences such as those found in cis-regulatory regions. We then compared "correct" alignments generated by a modified version of the ROSE simulation platform to alignments of the simulated derived sequences produced by eight pairwise alignment tools (Avid, BlastZ, Chaos, ClustalW, DiAlign, Lagan, Needle, and WABA) to determine the off-the-shelf performance of each tool. As expected, the ability to align noncoding sequences accurately decreases with increasing divergence for all tools, and declines faster in the presence of insertion/deletion evolution. Global alignment tools (Avid, ClustalW, Lagan, and Needle) typically have higher sensitivity over entire noncoding sequences as well as in constrained sequences. Local tools (BlastZ, Chaos, and WABA) have lower overall sensitivity as a consequence of incomplete coverage, but have high specificity to detect constrained sequences as well as high sensitivity within the subset of sequences they align. Tools such as DiAlign, which generate both local and global outputs, produce alignments of constrained sequences with both high sensitivity and specificity for divergence distances in the range of 1.25-3.0 substitutions per site.

CONCLUSION

For species with genomic properties similar to Drosophila, we conclude that a single pair of optimally diverged species analyzed with a high performance alignment tool can yield accurate and specific alignments of functionally constrained noncoding sequences. Further algorithm development, optimization of alignment parameters, and benchmarking studies will be necessary to extract the maximal biological information from alignments of functional noncoding DNA.

Functional dissection of the mouse tyrosinase locus control region identifies a new putative boundary activity

Locus control regions (LCRs) are complex high-order chromatin structures harbouring several regulatory elements, including enhancers and boundaries. We have analysed the mouse tyrosinase LCR functions, in vitro, in cell lines and, in vivo, in transgenic mice and flies. The LCR-core (2.1 kb), located at -15 kb and carrying a previously described tissue-specific DNase I hypersensitive site, operates as a transcriptional enhancer that efficiently transactivates heterologous promoters in a cell-specific orientation-independent manner. Furthermore, we have investigated the boundary activity of these sequences in transgenic animals and cells. In mice, the LCR fragment (3.7 kb) rescued a weakly expressed reference construct that displays position effects. In Drosophila, the LCR fragment and its core insulated the expression of a white minigene reporter construct from chromosomal position effects. In cells, sequences located 5' from the LCR-core displayed putative boundary activities. We have obtained genomic sequences surrounding the LCR fragment and found a LINE1 repeated element at 5'. In B16 melanoma and L929 fibroblast mouse cells, this element was found heavily methylated, supporting the existence of putative boundary elements that could prevent the spreading of condensed chromatin from the LINE1 sequences into the LCR fragment, experimentally shown to be in an open chromatin structure.

RETRACTED: A Mutant Form of MeCP2 Protein Associated with Human Rett Syndrome Cannot Be Displaced from Methylated DNA by Notch in Xenopus Embryos

MeCP2 is a DNA binding protein that represses transcription of methylated genes in vitro, but the endogenous function of MeCP2 in vivo is unclear. Here, we demonstrate that in Xenopus laevis embryos MeCP2 is a partner of the SMRT corepressor complex that regulates the expression of a neuronal repressor xHairy2a in differentiating neuroectoderm. The MeCP2/SMRT complex is bound to the promoter of the silenced xHairy2a gene and is displaced upon activation by the Notch intracellular domain (NICD). A truncated form of MeCP2 (R168X) found in patients with Rett syndrome cannot interact with the SMRT complex or fully activate xHairy2a during primary neurogenesis. This disruption of MeCP2 activity results in abnormal patterning of primary neurons during neuronal differentiation. Our results support a model whereby the dynamic association of MeCP2 with methylated DNA and the SMRT complex regulates a gene involved in cell fate decisions during primary neurogenesis in Xenopus.