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PubMed2004

Developmental constraint on gene duplicability in fruit flies and nematodes.

A previous study in nematodes suggested that developmental constraint reduces the duplicability of genes involved in early development. Recent large-scale gene expression studies of fly development enabled us to conduct a more detailed study of this issue. We found that the average duplicability of genes involved in embryonic development is indeed lower than that of genes involved in larval development but not significantly lower than that of genes involved in later stages of development. Moreover, in both flies and nematodes genes with multiple expression peaks do not seem to have a lower duplicability than do genes with a single expression peak. Thus, although developmental constraint does appear to reduce gene duplicability, the effect seems weak or at best moderate.

Animals↗

PubMed2000

Dysregulation of lymphocyte proliferation by chromosomal translocations and sequential genetic changes.

Enzymatically mediated rearrangement of Ig and T-cell receptor genes is essential for generating the huge molecular repertoire of the mammalian immune system, but it also carries a danger for the organism in the form of high risk zones for illegitimate juxtaposition of DNA from other areas of the genome. Translocation-dependent activation of oncogenes, transcription factors or developmental genes can trigger the development of neoplasia in a lineage-specific fashion. These events are not sufficient for tumorigenesis, however, since some of the most prominent tumor-associated translocations, such as Ig/myc and Ig/bcl-2, have been detected in normal individuals who did not develop tumors. Tumor development must, therefore, require subsequent genetic changes. Among them, the increased expression of genes that protect against apoptosis or, alternatively, mutations that cripple apoptosis-activating genes play a prominent role. Some of the translocations associated with T-cell leukemia, myeloid leukemia, and a variety of sarcomas act by generating fusion proteins. The participating genes encode transcription factors and/or developmental regulators. Fusion protein-expressing cells may serve as targets for specific interference with abnormal signaling pathways or for targeted immune attack. Using PCR to detect cells carrying such translocations is useful for tumor diagnosis, prognosis, and choice of therapy.

Abelson murine leukemia virus↗

PubMed2002

Ascidian gene-expression profiles.

With the advent of gene-expression profiling, a large number of genes can now be investigated simultaneously during critical stages of development. This approach will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.

Animals↗

PubMed1994

Developmental expression of murine retinoid X receptor (RXR) genes.

The developmental expression patterns of the three mouse retinoid X receptor genes (RXR alpha, beta and gamma) have been investigated by Northern blotting and in situ analysis of RNA transcript distribution, and compared to those of retinoic acid receptor (RAR) genes. RXR beta showed a diffuse and probably ubiquitous expression pattern at all developmental stages studied. RXR alpha also exhibited a diffuse expression at early developmental stages, but an enhanced in situ labelling was observed during late development in the epidermis and several other squamous epithelia. By contrast, RXR gamma apparently displayed a restricted expression in the myogenic lineage, i.e. in myotomes and subsequently in various differentiating muscles including those of the face and limbs. Apparently RXR gamma was not co-expressed with RAR beta and RAR gamma in these domains. RXR gamma transcripts were developmentally regulated in the otic epithelium, the retina, the pituitary and thyroid glands. In addition, RXR gamma was expressed in several discrete areas of the fetal central nervous system, namely in the diencephalon, the striatum and in part of the ventral horns of the spinal cord. In the two latter domains, there was a precise co-expression with RAR beta transcripts, although with quantitative differences, which suggests a possible preferential heterodimerization between these two retinoic acid receptors in the developing central nervous system.

Animals↗

PubMed2001

Post transcriptional control of gene expression in Leishmania.

Leishmania parasites are ancient eukaryotes, characterized by unusual molecular mechanisms. We have used the gene encoding for Hsp83 as a model system for studying regulatory mechanisms that control developmental gene regulation. We previously showed that protein coding genes are regulated exclusively by post-transcriptional mechanisms, while no transcriptional activation could be observed even for the conserved Hsp83 gene. We now show that processing and maturation of the Hsp83 polycistronic primary transcripts is more efficient at elevated temperatures. The mature transcripts are more stable during heat shock, with regulation conferred by 3' UTRs. Poly(A) tails of Hsp83 are approximately 30 nucleotides long, as common for other low eukaryotes. The mechanism that signals differential degradation is still unclear, since it was not possible to detect differences in deadenylation of Hsp83 transcripts at varying temperatures. Heat shock transcripts are preferentially translated at 33-37 degrees C, but unlike Drosophila, translational regulation is controlled by a region within the 3' UTR. Using this traditionally conserved system emphasizes that regulatory mechanisms in Leishmania differ from those prevailing in other eukaryotes.

3' Untranslated Regions↗

PubMed2006

MicroRNAs preferentially target the genes with high transcriptional regulation complexity.

Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level. However, it is still unclear why some genes are regulated by miRNAs but others are not, i.e. what principles govern miRNA regulation in animal genomes. In this study, we systematically analyzed the relationship between transcription factors (TFs) and miRNAs in gene regulation. We found that the genes with more TF-binding sites have a higher probability of being targeted by miRNAs and have more miRNA-binding sites on average. This observation reveals that the genes with higher cis-regulation complexity are more coordinately regulated by TFs at the transcriptional level and by miRNAs at the post-transcriptional level. This is a potentially novel discovery of mechanism for coordinated regulation of gene expression. Gene ontology analysis further demonstrated that such coordinated regulation is more popular in the developmental genes.

Chromosome Mapping↗

PubMed2006

Linking floral symmetry genes to breeding system evolution.

Understanding the genetic basis of ecologically important traits is a major focus of evolutionary research. Recent advances in molecular genetic techniques should significantly increase our understanding of how regulatory genes function. By contrast, our understanding of the broader macro-evolutionary implications of developmental gene function lags behind. Here we review published data on the floral symmetry gene network (FSGN), and conduct phylogenetic analyses that provide evidence of a link between floral symmetry and breeding systems in angiosperms via dichogamy. Our results suggest that known genes in the FSGN and those yet to be described underlie this association. We posit that the integration of floral symmetry and the roles of other regulatory genes in plant breeding system evolution will provide new insights about macro-evolutionary patterns and processes in flowering plants.

Biological Evolution↗

PubMed1999

Preservation of duplicate genes by complementary, degenerative mutations.

The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow 1996(p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh 1995 (p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff 1997 (p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. 1997 (p. 362)

Animals↗

PubMed2005

Human SRCAP and Drosophila melanogaster DOM are homologs that function in the notch signaling pathway.

The putative ATPase chromatin-remodeling machine SRCAP was identified in a yeast two-hybrid protein screen by interaction with the histone acetylase CBP. SRCAP is implicated in the transcriptional coactivation of cyclic AMP- and steroid-dependent promoters, but no natural chromosomal targets for SRCAP regulation have been identified. DOM is the unique SRCAP homolog in Drosophila melanogaster. The goal of this study was to test whether SRCAP is a functional homolog of DOM and to identify potential activities and targets of SRCAP in vivo. We show that human SRCAP complements recessive domino mutant phenotypes. This rescue depends on an intact ATPase homology domain. SRCAP colocalizes extensively with DOM on Drosophila polytene chromosomes and is recruited to sites of active transcription, such as steroid-regulated loci, but not to activated heat shock loci. We show that SRCAP recruits Drosophila CBP to ectopic chromosomal sites, providing the first evidence to suggest that SRCAP and CBP interact directly or indirectly on chromosomes. We show that DOM is a Notch pathway activator in Drosophila and that wild-type SRCAP-but not an ATPase domain mutant-can substitute for DOM in Notch-dependent wing development. We show that SRCAP potentiates Notch-dependent gene activation in HeLa cells. Taken together, these data implicate SRCAP and DOM in developmental gene activation.

Adenosine Triphosphatases↗

PubMed2003

Transcriptomal analysis of failing and nonfailing human hearts.

Heart failure is a multifactorial disease that may result from different initiating events. To contribute to an improved comprehension of normal cardiac function and the molecular events leading to heart failure, we performed large-scale gene expression analysis of failing and nonfailing human ventricle. Our aim was to define and compare expression profiles of 4 specific pathophysiological cardiac situations: 1) left ventricle (LV) from nonfailing heart; 2) LV from failing hearts affected by dilated cardiomyopathy (DCM); 3) LV from failing hearts affected by ischemic CM (ICM); 4) right ventricle (RV) from failing hearts affected by DCM or ICM. We used oligonucleotide arrays representing approximately 12,000 human genes. After stringent numerical analyses using several statistical tests, we identified 1,306 genes with a similar expression profile in all 4 cardiac situations, therefore representative of part of the human cardiac expression profile. A total of 95 genes displayed differential expression between failing and nonfailing heart samples, reflecting a reversal to developmental gene expression, dedifferentiation of failing cardiomyocytes, and involvement of apoptosis. Twenty genes were differentially expressed between failing LV and failing RV, identifying possible candidates for different functioning of both ventricles. Finally, no genes were found to be significantly differentially expressed between failing DCM and failing ICM LV, emphasizing that transcriptomal analysis of explanted hearts results mainly in identification of expression profiles of end-stage heart failure and less in determination of expression profiles of the underlying etiology. Taken together, our data resulted in identification of putative transcriptomal landmarks for normal and disturbed cardiac function.

Adolescent↗

PubMed1997

Cytosine methylation and the ecology of intragenomic parasites.

Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized intragenomic parasites that represent at least 35% of the genome. Transposon promoters are inactive when methylated and, over time, C-->T transition mutations at methylated sites destroy many transposons. Apart from that subset of genes subject to X inactivation and genomic imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a pattern that prevents transcription. It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.

Animals↗

PubMed2026

Transcriptome analysis of the pectoral fin degeneration in half-smooth tongue sole (Cynoglossus semilaevis).

Appendage degeneration is a notable morphological feature of some teleosts with specialized benthic lifestyles. The half-smooth tongue sole (Cynoglossus semilaevis) undergoes severe pectoral fin regression during metamorphosis. However, the molecular basis underlying rapid pectoral fin degeneration remains unclear. Here, we performed time-series transcriptome sequencing on pectoral fins at pre-metamorphosis, metamorphosis peak and post-metamorphosis to characterize the molecular changes associated with pectoral fin degeneration. Transcriptional dynamics and functional enrichment showed that no significant enrichment of classical apoptosis-related transcriptional pathways was detected during pectoral fin degeneration. Instead, sustained downregulation of twist1b, identified as a transcriptomic candidate, together with significant upregulation of ssh1, coupled with enrichment of lysosome and ubiquitin-proteasome system (UPS) pathways, suggested enhanced tissue remodeling during pectoral fin degeneration. Temporal expression clustering revealed heterochronic misalignment in the developmental gene expression: upstream initiator tbx5 was upregulated at early metamorphosis, while downstream maintenance signal fgf10 decreased synchronously. Distal patterning gene hoxd12a exhibited premature expression and rapid decay, losing sustained late-phase expression. Moreover, transient elevation of gli3 during metamorphosis may contribute to restricted distal fin growth. We conclude that pectoral fin degeneration in C. semilaevis is associated with heterochronic disruption of developmental signaling and extensive tissue remodeling. This study provides transcriptomic insights into pectoral fin degeneration in tongue soles and establishes a basis for future functional studies of appendage reduction in teleosts.

Animals↗

PubMed2003

Association of congenital diaphragmatic hernia with limb-reduction defects.

BACKGROUND: The pathogenesis of congenital diaphragmatic hernia (CDH), a severe birth defect, is not well understood; however, both developmental genes and environmental factors have been suggested to be involved. CDH is frequently associated with malformations of other structures, such as limbs, whose embryogenesis is better understood. An examination of the co-occurrence of developmental defects may provide clues as to the origin and timing of the insult to the diaphragm and limbs. Our focus was on CDH-associated limb-reduction defects (LRDs). METHODS: For this descriptive study, we reviewed the medical records of infants with a posterolateral (Bochdalek) CDH and an associated LRD among 146 patients from the Sophia Children's Hospital, and among 810 infants and 36 stillbirths from the California Birth Defects Monitoring Program (CBDMP). RESULTS: In the hospital group, 14 patients (10%) had an associated limb defect, of which about one-third were LRDs (of these, most were of a nonsevere type, such as hypoplasia of fingers). In the registry group, a limb defect was found in 162 cases (18.5%), 18 of which were mostly severe LRD (usually of the upper extremities). Additional congenital anomalies were observed in all CDH-LRD cases in both groups. CONCLUSIONS: In the registry group, 77.8% of LRDs were either bilateral or ipsilateral, and were mostly preaxial, suggesting an early embryological insult affecting both precursor anlages. These results, from large numbers of cases, support the notion of a developmental association between CDH and LRD, as has been observed in several knockout mice. Future analyses of candidate genes from patients with CDH and LRD may elucidate this developmental association in humans.

Female↗

PubMed2006

Compartments and the control of growth in the Drosophila wing imaginal disc.

The mechanisms that control organ growth are among the least known in development. This is particularly the case for the process in which growth is arrested once final size is reached. We have studied this problem in the wing disc of Drosophila, the developmental and growth parameters of which are well known. We have devised a method to generate entire fast-growing Minute(+) (M(+)) discs or compartments in slow developing Minute/+ (M/+) larvae. Under these conditions, a M(+) wing disc gains at least 20 hours of additional development time. Yet it grows to the same size of Minute/+ discs developing in M/+ larvae. We have also generated wing discs in which all the cells in either the anterior (A) or the posterior (P) compartment are transformed from M/+ to M(+). We find that the difference in the cell division rate of their cells is reflected in autonomous differences in the developmental progression of these compartments: each grows at its own rate and manifests autonomous regulation in the expression of the developmental genes wingless and vestigial. In spite of these differences, ;mosaic' discs comprising fast and slow compartments differentiate into adult wings of the correct size and shape. Our results demonstrate that imaginal discs possess an autonomous mechanism with which to arrest growth in anterior and posterior compartments, which behave as independent developmental units. We propose that this mechanism does not act by preventing cell divisions, but by lengthening the division cycle.

Animals↗

PubMed2005

Molecular characterization and embryonic expression of the family of N-methyl-D-aspartate receptor subunit genes in the zebrafish.

We present the cloning of 10 N-methyl-D-aspartate (NMDA) receptor subunits from the zebrafish. These subunits fall into five subtypes, each containing two paralogous genes. Thus, we report two NMDAR1 genes (NR1.1 and NR1.2), and eight NMDAR2 genes, designated NR2A.1 and NR2A.2, NR2B.1 and NR2B.2, NR2C.1 and NR2C.2, and NR2D.1 and NR2D.2. The predicted sequences of the NR1 paralogs display 90% identity to the human protein. The NR2 subunits show less identity, differing most at the N- and C-termini. The NR1 genes are both expressed embryonically, although in a nonidentical manner. NR1.1 is found in brain, retina, and spinal cord at 24 hours postfertilization (hpf). NR1.2 is expressed in the brain at 48 hpf but not in the spinal cord. NR2 developmental gene expression varies: both paralogs of the NR2A are expressed at 48 hpf in the retina, only one paralog of the NR2B is expressed at low levels in the heart at 48 hpf. Neither of the NR2C is expressed embryonically. Both paralogs of the NR2D are expressed: 2D.1 is in the forebrain, retina, and spinal cord at 24 hpf, whereas the 2D.2 is only found in the retina. Our findings demonstrate that the zebrafish can serve as a useful model system for investigating the role of NMDA receptors in the development of the nervous system.

Alternative Splicing↗

PubMed2002

Molecular genetic studies of human chromosome 7 in Russell-Silver syndrome.

Russell-Silver syndrome (RSS) is a form of congenital short stature characterized by severe growth retardation and variable dysmorphic features. In some RSS individuals, alterations in imprinted genes may be involved because approximately 7% of sporadic patients have been observed to have maternal uniparental disomy (mUPD) of chromosome 7. RSS patients with structural abnormalities of chromosome 7 have also been described. In these individuals the chromosome rearrangement could disrupt the balance of imprinted genes, contribute to a recessive form of RSS, or lead to haploinsufficiency of a crucial developmental gene product. Because the mechanism and molecular defects on chromosome 7 causing RSS are still unknown, we tested our collection of 77 RSS families for mUPD7 and were able to identify three new cases. We also characterized two RSS patients with de novo cytogenetic abnormalities involving the short arm of chromosome 7. One had a partial duplication [46, XX, dup(7)(p12 p14)] and the second contained a paracentric inversion [46, XY, inv(7)(p14 p21)]. Fluorescence in situ hybridization (FISH) mapping revealed that the breakpoints on 7p14 were localized to the same novel gene, C7orf10, which encompasses >700 kb of DNA. We also identified other transcription units from this immediate region, but all seem to be biallelically expressed when using a somatic cell hybrid assay.

Abnormalities, Multiple↗

PubMed2001

Pyk10, a seedling and root specific gene and promoter from Arabidopsis thaliana.

Pyk10 is a root and hypocotyl specific myrosinase from Arabidopsis thaliana. Northern analysis revealed the root specific expression of pyk10. In order to study the pyk10 promoter and the genomic structure of the gene, a genomic clone was isolated and sequenced. The clone contained the complete pyk10 gene and a promoter region of 3569 bp. The gene spans 2963 bp and consists of 12 exons and 11 introns, a structure that reflects the common gene organization of myrosinases. Within the promoter sequence, different development specific, organ specific, elicitor and plant hormone responsive regulatory elements could be identified, which also occur in other promoters. To determine the pattern of expression, four different 5'-promoter deletion fragments were linked to a ss-glucuronidase (gus) reporter gene and transformed into A. thaliana. The results demonstrated that the pyk10 promoter mediates a developmental gene activity with a strong emphasis in the root. Cis-acting sequences regulating root specific expression were identified to reside in the two promoter fragments B and C.

Journal Article↗

PubMed2002

Human limb malformations; an approach to the molecular basis of development.

Analysis of human inherited limb malformations and of mouse mutants copying individual human mutations team up to promote the understanding of vertebrate limb development as a model for molecular regulatory interactions in animals. The strength of the human genetic contribution lies in the increasingly complete information on the human genome, transcriptome and proteome, as well as in the wealth of individual mutations interfering with limb development available for study. Based on the strong fundament of the human genome project, mapping and identification of novel genes associated with limb defects extends considerably the range of candidates beyond the repertoire of developmental genes and pathways known from animals. Attempts to correlate genotype and phenotype uncover a very broad range of genetic heterogeneity, i.e. different genes underlying the same phenotype, or allelic heterogeneity between families, i.e. clinically distinct phenotypes associated with mutations affecting the same gene. Mechanisms other than simple Mendelian inheritance have to be taken into consideration. Phenotypic variability within families might be explained by different modifying genes or environmental influence, whereas asymmetry of limb defects within one patient may be caused by epigenetic factors, such as somatic mosaicism or X-inactivation, or by non-genetic factors. The intimate knowledge of the genes and events governing limb pattern formation in humans and animals will elucidate the regulatory interactions underlying normal and pathological development, homeostasis, and repair, and thus propose targets for preventive measures and novel approaches to therapeutic intervention in the new era of molecular medicine.

Bardet-Biedl Syndrome↗