The sequence of the human genome

In the name of the father: surnames and genetics

Hereditary surnames contain information about relatedness within populations. They have been used as crude indicators of population structure and migration events, and to subdivide samples for epidemiological purposes. In societies that use patrilineal surnames, a surname should correlate with a type of Y chromosome, provided certain assumptions are met. Recent studies involving Y-chromosomal haplotyping and surname analysis are promising and indicate that genealogists of the future could be turning to records written in DNA, as well as in paper archives, to solve their problems.

Automation in genotyping of single nucleotide polymorphisms

Automation for genotyping of single nucleotide polymorphisms (SNPs) can be split into the automation of the sample preparation and the automation of the analysis technology. SNP genotyping methods are reviewed and solutions for their automation discussed. A panacea for SNP genotyping does not exist. Different scientific questions require adapted solutions. The choice of a technology for SNP genotyping depends on whether few different SNPs are to be genotyped in many individuals, or many different SNPs are to be genotyped in few individuals. The requirements of throughput and the ease of establishing an SNP genotyping operation are important, as well as the degree of integration. The potential and state-of-the-art of different solutions are outlined.

Virogenomics: a novel approach to antiviral drug discovery

Target discovery in virology has been limited to the few open-reading frames encoded by viral genomes. However, several recent examples show that inhibiting host-cell proteins can prevent viral infection. The human genome sequence should, therefore, contain many more genes that are essential for viral propagation than viral genomes. A systematic approach to find these potential cellular antiviral targets is global host gene expression analysis using DNA microarrays. Several recent studies reveal both unique and common strategies by which viruses change the gene expression profile of the host cell. Moreover, work in progress shows that some of the host pathways discovered by expression profiling are important for viral replication. Thus, human genomics tools have the potential to deliver novel antiviral drugs.

Notl-Msell methylation-sensitive amplied fragment length polymorhism for DNA methylation analysis of human cancers

We have applied a methylation-sensitive restriction endonuclease, NotI, to the existing amplified fragment length polymorphism (AFLP) method and developed NotI-MseI methylation-sensitive-AFLP (MS-AFLP). NotI-MseI MS-AFLP allows the analysis of DNA methylation alterations at the NotI sites scattered over the genome. Hypermethylation and hypomethylation are visualized by the decrease and increase in the band intensity of DNA fingerprints. Identification of consistent changes can be facilitated through parallel electrophoresis of multiple samples. DNA fragments exhibiting alterations can be cloned from fingerprint bands by amplification of gel-eluted DNA with the same pair of primers used for radioactive fingerprint presentation. Fluorescent NotI-MseI MS-AFLP offers a safer method of studying the alterations in DNA methylation, and may be applied to the hybridization of DNA microarrays in the future. Using NotI-MseI MS-AFLP, we observed frequent hypomethylation of a satellite DNA repeat sequence in a majority of breast tumors.

Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks

In this post-sequencing era, geneticists can focus on functional genomics on a much larger scale than ever before. One goal is the discovery and elucidation of the intricate genetic networks that co-ordinate transcriptional activation in different regulatory circuitries. High-throughput gene expression measurement using DNA arrays has thus become routine strategy. This approach, however, does not directly identify gene loci that belong to the same regulatory group; e.g., those that are bound by a common (set of) transcription factor(s). Working in yeast, two groups have recently published an elegant method that could circumvent this problem, by combining chromatin immunoprecipitation and DNA microarrays.(1,2) The method is likely to provide a powerful tool for the dissection of global regulatory networks in eukaryotic cells.

Gene discovery using the serial analysis of gene expression technique: implications for cancer research

Cancer is a genetic disease. As such, our understanding of the pathobiology of tumors derives from analyses of the genes whose mutations are responsible for those tumors. The cancer phenotype, however, likely reflects the changes in the expression patterns of hundreds or even thousands of genes that occur as a consequence of the primary mutation of an oncogene or a tumor suppressor gene. Recently developed functional genomic approaches, such as DNA microarrays and serial analysis of gene expression (SAGE), have enabled researchers to determine the expression level of every gene in a given cell population, which represents that cell population's entire transcriptome. The most attractive feature of SAGE is its ability to evaluate the expression pattern of thousands of genes in a quantitative manner without prior sequence information. This feature has been exploited in three extremely powerful applications of the technology: the definition of transcriptomes, the analysis of differences between the gene expression patterns of cancer cells and their normal counterparts, and the identification of downstream targets of oncogenes and tumor suppressor genes. Comprehensive analyses of gene expression not only will further understanding of growth regulatory pathways and the processes of tumorigenesis but also may identify new diagnostic and prognostic markers as well as potential targets for therapeutic intervention.

Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era

The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make-up; however, the post-genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs.

Review article: the genetics of inflammatory bowel disease

Recent epidemiological, clinical and molecular studies have provided strong evidence that inherited predisposition is important in the pathogenesis of chronic inflammatory bowel diseases. The model most consistent with the epidemiological data suggests that Crohn's disease and ulcerative colitis are related polygenic diseases, sharing some but not all susceptibility genes. Investigators throughout the world have applied the complementary techniques of genome-wide scanning and candidate gene analysis. Four areas of linkage have been widely replicated on chromosomes 16 (IBD1), 12 (IBD2), 6 (IBD3-the HLA region), and most recently on chromosome 14. Fine mapping of these regions is underway. Of the 'positional' candidate genes, most attention has centred on the genes of the major histocompatibility complex. Genes within this region may determine disease susceptibility, behaviour, complications and response to therapy. Hope continues that studies of inflammatory bowel disease genetics will provide fresh insight into disease pathogenesis and soon deliver clinical applications.

Where will the genome lead us? Dentistry in the 21st century

BACKGROUND

Recent announcements of the deciphering and analysis of the human genome signal the inception of a new era of gene-based medicine. During the 21st century, patient treatment will be transformed and dentistry will be affected profoundly.

METHODS

The author explains the importance of the decoding of the genome and how--based on this now completely depicted molecular structure--genes build, maintain and control all the biological functions of humans and all other living organisms. The potential application of this knowledge to the practice of dentistry is addressed, as well as the ethical, legal and moral challenges to the profession engendered by this new technology.

CONCLUSION

During the next several decades, many of the current materials and methods will be abandoned in favor of emerging bioengineered technologies, genetically programmed for the prevention and treatment of oral disease as well as for the repair of damaged dental tissues.

PRACTICE IMPLICATIONS

The development and implementation of these innovative dental therapies will require intensive education of current practitioners. Considerable restructuring of dental school curricula will need to take place, and the emergence of a new dental specialty is anticipated.

Pre-mRNA splicing in the new millennium

The past year has witnessed refinements in models of spliceosome assembly pathways and in the understanding of how splicing factors of the serine/arginine-rich (SR) protein family function. The role of splicing in human genetic diseases has also received a lot of attention recently as exonic splicing enhancers become better understood.

Commensal host-bacterial relationships in the gut

One potential outcome of the adaptive coevolution of humans and bacteria is the development of commensal relationships, where neither partner is harmed, or symbiotic relationships, where unique metabolic traits or other benefits are provided. Our gastrointestinal tract is colonized by a vast community of symbionts and commensals that have important effects on immune function, nutrient processing, and a broad range of other host activities. The current genomic revolution offers an unprecedented opportunity to identify the molecular foundations of these relationships so that we can understand how they contribute to our normal physiology and how they can be exploited to develop new therapeutic strategies.

The core promoter of human thioredoxin reductase 1: cloning, transcriptional activity, and Oct-1, Sp1, and Sp3 binding reveal a housekeeping-type promoter for the AU-rich element-regulated gene

The selenoprotein thioredoxin reductase 1 (TrxR1) carries many vital antioxidant and redox regulatory functions. Its mRNA levels are known to be post-transcriptionally modulated via AUUUA motifs (AU-rich elements (AREs)), but the promoter yet remains unknown. Here we have cloned and determined the sequence of a 0.8-kilobase pair human genomic fragment containing the proximal promoter for TrxR1, which has transcriptional activity in several different cell types. The core promoter (-115 to +167) had an increased GC content and lacked TATA or CCAAT boxes. It contained a POU motif binding the Oct-1 transcription factor and two sites binding Sp1 and Sp3, which were identified with electrophoretic mobility shift assays using crude nuclear extracts of A549 cells. The TrxR1 promoter fulfills the typical criteria of a housekeeping gene. To our knowledge this is the first housekeeping-type promoter characterized for a gene with post-transcriptional regulation via ARE motifs generally possessed by transiently expressed proto-oncogenes, nuclear transcription factors, or cytokines and influencing mRNA stability in response to diverse exogenous factors. Expression of TrxR1 as an ARE-regulated housekeeping gene agrees with a role for the enzyme to maintain a balance between intracellular signaling via reactive oxygen species and protection of cells from excessive oxidative damage.

Microbial genes in the human genome: lateral transfer or gene loss?

The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.

Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions

The evolution of novelty in tightly integrated biological systems, such as hormones and their receptors, seems to challenge the theory of natural selection: it has not been clear how a new function for any one part (such as a ligand) can be selected for unless the other members of the system (e.g., a receptor) are already present. Here I show-based on identification and phylogenetic analysis of steroid receptors in basal vertebrates and reconstruction of the sequences and functional attributes of ancestral proteins-that the first steroid receptor was an estrogen receptor, followed by a progesterone receptor. Genome mapping and phylogenetic analyses indicate that the full complement of mammalian steroid receptors evolved from these ancient receptors by two large-scale genome expansions, one before the advent of jawed vertebrates and one after. Specific regulation of physiological processes by androgens and corticoids are relatively recent innovations that emerged after these duplications. These findings support a model of ligand exploitation in which the terminal ligand in a biosynthetic pathway is the first for which a receptor evolves; selection for this hormone also selects for the synthesis of intermediates despite the absence of receptors, and duplicated receptors then evolve affinity for these substances. In this way, novel hormone-receptor pairs are created, and an integrated system of increasing complexity elaborated. This model suggests that ligands for some "orphan" receptors may be found among intermediates in the synthesis of ligands for phylogenetically related receptors.

Critical care medicine in the 21st century: from CPR to PCR

As in other areas of medicine, the specialty of critical care medicine, which has made important contributions in the pathophysiology of critical illness, is facing challenges that must be recognized and addressed in the current century. In this review, we argue that the skill set required to adequately treat critically ill patients will also require knowledge of molecular biology for better diagnosis and treatment. The foundations of molecular biology and genetics are essential for the understanding of the mechanisms of disease. Incorporating molecular biology techniques in the research arsenal of the intensivist will provide the opportunity to dissect out and define the reversible and irreversible intracellular processes giving rise to the major causes of mortality in intensive care units. Two historical paradigms, the cardiopulmonary resuscitation and polymerase chain reaction, summarize how critical care medicine began, and how it could mature in the years to come.

Methylation matters

DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.

Human mast cell transcriptome project

After draft reading of the human genome sequence, systemic analysis of the transcriptome (the whole transcripts present in a cell) is progressing especially in commonly available cell types. Until recently, human mast cells were not commonly available. We have succeeded to generate a substantial number of human mast cells from umbilical cord blood and from adult peripheral blood progenitors. Then, we have examined messenger RNA selectively transcribed in these mast cells using high-density oligonucleotide probe arrays. Many unexpected but important transcripts were selectively expressed in human mast cells. We discuss the results obtained from transcriptome screening by introducing our data regarding mast-cell-specific genes.

The impact of the Human Genome Project on medical genetics

The near completion of the Human Genome Project stands as a remarkable achievement, with enormous implications for both science and society. For scientists, it is the first step in a complex process that will lead to important advances in the diagnosis and treatment of many diseases. Society, meanwhile, must prevent genetic discrimination, and protect genetic privacy through appropriate legislation.

Yesterday's polyploids and the mystery of diploidization

Thirty years after Susumu Ohno proposed that vertebrate genomes are degenerate polyploids, the extent to which genome duplication contributed to the evolution of the vertebrate genome, if at all, is still uncertain. Sequence-level studies on model organisms whose genomes show clearer evidence of ancient polyploidy are invaluable because they indicate what the evolutionary products of genome duplication can look like. The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one.

Protecting genetic privacy

This article outlines the arguments for and against new rules to protect genetic privacy. We explain why genetic information is different to other sensitive medical information, why researchers and biotechnology companies have opposed new rules to protect genetic privacy (and favour anti-discrimination laws instead), and discuss what can be done to protect privacy in relation to genetic-sequence information and to DNA samples themselves.

Complexity and power in case-control association studies

A general method is described for estimation of the power and sample size of studies relating a dichotomous phenotype to multiple interacting loci and environmental covariates. Either a simple case-control design or more complex stratified sampling may be used. The method can be used to design individual studies, to evaluate the power of alternative test statistics for complex traits, and to examine general questions of study design through explicit scenarios. The method is used here to study how the power of association tests is affected by problems of allelic heterogeneity and to investigate the potential role for collective testing of sets of related candidate genes in the presence of locus heterogeneity. The results indicate that allele-discovery efforts are crucial and that omnibus tests or collective testing of alleles can be substantially more powerful than separate testing of individual allelic variants. Joint testing of multiple candidate loci can also dramatically improve power, despite model misspecification and inclusion of irrelevant loci, but requires an a priori hypothesis defining the set of loci to investigate.

The Tec family of cytoplasmic tyrosine kinases: mammalian Btk, Bmx, Itk, Tec, Txk and homologs in other species

Cytoplasmic protein-tyrosine kinases (PTKs) are enzymes involved in transducing a vast number of signals in metazoans. The importance of the Tec family of kinases was immediately recognized when, in 1993, mutations in the gene encoding Bruton's tyrosine kinase (Btk) were reported to cause the human disease X-linked agammaglobulinemia (XLA). Since then, additional kinases belonging to this family have been isolated, and the availability of full genome sequences allows identification of all members in selected species enabling phylogenetic considerations. Tec kinases are endowed with Pleckstrin homology (PH) and Tec homology (TH) domains and are involved in diverse biological processes related to the control of survival and differentiation fate. Membrane translocation resulting in the activation of Tec kinases with subsequent Ca2+ release seems to be a general feature. However, nuclear translocation may also be of importance. The purpose of this essay is to characterize members of the Tec family and discuss their involvement in signaling. The three-dimensional structure, expression pattern and evolutionary aspects will also be considered.

Microfluidic arrays in genetic analysis

The goal of genetic analysis is to discover genetic markers that are informative for providing high confidence, positive predictive value in managing phenotypic outcomes. Primary consensus sequence data, genetic polymorphism databases and associated phenotype data are rapidly making genetic analysis more useful. Therefore, genetic analysis applications are gradually becoming more mainstream. The diversity and complexity of genetic analysis currently requires an array of analytical techniques, instrument platforms and software to support all the steps from data acquisition to interpretation. As supporting research technologies mature, they are incorporating increasing levels of automation, system integration and miniaturization. Microfluidic arrays are positioned to play a key role in routine genetic analysis, particularly as they begin to appear in more fully integrated analytical platforms.

Gene-diet interaction and plasma lipid response to dietary intervention

Research in the field of gene-diet interactions as determinants of plasma lipid response to dietary interventions has accumulated a substantial body of evidence during the past decade. Several candidate genes have shown some promise as potential markers of individual dietary responsiveness. Among the best characterized are the APOE, APOA4, APOB, APOC3, and LPL loci. Other genes are being continuously incorporated to this most interesting search. However, in very few cases has consensus been achieved about the usefulness of genetic markers as clinically significant predictors of dietary response. The increased ability to generate genotypic information, in combination with the knowledge from the human genome project and more comprehensive experimental designs, will dramatically improve our capacity to answer many of our current questions. It will also help to prove that knowledge of an individual's genetic background will facilitate more precise dietary counseling and intervention, and more efficacious primary and secondary coronary heart disease prevention.

The Surgeon General's Report and special-needs patients: a framework for action for children and their caregivers

The Surgeon General's Report, Oral Health in America, is the first comprehensive assessment of oral, dental, and craniofacial health in the history of our nation. The intent of this first-ever Report is to alert Americans to the full meaning of oral health and its importance to general health and well-being across the lifespan. Moreover, the Report has been released at a time in human history of enormous changes as well as opportunities. The convergence of public health policies, "quality of life" expectations, global informatics, a new century of biotechnology, the completion of the Human Genome Project, changes in the management of health care, and the acknowledgment of enormous health disparities herald a call to action. These profound dynamics particularly affect children and their caregivers and the multitude of social, economic, and health issues associated with special patients and developmental disabilities. This paper will highlight the issues, provide recommendations, and suggest a call to action.

Imaging biochemistry inside cells

Proteins provide the building blocks for multicomponent molecular units, or pathways, from which higher cellular functions emerge. These units consist of either assemblies of physically interacting proteins or dispersed biochemical activities connected by rapidly diffusing second messengers, metabolic intermediates, ions or other proteins. It will probably remain within the realm of genetics to identify the ensemble of proteins that constitute these functional units and to establish the first-order connectivity. The dynamics of interactions within these protein machines can be assessed in living cells by the application of fluorescence spectroscopy on a microscopic level, using fluorescent proteins that are introduced within these functional units. Fluorescence is sensitive, specific and non-invasive, and the spectroscopic properties of a fluorescent probe can be analysed to obtain information on its molecular environment. The development and use of sensors based on the genetically encoded variants of green-fluorescent proteins has facilitated the observation of 'live' biochemistry on a microscopic level, with the advantage of preserving the cellular context of biochemical connectivity, compartmentalization and spatial organization. Protein activities and interactions can be imaged and localized within a single cell, allowing correlation with phenomena such as the cell cycle, migration and morphogenesis.

Lithium-related genetics of bipolar disorder

Lithium is a potent prophylactic medication and mood stabilizer in bipolar disorder. However, clinical outcome is variable, and its therapeutic effect manifests after a period of chronic treatment, implying a progressive and complex biological response process. Signal transduction systems known to be perturbed by lithium involve phosphoinositide (PI) turnover, activation of the Wnt pathway via inhibition of glycogen synthase kinase-3beta (GSK-3beta), and a growth factor-induced, Akt-mediated signalling that promotes cell survival. These pathways, acting in synergy, probably prompt the amplification of lithium signal causing such immense impact on the neuronal network. The sequencing of the human genome presents an unparallelled opportunity to uncover the full molecular repertoire involved in lithium action. Interrogation of high-resolution expression microarrays and protein profiles represents a strategy that should help accomplish this goal. A recent microarray analysis on lithium-treated versus untreated PC12 cells identified multiple differentially altered transcripts. Lithium-perturbed genes, particularly those that map to susceptibility regions, could be candidate risk-conferring factors for mood disorders. Transcript and protein profiling in patients could reveal a lithium fingerprint for responsiveness or nonresponsiveness, and a signature motif that may be diagnostic of a specific phenotype. Similarly, lithium-sensitive gene products could provide a new generation of pharmacological targets.

The human genome: an immuno-centric view of evolutionary strategies

A hallmark of modern biology is the realization of the fundamental unity of biological processes in all life forms. Consequently, the complete genome sequencing of various bacteria, yeast (Saccharomyces cerevisiae), fly (Drosophila melanogaster) and worm (Caenorhabditis elegans) over the past five years has already had an impact on all of biology. "Model organisms" have contributed a great deal to immunology; for example, the Toll receptors of the fly provided the impetus for the investigation of Toll-like receptors, which proved to be fundamental elements in the mammalian innate immune system. The recent release of a draft sequence of the human genome provides the first panoramic view of the 30000-35000 human genes in the human genetic blueprint and provides a plethora of new details, the significance of which will take some time to appreciate. The over-riding concepts that emerge from these studies relate primarily to general evolutionary processes that are equally as relevant to immunology as they are to other disciplines of biology.

Computational inference of homologous gene structures in the human genome

With the human genome sequence approaching completion, a major challenge is to identify the locations and encoded protein sequences of all human genes. To address this problem we have developed a new gene identification algorithm, GenomeScan, which combines exon-intron and splice signal models with similarity to known protein sequences in an integrated model. Extensive testing shows that GenomeScan can accurately identify the exon-intron structures of genes in finished or draft human genome sequence with a low rate of false-positives. Application of GenomeScan to 2.7 billion bases of human genomic DNA identified at least 20,000-25,000 human genes out of an estimated 30,000-40,000 present in the genome. The results show an accurate and efficient automated approach for identifying genes in higher eukaryotic genomes and provide a first-level annotation of the draft human genome.

Genome mining for human cancer genes: wherefore art thou?

In an initial data-mining effort, the draft human genome was searched to find paralogs of known tumor suppressor genes, and for gene arrangements, which are typical of oncogenes, in cancer cells. The results were disappointing, indicating that although knowledge of the human genome will undoubtedly be of great help, other approaches to identify new oncogenes are needed.

Creation of genome-wide protein expression libraries using random activation of gene expression

Here we report the use of random activation of gene expression (RAGE) to create genome-wide protein expression libraries. RAGE libraries containing only 5 x 10(6) individual clones were found to express every gene tested, including genes that are normally silent in the parent cell line. Furthermore, endogenous genes were activated at similar frequencies and expressed at similar levels within RAGE libraries created from multiple human cell lines, demonstrating that RAGE libraries are inherently normalized. Pools of RAGE clones were used to isolate 19,547 human gene clusters, approximately 53% of which were novel when tested against public databases of expressed sequence tag (EST) and complementary DNA (cDNA). Isolation of individual clones confirmed that the activated endogenous genes can be expressed at high levels to produce biologically active proteins. The properties of RAGE libraries and RAGE expression clones are well suited for a number of biotechnological applications including gene discovery, protein characterization, drug development, and protein manufacturing.

Mitochondrial uncoupling proteins and phylogenesis--UCP4 as the ancestral uncoupling protein

We searched for the previously defined uncoupling protein (UCP) signatures [Jezek, P. and Urbánková, E. (2000) IUBMB Life 49, 63-70] in genomes of Drosophila melanogaster, Caenorhabditis elegans, Dictyostelium discoideum, and Arabidopsis thaliana. We identified four UCPs in Drosophila and one in Caenorhabditis or Dictyostelium as close relatives of human UCP4 (BMCP), but distant from UCP1, UCP2, UCP3, and two plant UCPs of Arabidopsis. But the third Arabidopsis UCP is the closest UCP4 relative. This suggests that UCP4 represents the ancestral UCP from which other mammalian and plant UCPs diverged. Speculations on UCP4 participation in apoptosis are thus supported by its early phylogenetic occurrence.