The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains ϳ16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.

Recombination is the exchange of information between two homologous chromosomes during meiosis. The rate of recombination per nucleotide, which profoundly affects the evolution of chromosomal segments, is calculated by comparing genetic and physical maps. Human physical maps have been constructed using cytogenetics, overlapping DNA clones and radiation hybrids; but the ultimate and by far the most accurate physical map is the actual nucleotide sequence. The completion of the draft human genomic sequence provides us with the best opportunity yet to compare the genetic and physical maps. Here we describe our estimates of female, male and sex-average recombination rates for about 60% of the genome. Recombination rates varied greatly along each chromosome, from 0 to at least 9 centiMorgans per megabase (cM Mb(-1)). Among several sequence and marker parameters tested, only relative marker position along the metacentric chromosomes in males correlated strongly with recombination rate. We identified several chromosomal regions up to 6 Mb in length with particularly low (deserts) or high (jungles) recombination rates. Linkage disequilibrium was much more common and extended for greater distances in the deserts than in the jungles.

A BSTR ACTThe recurring translocation t(11;16)-(q23;p13.3) has been documented only in cases of acute leukemia or myelodysplasia secondary to therapy with drugs targeting DNA topoisomerase II. We show that the MLL gene is fused to the gene that codes for CBP (CREB-binding protein), the protein that binds specifically to the DNAbinding protein CREB (cAMP response element-binding protein) in this translocation. MLL is fused in-frame to a different exon of CBP in two patients producing chimeric proteins containing the AT-hooks, methyltransferase homology domain, and transcriptional repression domain of MLL fused to the CREB binding domain or to the bromodomain of CBP. Both fusion products retain the histone acetyltransferase domain of CBP and may lead to leukemia by promoting histone acetylation of genomic regions targeted by the MLL AT-hooks, leading to transcriptional deregulation via aberrant chromatin organization. CBP is the first partner gene of MLL containing well defined structural and functional motifs that provide unique insights into the potential mechanisms by which these translocations contribute to leukemogenesis.The t(11;16)(q23;p13.3) is a rare recurring translocation that has been described in 11 patients to date (1). All of these patients have therapy-related acute leukemia of myeloid or lymphoid phenotype, or myelodysplasia, after exposure to DNA topoisomerase II inhibitors (anthracyclines or epipodophyllotoxins) for treatment of a primary malignancy.MLL (also called ALL1, Htrx, and HRX; refs. 2-6), which is located on chromosomal band 11q23, is involved in translocations with at least 40 different partner genes (7-9). These translocations result in acute leukemia, either lymphoblastic or myeloid͞monocytic, with a close correlation between the specific translocation and a particular leukemia phenotype. MLL also is involved in translocations that occur secondary to therapy of a primary malignant disease with drugs that target DNA topoisomerase II and result in therapy-related acute myeloid leukemia or acute lymphoblastic leukemia (10-14). The t(11;16)(q23;p13.3) occurs only in therapy-related leukemia or myelodysplasia, in contrast to other MLL translocations such as the t(9;11), t(4;11), or t(11;19), which are seen primarily in de novo leukemia with no more than about 5-10% having leukemia occurring after treatment.MLL codes for a very large protein, with a predicted molecular mass of 431 kDa (4-6). The protein contains several domains identified by homology to other proteins or by functional analysis. Three AT-hook DNA-binding domains near the amino terminus also are found in the high-mobility group proteins HMG-I(Y) (15). MLL contains a region of homology to mammalian DNA methyltransferases, transcriptional activation and repression domains, and a cysteine-rich region that forms three C4HC3 zinc fingers [plant homeodomain (PHD) or leukemia-associated-protein domains] (16-21). The PHD domain and the SET [Su(var)3-9 enhancer of zeste, and trithorax] domain at the carboxyl terminus are the regions...

Background Clostridium botulinum and related clostridial species express extremely potent neurotoxins known as botulinum neurotoxins (BoNTs) that cause long-lasting, potentially fatal intoxications in humans and other mammals. The amino acid variation within the BoNT is used to categorize the species into seven immunologically distinct BoNT serotypes (A–G) which are further divided into subtypes. The BoNTs are located within two generally conserved gene arrangements known as botulinum progenitor complexes which encode toxin-associated proteins involved in toxin stability and expression.Methodology/Principal FindingsBecause serotype A and B strains are responsible for the vast majority of human botulism cases worldwide, the location, arrangement and sequences of genes from eight different toxin complexes representing four different BoNT/A subtypes (BoNT/A1-Ba4) and one BoNT/B1 strain were examined. The bivalent Ba4 strain contained both the BoNT/A4 and BoNT/bvB toxin clusters. The arrangements of the BoNT/A3 and BoNT/A4 subtypes differed from the BoNT/A1 strains and were similar to those of BoNT/A2. However, unlike the BoNT/A2 subtype, the toxin complex genes of BoNT/A3 and BoNT/A4 were found within large plasmids and not within the chromosome. In the Ba4 strain, both BoNT toxin clusters (A4 and bivalent B) were located within the same 270 kb plasmid, separated by 97 kb. Complete genomic sequencing of the BoNT/B1 strain also revealed that its toxin complex genes were located within a 149 kb plasmid and the BoNT/A3 complex is within a 267 kb plasmid.Conclusions/SignificanceDespite their size differences and the BoNT genes they contain, the three plasmids containing these toxin cluster genes share significant sequence identity. The presence of partial insertion sequence (IS) elements, evidence of recombination/gene duplication events, and the discovery of the BoNT/A3, BoNT/Ba4 and BoNT/B1 toxin complex genes within plasmids illustrate the different mechanisms by which these genes move among diverse genetic backgrounds of C. botulinum.

The growing potential of quantum dots (QDs) in applications as diverse as biomedicine and energy has provoked much dialogue about their conceivable impact on human health and the environment at large. Consequently, there has been an urgent need to understand their interaction with biological systems. Parameters such as size, composition, surface charge, and functionalization can be modified in ways to either enhance biocompatibility or reduce their deleterious effects. In the current study, we simultaneously compared the impact of size, charge, and functionalization alone or in combination on biological responses using primary normal human bronchial epithelial cells. Using a suite of cellular end points and gene expression analysis, we determined the biological impact of each of these properties. Our results suggest that positively charged QDs are significantly more cytotoxic compared to negative QDs. Furthermore, while QDs functionalized with long ligands were found to be more cytotoxic than those functionalized with short ligands, negative QDs functionalized with long ligands also demonstrated size-dependent cytotoxicity. We conclude that QD-elicited cytotoxicity is not a function of a single property but a combination of factors. The mechanism of toxicity was found to be independent of reactive oxygen species formation, as cellular viability could not be rescued in the presence of the antioxidant n-acetyl cysteine. Further exploring these responses at the molecular level, we found that the relatively benign negative QDs increased gene expression of proinflammatory cytokines and those associated with DNA damage, while the highly toxic positive QDs induced changes in genes associated with mitochondrial function. In an attempt to tentatively "rank" the contribution of each property in the observed QD-induced responses, we concluded that QD charge and ligand length, and to a lesser extent, size, are key factors that should be considered when engineering nanomaterials with minimal bioimpact (charge> functionalization > size).

We have sequenced a contiguous 284,495-bp segment of DNA extending from the terminal (TTAGGG)n repeats of the short arm of chromosome 16, providing a full description of the transition from telomeric through subtelomeric DNA to sequences that are unique to the chromosome. To complement and extend analysis of the primary sequence, we have characterized mRNA transcripts, patterns of DNA methylation and DNase I sensitivity. Together with previous data these studies describe in detail the structural and functional organization of a human telomeric region.