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.

Cohesin complexes mediate sister-chromatid cohesion in dividing cells but may also contribute to gene regulation in postmitotic cells. How cohesin regulates gene expression is not known. Here we describe cohesin-binding sites in the human genome and show that most of these are associated with the CCCTC-binding factor (CTCF), a zinc-finger protein required for transcriptional insulation. CTCF is dispensable for cohesin loading onto DNA, but is needed to enrich cohesin at specific binding sites. Cohesin enables CTCF to insulate promoters from distant enhancers and controls transcription at the H19/IGF2 (insulin-like growth factor 2) locus. This role of cohesin seems to be independent of its role in cohesion. We propose that cohesin functions as a transcriptional insulator, and speculate that subtle deficiencies in this function contribute to 'cohesinopathies' such as Cornelia de Lange syndrome.

Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wildtype samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

Sister chromatids, the products of eukaryotic DNA replication, are held together after their synthesis by the chromosomal cohesin complex. This allows the spindle in mitosis to recognise pairs of replication products for segregation into opposite direction1-6. Cohesin forms large protein rings that may bind DNA strands by encircling7, but the characterisation of cohesin binding to chromosomes in vivo has remained vague. Here, we present high resolution analysis of cohesin association along budding yeast chromosomes III -VI. Cohesin localises almost exclusively between genes transcribed in converging direction. We find that not the underlying sequence, but active transcription positions cohesin at these sites. Cohesin is initially loaded onto chromosomes at separate places, marked by the Scc2/Scc4 cohesin loading complex8, from where it appears to slide to its more permanent locations. But even after sister chromatid cohesion is established changes in transcription lead to repositioning of cohesin. Thus a key architectural feature of mitotic chromosomes, the sites of cohesin binding and therefore most likely sister chromatid cohesion, display surprising flexibility. Cohesin localisation to places of convergent transcription is conserved in fission yeast, suggesting that it is a common feature of eukaryotic chromosomes.Correspondence and requests for materials should be addressed to F.U. (e-mail: frank.uhlmann@cancer.org.uk).. * these authors contributed equally Supplementary Information accompanies the paper on Nature's website (http://www.nature.com). Cohesin association with yeast and human chromosomes has been studied4,9-15, but the defining characteristics of association sites, and how cohesin gets to these sites, remained unclear. We analysed cohesin binding to chromosome VI of the budding yeast Saccharomyces cerevisiae by chromatin immunoprecipitation (ChIP) followed by hybridisation to a high-density oligonucleotide array16. The pattern of association in metaphase was similar for all cohesin subunits analysed, Scc1, Scc3, Smc3, and Pds5 ( Fig. 1, and Supplementary Figure S1). It was also similar before the establishment of sister chromatid cohesion, in cells arrested with the replication inhibitor hydroxyurea (Ref. 9, and Supplementary Figure S1). Cohesin bound 28 distinct sites, each spanning 1-4 kilobases (kb) in width. The intensity of association varied, with the strongest peaks found around the centromere, consistent with previous analyses9-11. The distance between neighbouring cohesin association sites ranged from 2 to 35 kb. Almost all cohesin association sites were centred in intergenic regions where genes from opposite strands converged (Fig. 1a), as previously suggested17. Using an additional high-density array, we also mapped the association of Scc1 with chromosomes III, IV, and V (Supplementary Table 1 and Figure S2). 91% (276 of 304) cohesin association sites identified lie at intergenic regions between converging genes, and of 328 convergent intergene regions 84% were bound by cohes...

Segregation of homologous maternal and paternal centromeres to opposite poles during meiosis I depends on post-replicative crossing over between homologous non-sister chromatids, which creates chiasmata and therefore bivalent chromosomes. Destruction of sister chromatid cohesion along chromosome arms due to proteolytic cleavage of cohesin's Rec8 subunit by separase resolves chiasmata and thereby triggers the first meiotic division. This produces univalent chromosomes, the chromatids of which are held together by centromeric cohesin that has been protected from separase by shugoshin (Sgo1/MEI-S332) proteins. Here we show in both fission and budding yeast that Sgo1 recruits to centromeres a specific form of protein phosphatase 2A (PP2A). Its inactivation causes loss of centromeric cohesin at anaphase I and random segregation of sister centromeres at the second meiotic division. Artificial recruitment of PP2A to chromosome arms prevents Rec8 phosphorylation and hinders resolution of chiasmata. Our data are consistent with the notion that efficient cleavage of Rec8 requires phosphorylation of cohesin and that this is blocked by PP2A at meiosis I centromeres.

[Keywords: Chromosome condensation; condensin; Scc2/4; tRNA genes; TFIIIC] Supplemental material is available at http://www.genesdev.org.

Recent advances in DNA sequencers are accelerating genome sequencing, especially in microbes, and complete and draft genomes from various species have been sequenced in rapid succession. Here, we present a comprehensive gene prediction tool, the MetaGeneAnnotator (MGA), which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths. The MGA integrates statistical models of prophage genes, in addition to those of bacterial and archaeal genes, and also uses a self-training model from input sequences for predictions. As a result, the MGA sensitively detects not only typical genes but also atypical genes, such as horizontally transferred and prophage genes in a prokaryotic genome. In this paper, we also propose a novel approach for analyzing the ribosomal binding site (RBS), which enables us to detect species-specific patterns of the RBSs. The MGA has the ingenious RBS model based on this approach, and precisely predicts translation starts of genes. The MGA also succeeds in improving prediction accuracies for short sequences by using the adapted RBS models (96% sensitivity and 93% specificity for 700 bp fragments). These features of the MGA expedite wide ranges of microbial genome studies, such as genome annotations and metagenome analyses.

This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production.