We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding ;183 haploid coverage of aligned sequence and close to 3003 clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed matepaired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased segments of up to 215 kb. We detect 226,529 intra-read indels, 5590 indels between mate-paired reads, 91 inversions, and four gene fusions. We use a novel approach for detecting indels between mate-paired reads that are smaller than the standard deviation of the insert size of the library and discover deletions in common with those detected with our intra-read approach. Dozens of mutations previously described in OMIM and hundreds of nonsynonymous single-nucleotide and structural variants in genes previously implicated in disease are identified in this individual. There is more genetic variation in the human genome still to be uncovered, and we provide guidance for future surveys in populations and cancer biopsies.[Supplemental material is available online at

Deletion of any one of three subunits of the yeast Mediator of transcriptional regulation, Med2, Pgd1 (Hrs1), and Sin4, abolished activation by Gal4-VP16 in vitro. By contrast, other Mediator functions, stimulation of basal transcription and of TFIIH kinase activity, were unaffected. A different but overlapping Mediator subunit dependence was found for activation by Gcn4. The genetic requirements for activation in vivo were closely coincident with those in vitro. A whole genome expression profile of a ⌬med2 strain showed diminished transcription of a subset of inducible genes but only minor effects on ''basal'' transcription. These findings make an important connection between transcriptional activation in vitro and in vivo, and identify Mediator as a ''global'' transcriptional coactivator.Mediator was discovered as an activity in a crude yeast fraction able to relieve activator inhibition (1) and required for an activator response in a partially reconstituted RNA polymerase II transcription system (2). Mediator was initially resolved to homogeneity (3) by displacement from a complex with polymerase II (''holoenzyme''), and proved to contain the products of three groups of genes: SRBs, recovered from a genetic screen for CTD-interacting proteins (4, 5); the SIN4͞ RGR1 group, whose founding members were obtained from screens for mutations affecting repression (5, 6); and the MED genes, not previously identified in any screen (7,8). Functional analysis of purified Mediator in a transcription system reconstituted from essentially homogeneous proteins revealed three biochemical activities, stimulation of basal transcription, support of activated transcription, and stimulation of CTD phosphorylation by TFIIH (3,8). Activated transcription occurred in the absence of TATA boxing-binding protein associated factors (TAFs), consistent with the lack of a TAF requirement for regulation of most yeast promoters in vivo (9-10). The outstanding question regarding Mediator has been whether it too might prove to be dispensable for regulation in vivo, or whether it plays a general role in activated transcription in vivo, in keeping with the biochemical results.Work done to date has begun to address the physiologic relevance of Mediator and the relationship between its functions in vivo and in vitro. Cells harboring a temperaturesensitive mutation in SRB4 ceased transcription of all promoters analyzed at the restrictive temperature, indicating a widespread requirement for Mediator, though not distinguishing between roles in basal and activated transcription (11). A temperature-sensitive mutation in MED6 was shown to diminish activation by Gal4 in vivo and by VP16 in vitro, but because two different activators were used, the effects could not be correlated (7). Finally, CTD truncation has been shown to impair activation in vivo (12) and in vitro (8); the CTD interacts with Mediator in vitro (8, 13), enabling a correlation, but only an indirect one.Here we use multiple activators and Mediator mutants in a combined biochemical...

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