Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

Within 15 years the web has grown from a group work tool for scientists at CERN into a global information space with more than a billion users. Currently, it is both returning to its roots as a read/write tool and also entering a new, more social and participatory stage. These trends have led to a feeling that the web is entering a ‘second phase’ – a new, ‘improved’ Web version 2.0. But how justified is this perception?

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What is Web 2.0? Ideas, technologies and implications for education

Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.

/pdf/rna-interference-biology-mechanism-and-applications-ww381qhd6t.pdf

RNA Interference: Biology, Mechanism, and Applications

Copy number variants (CNVs) contribute to human genetic and phenotypic diversity. However, the distribution of larger CNVs in the general population remains largely unexplored. We identify large variants in ∼2500 individuals by using Illumina SNP data, with an emphasis on “hotspots” prone to recurrent mutations. We find variants larger than 500 kb in 5%–10% of individuals and variants greater than 1 Mb in 1%–2%. In contrast to previous studies, we find limited evidence for stratification of CNVs in geographically distinct human populations. Importantly, our sample size permits a robust distinction between truly rare and polymorphic but low-frequency copy number variation. We find that a significant fraction of individual CNVs larger than 100 kb are rare and that both gene density and size are strongly anticorrelated with allele frequency. Thus, although large CNVs commonly exist in normal individuals, which suggests that size alone can not be used as a predictor of pathogenicity, such variation is generally deleterious. Considering these observations, we combine our data with published CNVs from more than 12,000 individuals contrasting control and neurological disease collections. This analysis identifies known disease loci and highlights additional CNVs (e.g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%–1%) CNVs in the general population, with insights relevant to future analyses of genetic disease.

https://www.cell.com/ajhg/pdf/S0002-9297(09)00002-0.pdf

Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

Materials and Methods related to gene targeting (e.g., gene targeting with transcription activator-like effector nucleases; “TALENS”) are provided.

Tal effector-mediated dna modification

NATURE REVIEWS | GENETICS VOLUME 4 | AUGUST 2003 | 581 have been known to transcribe in an unregulated way in yeast; if the same is true in Tetrahymena then their transcription betrays their existence to the genome surveillance machinery. Herein lies the next big question, for we still do not know the mechanism that underlies the deletion itself. Based on their data and previous observations, the authors propose that the dsRNA marks the DNA to be removed in a way that is similar to that in which RNA contributes to heterochromatin formation in fission yeast and plants, and to DNA methylation in plants. By extension, they suggest that RISC-like complex might mediate deletions, although a more prosaic culprit such as a nonspecific endonuclease or a recombinase cannot be ruled out at present. Magdalena Skipper References and links ORIGINAL RESEARCH PAPER Yao, M.-C. et al. Programmed DNA deletion as an RNA-guided system of genome defense. Science 300, 1581–1584 (2003)

Who's doing the dirty work for MYC?

Phase II of the International HapMap Project has just been published, adding substantial amounts of human genetic variation data to the Phase I release and providing important insights for the design of gene association studies. Phase II involved genotyping 3.1 million SNPs from the same populations as Phase I. The increased SNP density — to about one SNP per kilobase — provides higher-resolution fine-scale genetic maps, and facilitates detection and localization of recombination hotspots. Because the newly identified SNPs have lower minor allele frequencies than those from Phase I, rare variation is better represented. Importantly for genome-wide association studies, ~25–35% of all common SNPs are thought to have been genotyped, correlating with up to 95% of all common SNPs. Although currently available arrays capture 68–88% of this variation, analytical approaches that use the HapMap data can further increase the value of these arrays. The new data provide two important insights into the structure of linkage disequilibrium. First, the apparent long-range similarity among haplotypes reveals recent common ancestry and inbreeding within populations. The high-quality haplotype data is a further asset for genome-wide association studies, as haplotype-sharing approaches can complement standard SNP association tests and should be especially useful to identify potential rare variants that are associated with complex diseases. Second, despite high SNP density, no tag could be identified for up to 1% of all highfrequency SNPs (a tag is a SNP that provides information on other variants nearby). Most of these untaggable SNPs lie in recombination hotspots, suggesting that regions of interest that contain hotspots might require additional sequencing to identify variants. Another new insight is that hotspots account for ~60% of recombination in the human genome and for 6% of its sequence. Recombination is lower in transcribed genic regions and peaks 5′ of transcription start sites, although most hotspots do not lie in promoters. Average recombination rates vary among gene classes, with defense and immunity genes having the highest and chaperoneencoding genes having the lowest rates. The authors propose that recombination might be favoured in regions that are exposed to recurrent selection (for example, from the environment or by pathogens). Now that the fleshed out HapMap is available, what is the future of the HapMap project? Additional samples and populations will need to be sequenced and genotyped to provide information on rarer variants. Other important goals will involve generating molecular phenotypes for the HapMap samples and integrating SNP information with structural variation. Magdalena Skipper

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Genomics: HapMap Phase II unveiled

/pdf/transcriptomics-the-no-longer-uncharted-territory-4zvwg1uaoc.pdf

Transcriptomics: The no-longer uncharted territory

Damage takes control

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Magdalena Skipper

Papers

Who's doing the dirty work for MYC?

Genomics: HapMap Phase II unveiled

Transcriptomics: The no-longer uncharted territory

Damage takes control

Genomics: Of mice and... fish