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Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylatuon throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes. [ABSTRACT FROM AUTHOR]

Background: Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings. Results: We tested our aligner on synthetic data, a bisulfite-converted Arabidopsis library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP and BSMAP. Furthermore, BS Seeker is the only alignment tool that can explicitly account for tags which are generated by certain library construction protocols. Conclusions: BS Seeker provides fast and accurate mapping of bisulfite-converted reads. It can work with BS reads generated from the two different experimental protocols, and is able to efficiently map reads to large mammalian genomes. The Python program is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html. [ABSTRACT FROM AUTHOR]

This paper demonstrates that histone H3 lysine 27 methylation is a major gene-silencing histone modification in plants. [ABSTRACT FROM AUTHOR]

For each m × n real matrix A, let Null(A) be the right nullspace of A and let Q(A) be the set of m × n real matrices with the same sign pattern as A. If it is true for all à ∈ Q(A) that (i) Null(Ã) = {0}, then A is an L-matrix, and if it is true for all à ∈ Q(A) that (ii) Null(Ã) is a line penetrating the open positive orthant of Rn, then A is an S-matrix. When (i) or (ii) holds for each à ∈ Q(A) and (ii) applies to at least one, then A is a CS-matrix. It is known that the study of sign-solvability of linear systems may be decomposed into the study of L- and S-matrices, while the study of conditional sign-solvability may be decomposed into that of L- and CS-matrices. When sign-solvability and conditional sign-solvability are regarded as properties of systems of sign cones in Rm associated with the relevant matrices' columns, they have natural generalizations to systems of arbitrary subsets of Rm. This paper contains extended decomposition results for arbitrary systems in the case of sign-solvability, and in the case of conditional sign-solvability, for arbitrary systems of subsets in which each subset is relatively open in its linear span. [ABSTRACT FROM AUTHOR]

Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes. [ABSTRACT FROM AUTHOR]