In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs.

Reproduction-specific small RNAs are vital regulators of germline development in animals and plants. MicroRNA2118 (miR2118) is conserved in plants and induces the production of phased small interfering RNAs (phasiRNAs). To reveal the biological functions of miR2118, we describe here rice mutants with large deletions of the miR2118 cluster. Our results demonstrate that the loss of miR2118 causes severe male and female sterility in rice, associated with marked morphological and developmental abnormalities in somatic anther wall cells. Small RNA profiling reveals that miR2118-dependent 21-nucleotide (nt) phasiRNAs in the anther wall are U-rich, distinct from the phasiRNAs in germ cells. Furthermore, the miR2118-dependent biogenesis of 21-nt phasiRNAs may involve the Argonaute proteins OsAGO1b/OsAGO1d, which are abundant in anther wall cell layers. Our study highlights the site-specific differences of phasiRNAs between somatic anther wall and germ cells, and demonstrates the significance of miR2118/U-phasiRNA functions in anther wall development and rice reproduction.

Here we demonstrate a purely electrochemical approach for monitoring the electric field-induced melting of surface-bound DNA duplexes tethered to gold surfaces using standard surface attachment chemistry, i.e. single thiol-Au bonds. The sensitivity of square wave voltammetry is combined with the electric fields generated during programmed sequences of chronoamperometric pulses to enable a method for DNA analysis that can be carried out at room temperature without need for parallel spectroscopic monitoring. Electrochemical melting curves are obtained using both scanning potential pulses and constant potential pulses, which are analyzed to assess duplex stability and the extent of thiol desorption. The melting behavior is found to depend on the pulse potential and pule time. Under optimized conditions, thiol reduction is minimized and DNA duplexes can be discriminated based on the presence of a single base pair mismatch. The method is found to be less sensitive to the duplex length, presumably due to the rapid decay of the electric field away from the electrode surface. Based on these results, a simple model is proposed in which maintenance of the double-layer charge by accumulation of ions from the bulk of solution competes with electric field-induced loss of the negatively-charged DNA at a given applied potential.

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BackgroundNucleosome, the fundamental unit of chromatin, is formed by wrapping nearly 147bp of DNA around an octamer of histone proteins. This histone core has many variants that are different from each other by their biochemical compositions as well as biological functions. Although the deposition of histone variants onto chromatin has been implicated in many important biological processes, such as transcription and replication, the mechanisms of how they are deposited on target sites are still obscure.ResultsBy analyzing genomic sequences of nucleosomes bearing different histone variants from human, including H2A.Z, H3.3 and both (H3.3/H2A.Z, so-called double variant histones), we found that genomic sequence contributes in part to determining target sites for different histone variants. Moreover, dinucleotides CA/TG are remarkably important in distinguishing target sites of H2A.Z-only nucleosomes with those of H3.3-containing (both H3.3-only and double variant) nucleosomes.ConclusionsThere exists a DNA-related mechanism regulating the deposition of different histone variants onto chromatin and biological outcomes thereof. This provides additional insights into epigenetic regulatory mechanisms of many important cellular processes.

Abstract-Post-translational modifications (PTMs) of histone proteins play critical roles in establishing functionally separated domains on chromatin and regulating important biological processes, such as transcription. These modifications often act in cooperative manner, forming complicated "histone codes". Elucidation of functional relationships among them will, therefore, significantly increase our understanding of cell differentiation, development, and cancer pathogenesis. Biological evidence has shown that nucleosome positioning can provide invaluable information about interactive effects of PTMs. However, to our knowledge, none of previous works has exploited this information in the reconstruction of histone modification networks.We propose a computational approach based on Bayesian network to reconstruct a network representing functional relationships of histone modifications. Our approach employed the search-and-score method to infer the network structure using interactive information of histone modifications, which is measured by the correlation between each modification with nucleosome positioning. When applied on human CD4+ T cell ChIP-Seq dataset, containing 38 different histone modifications and binding information of three other proteins, H2A.Z, PolII and CTCF, our method not only outperformed previous approaches in recovering known relationships but also suggested many new ones, confirming its validity and efficiency. Our unbiased method for inferring the network structure can also be applied to reconstruct interaction networks of other epigenetic factors.

BackgroundEukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by regulating the accessibility of regulatory elements to biological machineries. Although it has been known that various factors, such as DNA sequences, histone modifications, and chromatin remodelling complexes, could affect nucleosome stability, the mechanisms of how they regulate this stability are still unclear.ResultsIn this paper, we propose a novel computational method based on rule induction learning to characterize nucleosome dynamics using both genomic and histone modification information. When applied on S. cerevisiae data, our method produced totally 98 rules characterizing nucleosome dynamics on chromosome III and promoter regions. Analyzing these rules we discovered that, some DNA motifs and post-translational modifications of histone proteins play significant roles in regulating nucleosome stability. Notably, these DNA motifs are strong determinants for nucleosome forming and inhibiting potential; and these histone modifications have strong relation with transcriptional activities, i.e. activation and repression. We also found some new patterns which may reflect the cooperation between these two factors in regulating the stability of nucleosomes.ConclusionDNA motifs and histone modifications can individually and, in some cases, cooperatively regulate nucleosome stability. This suggests additional insights into mechanisms by which cells control important biological processes, such as transcription, replication, and DNA repair.

MotivationHistone proteins are subject to various posttranslational modifications (PTMs). Elucidating their functional relationships is crucial toward understanding many biological processes. Bayesian network (BN)-based approaches have shown the advantage of revealing causal relationships, rather than simple cooccurrences, of PTMs. Previous works employing BNs to infer causal relationships of PTMs require that all confounders should be included. This assumption, however, is unavoidably violated given the fact that several modifications are often regulated by a common but unobserved factor. An existing non-parametric method can be applied to tackle the problem but the complexity and inflexibility make it impractical.ResultsWe propose a novel BN-based method to infer causal relationships of histone modifications. First, from the evidence that nucleosome organization in vivo significantly affects the activities of PTM regulators working on chromatin substrate, hidden confounders of PTMs are selectively introduced by an information-theoretic criterion. Causal relationships are then inferred from a network model of both PTMs and the derived confounders. Application on human epigenomic data shows the advantage of the proposed method, in terms of computational performance and support from literature. Requiring less strict data assumptions also makes it more practical. Interestingly, analysis of the most significant relationships suggests that the proposed method can recover biologically relevant causal effects between histone modifications, which should be important for future investigation of histone crosstalk.