ATP-dependent chromatin remodeling complex SWI/SNF in cardiogenesis and cardiac progenitor cell development

The recent identification of cardiac progenitor cells (CPCs) provides a new paradigm for studying and treating heart disease.To realize the full potential of CPCs for therapeutic purposes,it is essenti...     

The ways of PARP

Two papers in this issue of Cell describe two roles of poly(ADP-ribose) polymerase (PARP) in modulating chromatin structure: as a structural component replacing linker histone (Kim et al., 2004) and as a constituent of a corepressor complex poised to dismiss repression upon receipt of an activating signal (Ju et al., 2004).     

Stopping for FISH and chips along the chromatin fiber superhighway

Gilbert et al. (2004) report in a recent issue of Cell on the analysis of chromatin fiber structure across the human genome. They show that compact chromatin fibers are composed of heterochromatin but also contain some active genes, while open chromatin fibers correlate with regions of highest gene density, but not with gene expression.     

A crack in histone lysine methylation

Histone lysine methylation is regarded as a very stable modification with important functions in epigenetic gene control and for organizing chromatin domains. While more robust modifications of the chromatin template are essential to stabilize epigenetic information, there is now the first evidence for a histone lysine demethylase that reverts an activating methyl mark to the unmodified state (Shi et al., 2004 [this issue of Cell]).     

Watching the DNA repair ensemble dance

Repair of damaged DNA is a dynamic process that requires careful orchestration of a multitude of enzymes, adaptor proteins, and chromatin constituents. In this issue of Cell, Lisby et al. (2004) provide a visual glimpse into how the diverse signaling and repair machines are organized in space and time around the deadliest genetic lesions--the DNA double-strand breaks.     

采自云南热带雨林的中国多孔菌两新记录种

<正>1 INTRODUCTION Wood-rotting fungi have been intensively studied in China (Dai & Niemel? 2002; Dai et al. 2003, 2004a, 2004b; Dai & Penttil? 2006), and some new species and new records were found from     

O2 sensing: only skin deep?

In this issue, two papers implicate histone H3 lysine 56 acetylation in histone deposition in chromatin. Li et al. (2008) show that acetylation of H3K56 promotes S phase chromatin assembly that is mediated by the histone chaperones CAF-1 and Rtt106. Chen et al. (2008) establish that the acetylation mark promotes chromatin reassembly following DNA double-strand break repair.     

CAR: three new models for a problem child

By comparison with its older and better-behaved cousins in the nuclear receptor superfamily, CAR (NR1I3) has always been an oddball. Three new crystal structures recently described in Molecular Cell reveal the molecular basis for some of its bad habits (Xu et al., 2004; Suino et al., 2004; Shan et al., 2004).     

When pouring water on the fire makes it burn brighter

By comparison with its older and better-behaved cousins in the nuclear receptor superfamily, CAR (NR1I3) has always been an oddball. Three new crystal structures recently described in Molecular Cell reveal the molecular basis for some of its bad habits (Xu et al., 2004; Suino et al., 2004; Shan et al., 2004).     

Heterotrimeric G proteins: new tricks for an old dog

Heterotrimeric G proteins are well known for their function in signal transduction downstream of seven transmembrane receptors. More recently, however, genetic analysis in C. elegans and in Drosophila has revealed a second, essential function of these molecules in positioning the mitotic spindle and attaching microtubules to the cell cortex. Five new publications in Cell (Afshar et al., 2004; Du and Macara, 2004 [this issue of Cell]; Hess et al., 2004), Developmental Cell (Martin-McCaffrey et al., 2004), and Current Biology (Couwenbergs et al., 2004) show that this function is conserved in vertebrates and--like the classical pathway--involves cycling of G proteins between GDP and GTP bound conformations.     

The anchorosome, a special chromatin granule for the anchorage of the interphase chromosome to the nuclear envelope

Peripheral chromatin granules bound to the nuclear envelope of rat liver nuclei have been further investigated. Judging by the results of Staphylococcal nuclease digestion of nuclei and electron microscopical observations, the peripheral granules have nucleosomal organization. As shown by ultraviolet radiation DNA-protein cross-linkage, the histone-like proteins present in the peripheral chromatin instead of histone H1 (Fais et al., 1982) are in close contact with DNA. The peripheral chromatin contains a DNA firmly bound to the lamina. This DNA, resistant to extraction in high salt, heparin and SDS, is protected against a DNase attack since, as shown by DNA electrophoresis data, high molecular weight molecules (up to 20 kbas) are still present in the lamina residue. However, the high molecular weight DNA disappeared if the nuclear envelope fraction was again DNase-digested after high salt treatment. Altogether, the data of the previous (Fais et al., 1982; Prusov et al., 1980: Prusov et al., 1982) and the present investigations demonstrate that the peripheral chromatin granules are endowed with properties which distinguish them from the bulk chromatin and account for the chromosome bond to the nuclear envelope during interphase. This is why we suggest the term "anchorosome" for the peripheral protein granule attached to the nuclear envelope.     

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.Chromatin has a major impact on genome organization and gene activity. Differential accessibility of DNA is thought to be a major consequence of locally different chromatin composition and structure (Li et al., 2007). Chromatin sensitivity to nucleases has proven to be a powerful tool to probe DNA accessibility in chromatin. Frequently used nucleases include DNase, micrococcal nuclease, and restriction enzymes. The resolution of restriction enzymes is limited by their sequence specificity, and micrococcal nuclease is more often used to determine nucleosome occupancy (Schones and Zhao, 2008). Chromatin sensitivity to DNase I has often been used to define the “openness” of chromatin relative to its higher order structures. Its applicability has been manifested by detecting regulatory elements, such as promoters, enhancers, and insulators, as DNase I-hypersensitive sites (Wang and Simpson, 2001; Crawford et al., 2004, 2006; Dorschner et al., 2004; Sabo et al., 2006; Boyle et al., 2008; Naughton et al., 2010; Pique-Regi et al., 2011). DNase I sensitivity can also be used as a measure for the general accessibility of chromatin (Weil et al., 2004).Initially, the chromatin accessibility of local genomic regions to DNase I was probed by Southern blotting (Mather and Perry, 1983; Bender et al., 2000; Wang and Simpson, 2001; Bulger et al., 2003). However, Southern blotting is tedious and lacks sensitivity, and the interpretation of results can be challenging. Therefore, analysis methods based on PCR have been developed (Pfeifer and Riggs, 1991; Feng and Villeponteau, 1992; McArthur et al., 2001; Dorschner et al., 2004; Martins et al., 2007). In recent years, DNase I assays were coupled to high-throughput genome-wide profiling strategies such as genome tiling arrays and next-generation sequencing (Crawford et al., 2004, 2006; Sabo et al., 2004, 2006; Weil et al., 2004). While much has been learned about the accessibility of chromatin in animal and yeast systems, our knowledge of chromatin accessibility in plants is limited. Most studies have focused on selected genomic regions such as the general regulatory factor1 (GRF1) gene and the alcohol dehydrogenase1 (Adh1) and Adh2 genes in maize (Zea mays; Paul and Ferl, 1998a, 1998b) or the GRF gene, the Adh gene, and an 80-kb genomic region harboring 30 protein-coding genes in Arabidopsis (Arabidopsis thaliana; Vega-Palas and Ferl, 1995; Paul and Ferl, 1998a, 1998b; Kodama et al., 2007). The technique used in these reports was exclusively DNase I treatment and analysis of accessibility using Southern blotting. More recently, we have combined the DNase I sensitivity assay with whole-genome tiling arrays in Arabidopsis to generate a genome-wide chromatin accessibility profile (Shu et al., 2012).Here, we present a robust, optimized DNase I sensitivity assay protocol for Arabidopsis tissues based on PCR. This protocol can be adapted to different samples or experimental objectives; the strategies for optimizing each step are also discussed. Analysis of relatively large fragments by PCR has proven to be highly robust as a first step in probing DNase I sensitivity in any region of the genome. We also introduce a new strategy for presenting the DNase I sensitivity of the tested regions using a decay constant calculated by fitting PCR product intensity values from a gradient digestion. In this way, the sensitivity of each region is characterized by a single value, facilitating comparisons between different regions or samples. Finally, we describe how our protocol can be combined with genomic techniques for genome-wide profiles of chromatin accessibility.     

mRNA turnover meets RNA interference

By using two very different approaches, recent work by Gazzani et al. (2004) and Souret et al. (2004) reveal a fundamental link between mRNA degradation and RNA silencing pathways in Arabidopsis.     

Unraveling epigenetic landscapes: the enigma of enhancers

In recent publications in Nature and PNAS, Rada-Iglesias et?al. (2010) and Creyghton et?al. (2010) have uncovered unique chromatin signatures of developmental enhancers marking active, primed, or silent genes in human and mouse embryonic stem cells.     

Silence of the rings

Two recent papers (de Napoles et al., 2004 and Wang et al., 2004) have linked monoubiquitylation of histone H2A to the activities of E3 ubiquitin ligases that reside in Polycomb-group repressor complexes.     

A two-way street: LSD1 regulates chromatin boundary formation in S. pombe and Drosophila

Two recent studies in Molecular Cell (Lan et al., 2007; Rudolph et al., 2007) implicate histone demethylation by LSD1 in the regulation of boundaries between silenced and active chromatin domains in both fission yeast and flies, but by distinct mechanisms.