Mapping and analysis of chromatin state dynamics in nine human cell types

Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.     

A unique chromatin signature uncovers early developmental enhancers in humans

Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.     

Alternative sets of DNase I-hypersensitive sites characterize the various functional states of the chicken lysozyme gene

The structural organization of chromatin is thought to determine the state of differentiation and activity of eukaryotic genes. Local interruptions of the regular nucleosomal array, the so-called DNase-hypersensitive sites, may indicate regions of the genome which play a critical part in regulation of differential gene activity. We present here two new observations on the chromatin structure of the chicken lysozyme gene, which strongly support a regulatory function for these sites. First, different sets of DNase I-hypersensitive sites have been found upstream from the promoter, depending on whether the gene is constitutively expressed (cultured macrophages) or in the steroid hormone-controlled state (oviduct). It seems, therefore, that diverse modes of regulation of the same gene are associated with discrete patterns of DNase I hypersensitivity. Second, one of the DNase I-hypersensitive sites in the oviduct chromatin disappears and reappears on steroid hormone withdrawal and secondary induction. These reversible changes in a narrow chromatin region reflect the transition from the potentially active to the active state of the lysozyme gene.     

Determinants of nucleosome organization in primary human cells

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.     

Novel developmental specificity in the nervous system of transgenic animals expressing growth hormone fusion genes

The development of methods for introducing foreign genes into the germ line of mice provides an approach for studying mechanisms underlying inducible and developmental gene regulation. Transgenic animals expressing foreign genes have thus been used to test models of the role played by specific DNA sequences in determining cell-specific expression. Results from these experiments suggest that tissue-specific expression is the consequence of a cis-acting regulatory sequence. However, these results do not exclude the possibility that cell-specific expression of some genes might be 'coded' by combinations of regulatory elements. We have previously described the production of transgenic mice from eggs microinjected with metallothionein-I/growth hormone (MGH) fusion genes, and now demonstrate that the juxtaposition of sequences from two different genes can be deciphered by cells to generate novel tissue specificities. Although expression of the endogenous metallothionein and growth hormone genes has not been detected in neuronal cells, transgenic mice clearly express an MGH fusion gene in a restricted subset of neurones. These results suggest a model in which tissue-specific patterns of expression of certain genes are determined by combinations of cis-acting regulatory sequences.     

原生动物四膜虫(TetrahymenaS1)高迁移率非组蛋白的研究

利用原生动物四膜虫(Tetrahymena shanghaiensis S1)作材料,经高氯酸抽提,丙酮沉淀等方法,制备取得高迁移率的非组蛋白。在高分辨率的乙酸一脲电泳图谱上,具有小牛胸腺所具有的典型的全部蛋白带。此外还含有一些未经检测的蛋白带。作者认为这些多余蛋白带可能是四膜虫所特有的高迁移率的非组蛋白。