H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

Compared with histone H3, acetylation of H4 tails has not been well studied, especially in mammalian cells. Yet, H4K16 acetylation is of particular interest because of its ability to decompact nucleosomes in vitro and its involvement in dosage compensation in flies. Here we show that, surprisingly, loss of H4K16 acetylation does not alter higher-order chromatin compaction in vivo in mouse embryonic stem cells (ESCs). As well as peaks of acetylated H4K16 and KAT8 histone acetyltransferase at the transcription start sites of expressed genes, we report that acetylation of H4K16 is a new marker of active enhancers in ESCs and that some enhancers are marked by H3K4me1, KAT8, and H4K16ac, but not by acetylated H3K27 or EP300, suggesting that they are novel EP300 independent regulatory elements. Our data suggest a broad role for different histone acetylation marks and for different histone acetyltransferases in long-range gene regulation.</jats:p

SBE6, a novel long-range enhancer involved in driving Sonic Hedgehog expression in neural progenitor cells

The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene (<i>Shh</i>) that plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells both <i>in vivo</i> and <i>in vitro. Shh</i> expression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh-Shh-brain-enhancer-6 (SBE6) that is located 100 kb upstream of <i>Shh</i> and that is required for the proper induction of <i>Shh</i> expression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled to <i>in vivo</i> testing, can be used to identify new cell-type specific <i>cis</i>-regulatory elements and points to yet further complexity in the control of <i>Shh</i> expression during embryonic brain development

DESIGN OF GEODETIC NETWORKS BASED ON OUTLIER IDENTIFICATION CRITERIA: AN EXAMPLE APPLIED TO THE LEVELING NETWORK

We present a numerical simulation method for designing geodetic networks. The quality criterion considered is based on the power of the test of data snooping testing procedure. This criterion expresses the probability of the data snooping to identify correctly an outlier. In general, the power of the test is defined theoretically. However, with the advent of the fast computers and large data storage systems, it can be estimated using numerical simulation. Here, the number of experiments in which the data snooping procedure identifies the outlier correctly is counted using Monte Carlos simulations. If the network configuration does not meet the reliability criterion at some part, then it can be improved by adding required observation to the surveying plan. The method does not use real observations. Thus, it depends on the geometrical configuration of the network; the uncertainty of the observations; and the size of outlier. The proposed method is demonstrated by practical application of one simulated leveling network. Results showed the needs of five additional observations between adjacent stations. The addition of these new observations improved the internal reliability of approximately 18%. Therefore, the final designed network must be able to identify and resist against the undetectable outliers – according to the probability levels

Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle

Even though every cell in a multicellular organism contains the same genes, the differing spatiotemporal expression of these genes determines the eventual phenotype of a cell. This means that each cell type contains a specific epigenetic program that needs to be replicated through cell divisions, along with the genome, in order to maintain cell identity. The stable inheritance of these programs throughout the cell cycle relies on several epigenetic mechanisms. In this review, DNA methylation and histone methylation by specific histone lysine methyltransferases (KMT) and the Polycomb/Trithorax proteins are considered as the primary mediators of epigenetic inheritance. In addition, non-coding RNAs and nuclear organization are implicated in the stable transfer of epigenetic information. Although most epigenetic modifications are reversible in nature, they can be stably maintained by self-recruitment of modifying protein complexes or maintenance of these complexes or structures through the cell cycle

Molecular marks for epigenetic identification of developmental and cancer stem cells

Epigenetic regulations of genes by reversible methylation of DNA (at the carbon-5 of cytosine) and numerous reversible modifications of histones play important roles in normal physiology and development, and epigenetic deregulations are associated with developmental disorders and various disease states, including cancer. Stem cells have the capacity to self-renew indefinitely. Similar to stem cells, some malignant cells have the capacity to divide indefinitely and are referred to as cancer stem cells. In recent times, direct correlation between epigenetic modifications and reprogramming of stem cell and cancer stem cell is emerging. Major discoveries were made with investigations on reprogramming gene products, also known as master regulators of totipotency and inducer of pluoripotency, namely, OCT4, NANOG, cMYC, SOX2, Klf4, and LIN28. The challenge to induce pluripotency is the insertion of four reprogramming genes (Oct4, Sox2, Klf4, and c-Myc) into the genome. There are always risks of silencing of these genes by epigenetic modifications in the host cells, particularly, when introduced through retroviral techniques. In this contribution, we will discuss some of the major discoveries on epigenetic modifications within the chromatin of various genes associated with cancer progression and cancer stem cells in comparison to normal development of stem cell. These modifications may be considered as molecular signatures for predicting disorders of development and for identifying disease states