We have isolated the gene for a protein designated CCAl. This protein can bind t o a region of the promoter of an Arabidopsis light-harvesting chlorophyll a/b protein gene, Lhcb7*3, which is necessary for its regulation by phytochrome. The CCAl protein interacted with two imperfect repeats in the Lhcb7*3 promoter, AAA/,AATCT, a sequence that is conserved in Lhcb genes. A region near the N terminus of CCA1, which has some homology t o the repeated sequence found in the DNA binding domain of Myb proteins, is required for binding t o the Lhcb7*3 promoter. Lines of transgenic Arabidopsis plants expressing antisense RNA for CCAl showed reduced phytochrome induction of the endogenous Lhcb7*3 gene, whereas expression of another phytochrome-regulated gene, rbcS-7A, which encodes the small subunit of ribulose-1 ,Bbisphosphate carboxylase/oxygenase, was not affected. Thus, the CCAl protein acts as a specific activator of Lhcb7*3 transcription in response t o brief red illumination. The expression of CCAl RNA was itself transiently increased when etiolated seedlings were transferred t o light. We conclude that the CCAl protein is a key element in the functioning of the phytochrome signal transduction pathway leading t o increased transcription of this Lhcb gene in Arabidopsis.

Imperfect maintenance of genome integrity has been postulated to be an important cause of aging. Here we provide support for this hypothesis by demonstrating that the disruption of PASG (lsh), a SNF2-like factor that facilitates DNA methylation, causes global hypomethylation, developmental growth retardation and a premature aging phenotype. PASG mutant mice display signs of growth retardation and premature aging, including low birth weight, failure to thrive, graying and loss of hair, reduced skin fat deposition, osteoporosis, kyphosis, cachexia, and premature death. Fibroblasts derived from PASG mutant embryos show a replicative senescence phenotype. Both PASG mutant mice and fibroblasts demonstrate a markedly increased expression of senescence-associated tumor suppressor genes, such as p16 INK4a, that is independent of promoter methylation, but, instead, is associated with down-regulation of bmi-1, a negative regulator of p16 INK4a. These studies show that PASG is essential for properly maintaining DNA methylation and gene expression patterns that are required for normal growth and longevity. PASG mutant mice provide a useful model for the study of aging as well as the mechanisms regulating epigenetic patterning during development and postnatal life.

The use of an HPLC bioactivity profiling/microtiter plate technique in conjunction with capillary probe NMR instrumentation and access to appropriate databases effectively short-circuits conventional dereplication procedures, necessarily based on multimilligram extracts, to a single, more rapid submilligram operation. This approach to dereplication is illustrated using fungal or bacterial extracts that contain known compounds. In each case the dereplication steps were carried out on microgram quantities of extract and demonstrate the discriminating power of (1)H NMR spectroscopy as a definitive dereplication tool.

Enhancers play a pivotal role in regulating the transcription of distal genes. Although certain chromatin features, such as the histone acetyltransferase P300 and the histone modification H3K4me1, indicate the presence of enhancers, only a fraction of enhancers are functionally active. Individual chromatin marks, such as H3K27ac and H3K27me3, have been identified to distinguish active from inactive enhancers. However, the systematic identification of the most informative single modification, or combination thereof, is still lacking. Furthermore, the discovery of enhancer RNAs (eRNAs) provides an alternative approach to directly predicting enhancer activity. However, it remains challenging to link chromatin modifications to eRNA transcription. Herein, we develop a logistic regression model to unravel the relationship between chromatin modifications and eRNA synthesis. We perform a systematic assessment of 24 chromatin modifications in fetal lung fibroblast and demonstrate that a combination of four modifications is sufficient to accurately predict eRNA transcription. Furthermore, we compare the ability of eRNAs and H3K27ac to discriminate enhancer activity. We demonstrate that eRNA is more indicative of enhancer activity. Finally, we apply our fibroblast trained model to six other cell-types and successfully predict eRNA synthesis. Thus, we demonstrate the learned relationships are general and independent of cell-type. We provided a powerful tool to identify active enhancers and reveal the relationship between chromatin modifications, eRNA production and enhancer activity.