FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

Motivation: Next generation sequencing technology generates high-throughput data, which allows us to detect fusion genes at both transcript and genomic levels. To detect fusion genes, the current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of reads that span fusion junctions. Thus there is a need to develop an efficient aligner to detect fusion events by accurate mapping of these junction-spanning single reads, particularly when the read gets longer with the improvement in sequencing technology.

Identification of the major sites of phosphorylation in IGF binding protein-3.

Insulin-like growth factor binding protein-3 (IGFBP-3) is the major carrier of insulin-like growth factor I and II in the circulation. IGFBP-3 is secreted by various tissues and cell lines as a glycosylated phosphoprotein. We have identified two major serine phosphorylation sites located at amino acids 111 and 113 of the human protein.

InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface.

InfoTrac TFD provides a graphical user interface (GUI) for viewing and manipulating datasets in the Transcription Factor Database, TFD. The interface was developed in Filemaker Pro 2.0 by Claris Corporation, which provides cross platform compatibility between Apple Macintosh computers running System 7.

Localization of the approximately 12 kDa M(r) discrepancy in gel migration of the mouse glucocorticoid receptor to the major phosphorylated cyanogen bromide fragment in the transactivating domain.

The intact wild-type mouse glucocorticoid receptor has a theoretical molecular weight of approximately 96 kDa based on amino acid sequence, but on SDS-polyacrylamide gel electrophoresis it migrates as a protein of approximately 98 kDa. It is not known where the unusual primary structure or covalent modification responsible for this anomalous migration is located within the amino acid chain. In the course of examining the pattern of fragmentation of 32P-labeled glucocorticoid receptors from Chinese hamster ovary (CHO) cells containing amplified mouse receptor cDNA, we have found a localized region in the amino-terminal half of the receptor that accounts for this anomalous behavior.

Cytoplasmic phospholipase A2 activity and gene expression are stimulated by tumor necrosis factor: dexamethasone blocks the induced synthesis.

The interaction of tumor necrosis factor alpha (TNF) with its two membrane-bound receptors initiates intracellular events in which arachidonic acid and its derivatives are involved. In HeLa cells, TNF treatment induces an arachidonic acid-selective, Ca(2+)-dependent cellular phospholipase A2 (cPLA2). By itself, TNF causes a modest increase in cPLA2 activity, but with the Ca2+ ionophore A23187 it provides a strong synergistic action.

Cloning and transcriptional regulation of a novel adipocyte-specific gene, FSP27. CAAT-enhancer-binding protein (C/EBP) and C/EBP-like proteins interact with sequences required for differentiation-dependent expression.

We have reported previously the cloning of several cDNAs whose mRNAs are induced during differentiation of the adipogenic cell line TA1. Here we characterize an adipocyte-specific gene, which we refer to as FSP27 (formerly clone 47), that encodes a protein of 27 kDa, the sequence of which is unrelated to any in the current data banks. The FSP27 promoter confers adipocyte-specific expression to a heterologous reporter gene in transfected adipogenic cell lines, e.

Surface expression of erbB-2 protein is post-transcriptionally regulated in mammary epithelial cells by epidermal growth factor and by the culture density.

The control of expression of the erbB-2 protein was examined in two mammary epithelial cells lines, HC11 and 31E. The erbB-2 protein content varied dramatically depending upon cell density and upon the presence of epidermal growth factor (EGF) in the culture medium. The changes in protein content were not due to variation in the erbB-2 mRNA level.

Overexpression of the glucocorticoid receptor represses transcription from hormone responsive and non-responsive promoters.

The glucocorticoid receptor (GR) is a regulable transcription factor which can bind to DNA response elements in the vicinity of inducible gene promoters and enhance the rate of transcription initiation. The concentration of endogenously expressed GR has been shown to limit the magnitude of the transcriptional induction response in cultured cells. We have investigated the consequence of increased GR expression on the transcriptional activity of a hormone responsive promoter, the MMTV LTR, and on three non-responsive promoters, the RSV LTR, the SV40 early promoter and the c-fos promoter in transiently transfected cells.

Localization of the vicinal dithiols involved in steroid binding to the rat glucocorticoid receptor.

Our previous studies with the thiol-specific reagent methyl methanethiolsulfonate (MMTS) and the vicinal dithiol-specific reagent sodium arsenite have established that 2 spatially close thiols (i.e. vicinal dithiols) are involved in steroid binding to the intact 98 K rat glucocorticoid receptor.

Hormone-dependent phosphorylation of the glucocorticoid receptor occurs mainly in the amino-terminal transactivation domain.

Phosphorylation of glucocorticoid receptors is increased by hormone binding and has been implicated in transcriptional regulation. We performed a phosphoamino acid analysis and identified the phosphorylated regions of the glucocorticoid receptor with respect to its functional domains before and after hormone activation. Receptor was isolated by immunoprecipitation from [32P]orthophosphate-labeled FTO 2B rat hepatoma cells grown in the absence or presence of glucocorticoids.

Down-regulation and phosphorylation of glucocorticoid receptors in cultured cells. Investigations with a monospecific antiserum against a bacterially expressed receptor fragment.

The expression of the glucocorticoid receptor (GR) gene and the phosphorylation of the GR protein has been studied as a function of time after hormone addition to NIH 3T3 cells. We detected a ligand-induced decrease of GR gene expression at both the level of RNA and protein. GR mRNA declined to 25% of the control within 3 h of dexamethasone treatment and remained at this level for at least 24 h.