Understanding the complexity and dynamics of cancer cells in response to effective therapy requires hypothesis-driven, quantitative, and high-throughput measurement of genes and proteins at both spatial and temporal levels. This study was designed to gain insights into molecular networks underlying the clinical synergy between retinoic acid (RA) and arsenic trioxide (ATO) in acute promyelocytic leukemia (APL), which results in a high-quality disease-free survival in most patients after consolidation with conventional chemotherapy. We have applied an approach integrating cDNA microarray, 2D gel electrophoresis with MS, and methods of computational biology to study the effects on APL cell line NB4 treated with RA, ATO, and the combination of the two agents and collected in a time series. Numerous features were revealed that indicated the coordinated regulation of molecular networks from various aspects of granulocytic differentiation and apoptosis at the transcriptome and proteome levels. These features include an array of transcription factors and cofactors, activation of calcium signaling, stimulation of the IFN pathway, activation of the proteasome system, degradation of the PML-RAR␣ oncoprotein, restoration of the nuclear body, cell-cycle arrest, and gain of apoptotic potential. Hence, this investigation has provided not only a detailed understanding of the combined therapeutic effects of RA͞ATO in APL but also a road map to approach hematopoietic malignancies at the systems level.systems biology ͉ self-organizing map A cute promyelocytic leukemia (APL) is a form of acute myeloid leukemia that responds remarkably to the effect of differentiation-induction by all-trans-retinoic acid and the differentiation͞ apoptosis-inducing effect of arsenic trioxide (ATO). Cytogenetically, a translocation t(15;17)(q22;q21) is found in most APL patients, resulting in the formation of the promyelocytic leukemiaretinoic acid receptor ␣ (PML-RAR␣) fusion gene (1). The chimeric protein encoded by the fusion gene oligomerizes with retinoid-X receptor (RXR) and disrupts the retinoic acid (RA) signal pathway, which is essential for granulocytic differentiation. PML-RAR␣ can also form a homodimer that competes with RAR␣ for binding to the RA-response elements of target genes and binds to the corepressor (CoR) complex with a much higher affinity than does the wild-type RAR␣͞RXR. This change leads to transcriptional repression under physiological concentrations of RA and, thus, blocks cell differentiation. Pharmacological concentrations of RA can convert the PML-RAR␣ fusion protein from a transcription repressor to a transcription activator, resulting in the release of the CoR and the recruitment of a coactivator (CoA) complex. The RA treatment can also trigger degradation of the PML-RAR␣ protein via the ubiquitin͞proteasome (U͞P) pathway and, thus, trigger reassembly of the nuclear body (NB) (2). On the other hand, ATO induces partial differentiation and͞or apoptosis of APL cells in a dose-dependent manner. Importantly, cellular and m...

Histone methylation plays an important role in eukaryotic transcriptional regulation. A number of histone methyltransferases (HMTases) with distinct functions have been identified. The HSPC069/HYPB gene was originally isolated from the human hematopoietic stem/progenitor cells (HSPCs), and it was also identified as a huntingtin interacting protein, implicated in the pathogenesis of Huntington disease (HD). However, its biochemical function is poorly understood. Here we report the structural and functional characterization of the huntingtin interacting protein B (HYPB). 1) The triplicate AWS-SET-PostSET domains mediate a histone H3 lysine 36 specific HMTase activity. 2) A low charged region that is rich in glutamine and proline has been characterized as a novel transcriptional activation domain. The structural features of this region are evolutionarily conserved in vertebrates. 3) Coimmunoprecipitation assays indicate that HYPB protein associates with hyperphosphorylated RNA polymerase II (RNAPII) but not the unphosphorylated form. Furthermore, the RNAPII-association region of HYPB protein has been identified to encompass the C-terminal 142 amino acids. Thus, our results suggest that HYPB HMTase may coordinate histone methylation and transcriptional regulation in mammals and open perspective for the further study of the potential roles of HYPB protein in hematopoiesis and pathogenesis of HD.Nucleosome, the bead-like unit of DNA packaging in eukaryotic cells, consists of DNA wound around a protein core made up of eight histone molecules. Covalent modifications of the N-terminal tails of the core histones have emerged as key regulatory mechanisms of gene expression (1-3). These histone modifications, including acetylation, phosphorylation, ubiquitination, and methylation, create both synergistic and antagonistic signals that correlate with the transcriptional activity of a gene, through recruiting/dispelling some protein complexes or through changing the structure of chromatin to allow access for RNA polymerase to initiate transcription. Moreover, these histone modifications and the consequent changes in chromatin structure may serve as an epigenetic marking system that is responsible for establishing and maintaining the heritable programs of gene expression during cellular differentiation and organism development (4, 5).Methylations of histone lysine residues, with exception of H3 lysine 79, are catalyzed by a family of SET domain-containing proteins (6). The SET domain is an evolutionarily conserved, ϳ130-amino acid sequence motif. It was originally identified in members of polycomb group (PcG), trithorax group (trxG), and Su(var) genes and was named after the genes Su(var)3-9, Enhancer of zeste (E(z)) and trithorax (trx) (7). Not all SET domain-containing proteins possess histone methyltransferase (HMTase) 5 activities. The cysteine-rich regions adjacent to the SET domains are also required (8,9). In addition to the SET domains, most HMTases carry other functional domains such as transcriptional activation or re...