LinkNMF: Identification of histone modification modules in the human genome using nonnegative matrix factorization

Histone modifications are ubiquitous processes involved in various cellular mechanisms. Systemic analysis of multiple chromatin modifications has been used to characterize various chromatin states associated with functional DNA elements, gene expression, and specific biological functions. However, identification of modular modification patterns is still required to understand the functional associations between histone modification patterns and specific chromatin/DNA binding factors. To recognize modular modification patterns, we developed a novel algorithm that combines nonnegative matrix factorization (NMF) and a clique-detection algorithm. We applied it, called LinkNMF, to generate a comprehensive modification map in human CD4 + T cell promoter regions. Initially, we identified 11 modules not recognized by conventional approaches. The modules were grouped into two major classes: gene activation and repression. We found that genes targeted by each module were enriched with distinguishable biological functions, suggesting that each modular pattern plays a unique functional role. To explain the formation of modular patterns, we investigated the module-specific binding patterns of chromatin regulators. Application of LinkNMF to histone modification maps of diverse cells and developmental stages will be helpful for understanding how histone modifications regulate gene expression. The algorithm is available on our website at biodb.kaist.ac.kr/LinkNMF.     

Histone modifying enzymes and cancer: going beyond histones

Mutations in the molecular pathways that regulate cell proliferation, differentiation, and cell death all contribute to cancer formation. Enzymes that covalently modify histones affect these pathways by controlling the dynamic remodeling of chromatin structure. This article reviews several connections between histone modifying enzymes and cancer that are likely mediated via both histone and non-histone substrates. We propose that multiple protein modifications, including phosphorylation, methylation, and acetylation, cross regulate one another to coordinate intermolecular signaling, and that miscues in this regulation can lead to oncogenesis.     

Estrogen regulation of trefoil factor 1 expression by estrogen receptor alpha and Sp proteins

Estrogen-responsive genes in human breast cancer cells often have an estrogen response element (ERE) positioned next to an Sp1 binding site. In chromatin immunoprecipitation (ChIP) assays, we investigated the binding of estrogen receptor alpha (ER), Sp1, and Sp3 to the episomal and native estrogen-responsive trefoil factor 1 (TFF1; formerly pS2) promoter in MCF-7 breast cancer cells. Mutation of the Sp site upstream of the ERE reduced estrogen responsiveness and prevented binding of Sp1 and Sp3, but not ER to the episomal promoter. In the absence of estradiol (E2), Sp1, Sp3, histone deacetylase 1 (HDAC), and HDAC2, and low levels of acetylated H3 and H4 are associated with the native promoter, with the histones being engaged in dynamic reversible acetylation. Following E2 addition, levels of ER and acetylated H3 and H4 bound to the native promoter increases. There is clearance of Sp1, but not of Sp3, from the promoter while HDAC1 and HDAC2 remain bound. These data are consistent with a model in which Sp1 or Sp3 aid in recruitment of HDACs and histone acetyltransferases (HATs) to mediate dynamic acetylation of histones associated with the TFF1 promoter, which is in a state of readiness to respond to events occurring following the addition of estrogen.     

Rice histone deacetylase genes display specific expression patterns and developmental functions

Histone deacetylases (HDAC) are important in plant gene expression. Here we show that the expression of rice HDAC genes is both tissue/organ-specific, and most of them are responsive to drought or salt stresses. Over-expression of several rice HDACs did not produce any visible phenotype, whereas down-regulation of a few HDAC genes affected different developmental aspects. Specifically, down-regulation of HDA703 by amiRNA reduced rice peduncle elongation and fertility, while inactivation of a closely related homolog HDA710 by RNAi affected vegetative growth. HDA704 RNAi altered plant height and flag leaf morphology. Down-regulation of HDT702 led to the production of narrowed leaves and stems. These data suggest that rice HDAC genes may have divergent developmental functions compared with closely related homologs in Arabidopsis.     

Structural characterization of Set1 RNA recognition motifs and their role in histone H3 lysine 4 methylation

The yeast Set1 histone H3 lysine 4 (H3K4) methyltransferase contains, in addition to its catalytic SET domain, a conserved RNA recognition motif (RRM1). We present here the crystal structure and the secondary structure assignment in solution of the Set1 RRM1. Although RRM1 has the expected betaalphabetabetaalphabeta RRM-fold, it lacks the typical RNA-binding features of these modules. RRM1 is not able to bind RNA by itself in vitro, but a construct combining RRM1 with a newly identified downstream RRM2 specifically binds RNA. In vivo, H3K4 methylation is not affected by a point mutation in RRM2 that preserves Set1 stability but affects RNA binding in vitro. In contrast mutating RRM1 destabilizes Set1 and leads to an increase of dimethylation of H3K4 at the 5'-coding region of active genes at the expense of trimethylation, whereas both, dimethylation decreases at the 3'-coding region. Taken together, our results suggest that Set1 RRMs bind RNA, but Set1 RNA-binding activity is not linked to H3K4 methylation.