HMO1 is a high-mobility group B protein that plays a role in transcription of genes encoding rRNA and ribosomal proteins (RPGs) in Saccharomyces cerevisiae. This study uses genome-wide chromatin immunoprecipitation to study the roles of HMO1, FHL1, and RAP1 in transcription of these genes as well as other RNA polymerase II-transcribed genes in yeast. The results show that HMO1 associates with the 35S rRNA gene in an RNA polymerase I-dependent manner and that RPG promoters (138 in total) can be classified into several distinct groups based on HMO1 abundance at the promoter and the HMO1 dependence of FHL1 and/or RAP1 binding to the promoter. FHL1, a key regulator of RPGs, binds to most of the HMO1-enriched and transcriptionally HMO1-dependent RPG promoters in an HMO1-dependent manner, whereas it binds to HMO1-limited RPG promoters in an HMO1-independent manner, irrespective of whether they are transcribed in an HMO1-dependent manner. Reporter gene assays indicate that these functional properties are determined by the promoter sequence.The yeast ribosome is composed of four rRNAs and 79 ribosomal proteins (RPs) (58, 73). Yeast rRNA genes occur as a tandem repeat of approximately 150 copies. The 25S, 18S, and 5.8S RNAs are transcribed by RNA polymerase I (Pol I), 5S RNA is transcribed by RNA Pol III, and the 138 RP genes (RPGs) are transcribed by RNA Pol II (58,73). In a rapidly growing cell, transcription of rRNA and RPGs accounts for approximately 60% of total transcription and 50% of Pol IImediated transcription, respectively (73), representing a large fraction of the total energy consumption of the cell. Little is known about the regulatory mechanisms involved in coordinating the transcription of rRNA and RPGs under various growth conditions. Recent studies showed that the TOR complex 1 (TORC1) plays a central role in regulating transcription of rRNA and RPGs in response to changes in the abundance of extracellular nutrients (44). Under favorable nutrient conditions, TORC1 is localized to the nucleus and directly binds to the 35S rDNA promoter to activate transcription by Pol I (36). TORC1 also indirectly regulates Pol II-mediated RPG transcription by recruiting IFH1, a coactivator for FHL1 (45,58,60,72). FHL1 was originally identified as a suppressor of a Pol III mutant (24) and was later shown to be important for RPG transcription (27,34,45,58,60,72). Under poor nutrient conditions, TORC1 is exported from the nucleus to the cytoplasm, so that the synthesis of 35S rRNA is substantially diminished (36). Concurrently, CRF1, a corepressor for FHL1, displaces IFH1 from RPG promoters to inhibit RPG transcription (45).HMO1 is a member of the high-mobility group B (HMGB) protein family, which include nonhistone proteins that bind to and have diverse roles in eukaryotic chromatin. HMGB proteins contain one or more distinctive DNA-binding motifs known as "HMG boxes" (11, 69). The HMG box is a conserved protein structural motif, in which three alpha helices are arranged in an L shape (55, 74). As the HMG box domain binds...

A switchlike response in nuclear factor-κB (NF-κB) activity implies the existence of a threshold in the NF-κB signaling module. We show that the CARD-containing MAGUK protein 1 (CARMA1, also called CARD11)-TAK1 (MAP3K7)-inhibitor of NF-κB (IκB) kinase-β (IKKβ) module is a switch mechanism for NF-κB activation in B cell receptor (BCR) signaling. Experimental and mathematical modeling analyses showed that IKK activity is regulated by positive feedback from IKKβ to TAK1, generating a steep dose response to BCR stimulation. Mutation of the scaffolding protein CARMA1 at serine-578, an IKKβ target, abrogated not only late TAK1 activity, but also the switchlike activation of NF-κB in single cells, suggesting that phosphorylation of this residue accounts for the feedback.

Acquired drug resistance is the major reason why patients fail to respond to cancer therapies. It is a challenging task to determine the tipping point of endocrine resistance and detect the associated molecules. Derived from new systems biology theory, the dynamic network biomarker (DNB) method is designed to quantitatively identify the tipping point of a drastic system transition and can theoretically identify DNB genes that play key roles in acquiring drug resistance. We analyzed time-course mRNA sequence data generated from the tamoxifen-treated estrogen receptor (ER)-positive MCF-7 cell line, and identified the tipping point of endocrine resistance with its leading molecules. The results show that there is interplay between gene mutations and DNB genes, in which the accumulated mutations eventually affect the DNB genes that subsequently cause the change of transcriptional landscape, enabling full-blown drug resistance. Survival analyses based on clinical datasets validated that the DNB genes were associated with the poor survival of breast cancer patients. The results provided the detection for the pre-resistance state or early signs of endocrine resistance. Our predictive method may greatly benefit the scheduling of treatments for complex diseases in which patients are exposed to considerably different drugs and may become drug resistant.

Saccharomyces cerevisiae HMO1, a high mobility group B (HMGB) protein, associates with the rRNA locus and with the promoters of many ribosomal protein genes (RPGs). Here, the Sos recruitment system was used to show that HMO1 interacts with TBP and the N-terminal domain (TAND) of TAF1, which are integral components of TFIID. Biochemical studies revealed that HMO1 copurifies with TFIID and directly interacts with TBP but not with TAND. Deletion of HMO1 (Δhmo1) causes a severe cold-sensitive growth defect and decreases transcription of some TAND-dependent genes. Δhmo1 also affects TFIID occupancy at some RPG promoters in a promoter-specific manner. Interestingly, over-expression of HMO1 delays colony formation of taf1 mutants lacking TAND (taf1ΔTAND), but not of the wild-type strain, indicating a functional link between HMO1 and TAND. Furthermore, Δhmo1 exhibits synthetic growth defects in some spt15 (TBP) and toa1 (TFIIA) mutants while it rescues growth defects of some sua7 (TFIIB) mutants. Importantly, Δhmo1 causes an upstream shift in transcriptional start sites of RPS5, RPS16A, RPL23B, RPL27B and RPL32, but not of RPS31, RPL10, TEF2 and ADH1, indicating that HMO1 may participate in start site selection of a subset of class II genes presumably via its interaction with TFIID.

In unicellular and multicellular eukaryotes, elaborate gene regulatory mechanisms facilitate a broad range of biological processes from cell division to morphological differentiation. In order to fully understand the gene regulatory networks involved in these biological processes, the spatial and temporal patterns of expression of many thousands of genes will need to be determined in real time in living organisms. Currently available techniques are not sufficient to achieve this goal; however, novel methods based on magnetic resonance (MR) imaging may be particularly useful for sensitive detection of gene expression in opaque tissues. This report describes a novel reporter gene system that monitors gene expression dynamically and quantitatively, in yeast cells, by measuring the accumulation of inorganic polyphosphate (polyP) using MR spectroscopy (MRS) or MR spectroscopic imaging (MRI). Because this system is completely non-invasive and does not require exogenous substrates, it is a powerful tool for studying gene expression in multicellular organisms, as well.

The micromeres of sea urchin embryos have two functions: to promote the autonomous differentiation of skeletogenic cells and to induce endomesodermal tissues. Micromere specification is controlled by a double-repression gate consisting of two repressors, Pmar1 and HesC. Micro1/pmar1 encodes a transcriptional repressor with a paired-type N-terminal homeodomain and two C-terminal serine-rich repeats, each of which includes a sequence similar to engrailed homology region 1, which interacts with the co-repressor Groucho. To understand the molecular mechanisms of the double-repression gate, we examined the correlation between the structure and function of micro1. Phenotypic and gene expression pattern analyses of embryos injected with mutated micro1 mRNA revealed that micro1 consists of five functional domain and motifs; namely, a DNA-binding homeodomain, a nuclear localization signal in the C-terminal flanking region of the homeodomain, and two eh1-like motifs plus a short C-terminal stretch that together mediate transcriptional repression. Our data suggest that micro1 represses target genes, including hesC, via two redundant means: its eh1-like and C-terminal motifs. The C-terminal motif requires unidentified sequences for micro1 function; a micro1 mutant with the motif but lacking the unidentified sequences failed to trigger the double-repression gate for early micromere regulatory genes, except for delta, though it did repress hesC. Our results suggest that the spatial regulation of primary mesenchyme cell specification genes, including tbr, alx1, and ets1, may be different from that of delta.

General transcription factor TFIID is comprised of TATAbinding protein (TBP) and TBP-associated factors (TAFs), together playing critical roles in regulation of transcription initiation. The TAF N-terminal domain (TAND) of yeast TAF1 containing two subdomains, TAND1 (residues 10 -37) and TAND2 (residues 46 -71), is sufficient to interact with TBP and suppress the TATA binding activity of TBP. However, the detailed structural analysis of the complex between yeast TBP and TAND12 (residues 6 -71) was hindered by its poor solubility and stability in solution. Here we report a molecular engineering approach where the N terminus of TBP is fused to the C terminus of TAND12 via linkers of various lengths containing (GGGS) n sequence, (n ‫؍‬ 1, 2, 3). The length of the linker within the TAND12-TBP fusion has a significant effect on solubility and stability (SAS). The construct with (GGGS) 3 linker produces the best quality single-quantum-coherence (HSQC) NMR spectrum with markedly improved SAS. In parallel to these observations, the TAND12-TBP fusion exhibits marked reduction of TBP function in binding to TAF1 as well as temperature sensitivity in in vivo yeast cell growth. Remarkably, the temperature sensitivity was proportional to the length of the linker in the fusions: the construct with (GGGS) 3 linker did not grow at 20°C, while those with (GGGS) 1 and (GGGS) 2 linkers did. These results together indicate that the native interaction between TBP and TAND12 is well maintained in the TAND12-(GGGS) 3 -TBP fusion and that this fusion approach provides an excellent model system to investigate the structural detail of the TBP-TAF1 interaction.

CRK and CRKL (CRK-like) encode adapter proteins with similar biochemical properties. Here, we show that a 50% reduction of the family-combined dosage generates developmental defects, including aspects of DiGeorge/del22q11 syndrome in mice. Like the mouse homologs of two 22q11.21 genes CRKL and TBX1, Crk and Tbx1 also genetically interact, thus suggesting that pathways shared by the three genes participate in organogenesis affected in the syndrome. We also show that Crk and Crkl are required during mesoderm development, and Crk/Crkl deficiency results in small cell size and abnormal mesenchyme behavior in primary embryonic fibroblasts. Our systems-wide analyses reveal impaired glycolysis, associated with low Hif1a protein levels as well as reduced histone H3K27 acetylation in several key glycolysis genes. Furthermore, Crk/Crkl deficiency sensitizes MEFs to 2-deoxy-D-glucose, a competitive inhibitor of glycolysis, to induce cell blebbing. Activated Rapgef1, a Crk/Crkl-downstream effector, rescues several aspects of the cell phenotype, including proliferation, cell size, focal adhesions, and phosphorylation of p70 S6k1 and ribosomal protein S6. Our investigations demonstrate that Crk/Crkl-shared pathways orchestrate metabolic homeostasis and cell behavior through widespread epigenetic controls.