Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes

Proteolytic processing of the CUX1 transcription factor generates an isoform, p110 that accelerates entry into S phase. To identify targets of p110 CUX1 that are involved in cell cycle progression, we performed genome-wide location analysis using a promoter microarray. Since there are no antibodies that specifically recognize p110, but not the full-length protein, we expressed physiological levels of a p110 isoform with two tags and purified chromatin by tandem affinity purification (ChAP). Conventional ChIP performed on synchronized populations of cells confirmed that p110 CUX1 is recruited to the promoter of cell cycle-related targets preferentially during S phase. Multiple approaches including silencing RNA (siRNA), transient infection with retroviral vectors, constitutive expression and reporter assays demonstrated that most cell cycle targets are activated whereas a few are repressed or not affected by p110 CUX1. Functional classes that were over-represented among targets included DNA replication initiation. Consistent with this finding, constitutive expression of p110 CUX1 led to a premature and more robust induction of replication genes during cell cycle progression, and stimulated the long-term replication of a plasmid bearing the oriP replicator of Epstein Barr virus (EBV).The pc3oriPE plasmid and helpful advices were kindly provided by Dr Lori Frappier. A.N. is the recipient of a scholarship from the Fonds de la Recherche en Sante´ du Québec. C.V. is the recipient of a studentship from the McGill University Cancer Consortium Training Grant in Cancer Research (sponsored by CIHR). F.R. holds a new investigator award from the CIHR. This research was supported by grant No. 014288 from the Canadian Cancer Society to A.N. and a grant from Genome Canada/ Génome Québec to F.R and A.N. Funding to pay the Open Access publication charges for this article was provided by grant No. 014288 from the Canadian Cancer Society to A.N

Long-range transcriptional regulation by the p110 CUX1 homeodomain protein on theENCODE array

Abstract Background Overexpression of the Cut homeobox 1 gene, CUX1, inverselycorrelates with patient survival in breast cancers. Cell-based assays andmolecular studies have revealed that transcriptional regulation byCUX1 involves mostly the proteolytically processed p110isoform. As there is no antibody specific to p110 CUX1 only, an alternatestrategy must be employed to identify its targets. Results We expressed physiological levels of a tagged-p110 CUX1 protein and performedchromatin affinity purification followed by hybridization on ENCODE andpromoter arrays. Targets were validated by chromatin immunoprecipitation andtranscriptional regulation by CUX1 was analyzed in expression profiling andRT-qPCR assays following CUX1 knockdown or p110 CUX1 overexpression.Approximately 47% and 14% of CUX1 binding sites were respectively mappedless than 4 Kbp, or more than 40 Kbp, away from a transcription start site.More genes exhibited changes in expression following CUX1 knockdown thanp110 CUX1 overexpression. CUX1 directly activated or repressed 7.4% and 8.4%of putative targets identified on the ENCODE and promoter arraysrespectively. This proportion increased to 11.2% for targets with 2 bindingsites or more. Transcriptional repression was observed in a slightly higherproportion of target genes. The CUX1 consensus binding motif, ATCRAT, wasfound at 47.2% of the CUX1 binding sites, yet only 8.3% of the CUX1consensus motifs present on the array were bound in vivo. Thepresence of a consensus binding motif did not have an impact on whether atarget gene was repressed or activated. Interestingly, the distance betweena binding site and a transcription start site did not significantly reducedthe ability of CUX1 to regulate a target gene. Moreover, CUX1 not only wasable to regulate the next adjacent gene, but also regulated the gene locatedbeyond this one as well as the gene located further away in the oppositedirection. Conclusion Our results demonstrate that p110 CUX1 can activate or repress transcriptionwhen bound at a distance and can regulate more than one gene on certaingenomic loci. </jats:sec

Kinetic and thermodynamic investigation of Arthrospira (Spirulina) platensis fed-batch cultivation in a tubular photobioreactor using urea as nitrogen source

BACKGROUND: Fed-batch culture allows the cultivation of Arthrospira platensis using urea as nitrogen source. Tubular photobioreactors substantially increase cell growth, but the successful use of this cheap nitrogen source requires a knowledge of the kinetic and thermodynamic parameters of the process. This work aims at identifying the effect of two independent variables, temperature (T) and urea daily molar flow-rate (U), on cell growth, biomass composition and thermodynamic parameters involved in this photosynthetic cultivation. RESULTS: The optimal values obtained were T = 32 degrees C and U = 1.16 mmol L-1 d-1, under which the maximum cell concentration was 4186 +/- 39 mg L-1, cell productivity 541 +/- 5 mg L-1 d-1 and yield of biomass on nitrogen 14.3 +/- 0.1 mg mg-1. Applying an Arrhenius-type approach, the thermodynamic parameters of growth (?H* = 98.2 kJ mol-1; ?S* = - 0.020 kJ mol-1 K-1; ?G* = 104.1 kJ mol-1) and its thermal inactivation (Delta H-D(0) =168.9 kJ mol-1; Delta S-D(0) = 0.459 kJ mol-1 K-1; Delta G(D)(0) =31.98 kJ mol-1) were estimated. CONCLUSIONS: To maximize cell growth T and U were simultaneously optimized. Biomass lipid content was not influenced by the experimental conditions, while protein content was dependent on both independent variables. Using urea as nitrogen source prevented the inhibitory effect already observed with ammonium salts. Copyright (c) 2012 Society of Chemical IndustryCNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico), Sao Paulo-BrazilCNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico), Sao PauloBrazi

Flocculant and Chemical Properties of a Polysaccharide from <i>Pullularia pullulans</i>

An extracellular polysaccharide, PP-floc, was synthesized from glucose by Pullularia pullulans (or Aureobasidium pullulans ) in a pilot plant batch fermentor containing 175 liters of culture medium. At 58 h of fermentation, the concentration of PP-floc was 1.03 g/100 ml, giving a 25.8% conversion of initial glucose to polysaccharide. The flocculant activity of the culture medium increased during the fermentation process and reached its maximum at 50 h of culture age. Less PP-floc (0.33 lb/ton of slimes [approximately 149.7 g/0.907 t]) was required to give the same flocculant activity as a synthetic polymer of acrylamide, Separan NP-10 (0.5 lb/ton of slimes [approximately 226.8 g/0.907 t]), at all temperatures from 25 to 100 C. The degree of inactivation of PP-floc and Separan NP-10 at elevated temperatures was almost identical, and they were completely inactivated at about the same temperature (80 C). PP-floc also gave better compaction of slimes than Separan NP-10 at all temperatures tested. PP-floc was soluble in water and its specific optical rotation was [α] D 25 + 194° in water (c, 0.4). PP-floc contained 83.3% carbohydrate, 3.2% protein, and 8.1% water. Glucose was found to be the principal sugar monomer with traces (&gt;5%) of galactose and mannose present. Structural studies on the fractions of purified polysaccharide by methylation and by periodate oxidation techniques prove that PP-floc is linear and composed of α-(1 → 4) and α-(1 → 6) glucopyranosyl units in the approximate ratio of 2:1. The action of pullulanase on crude PP-floc suggested the ordered arrangement of two consecutive α-(1 → 4)-linked glucopyranosyl units flanked by α-(1 → 6)-linked glucopyranose residues. </jats:p