Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.

;We characterized three Arabidopsis genes, AtpOMT1, AtpDCT1 and AtpDCT2, localized on chromosome 5 and homologous to spinach chloroplastic 2-oxoglutarate/malate transporter (OMT) gene. The yeast-expressed recombinant AtpOMT1 protein transported malate and 2-oxoglutarate but not glutamate. By contrast, the recombinant AtpDCT1 protein transported 2-oxoglutarate and glutamate at similar affinities in exchange for malate. These findings suggested that AtpOMT1 is OMT and AtpDCT1 is a general dicarboxylate transporter (DCT). The recombinant proteins could also transport oxaloacetate at the same binding sites for dicarboxylates. In particular, the AtpOMT1 had a K m value for oxaloacetate one order of magnitude lower than those for malate and 2-oxoglutarate. Although the transcripts for the three genes were accumulated in all tissues examined, the expression of the genes in leaf tissues was light inducible. The expression of the three genes was also induced by nitrate supplement but the induction was most prominent and transient in AtpOMT1 similar to nitrate reductase gene. These findings lead to a proposition that AtpOMT1 functions as an oxaloacetate transporter in the malate-oxaloacetate shuttle across chloroplast membranes. We identified T-DNA insertional mutants of AtpOMT1 and AtpDCT1. Although the AtpOMT1 mutants could grow normally in normal air, the AtpDCT1 mutants were non-viable under the same conditions. The AtpDCT1 mutants were able to grow under the high CO 2 condition to suppress photorespiration. These findings suggested that at least AtpDCT1 is a necessary component for photorespiratory nitrogen recycling.

SummaryLight-induced lumenal acidi®cation controls the ef®ciency of light harvesting by inducing thermal dissipation of excess absorbed light energy in photosystem II. We isolated an Arabidopsis mutant, pgr1 (proton gradient regulation), entirely lacking thermal dissipation, which was observed as little nonphotochemical quenching of chlorophyll¯uorescence. Map-based cloning showed that pgr1 had a point mutation in petC encoding the Rieske subunit of the cytochrome b 6 f complex. Although the electron transport rate was not affected at low light intensity, it was signi®cantly restricted at high light intensity in pgr1, indicating that the lumenal acidi®cation was not suf®cient to induce thermal dissipation. This view was supported by (i) slow de-epoxidation of violaXanthin, which is closely related to lumenal acidi®cation, and (ii) reduced 9-aminoacridine¯uorescence quenching. Although lumenal acidi®cation was insuf®cient to induce thermal dissipation, growth rate was not affected under low light growth conditions in pgr1. These results suggest that thermal dissipation is precisely regulated by lumenal pH to maintain maximum photosynthetic activity. We showed that pgr1 was sensitive to changes in light conditions, demonstrating that maximum activity of the cytochrome b 6 f complex is indispensable for short-term acclimation.

Alkaline hydrolysis liberated ferulic and diferulic acid from polysaccharides of the Avena coleoptile (Avena sativa L. cv. Victory I) cell walls. The amount of the two phenolic acids bound to cell walls increased substantially at day 4–5 after sowing, when the growth rate of the coleoptile started to decrease. The level of these acids was almost constant from the tip to base in 3‐day‐old coleoptiles, but increased toward the basal zone in 4‐ and 5‐day‐old ones. The ratio of diferulic acid to ferulic acid was almost constant irrespective of coleoptile age and zone. An increase in the amount of ferulic and diferulic acids bound to cell wall polysaccharides correlated with a decrease in extensibility and with an increase in minimum stress‐relaxation time and relaxation rate of the cell wall. The level of lignin in the cellulose fraction increased as coleoptiles aged, but this increase did not correlate with changes in mechanical properties of the cell walls. These results suggest that ferulic acid, ester‐linked to cell wall polysaccharides, is oxidized to give diferulic acid, which makes the cell wall mechanically rigid by cross‐linking matrix polysaccharides and results in limited cell extension growth. In addition, it is probable that the step of feruloylation of cell wall polysaccharides is rate‐limiting in the formation of in‐termolecular bridges by diferulic acid in Avena coleoptile cell walls.

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