Ken-ichi Wakabayashi

The Peroxisome Proliferator-Activated Receptor γ/Retinoid X Receptor α Heterodimer Targets the Histone Modification Enzyme PR-Set7/Setd8 Gene and Regulates Adipogenesis through a Positive Feedback Loop

ABSTRACT Control of cell differentiation occurs through transcriptional mechanisms and through epigenetic modification. Using a chromatin immunoprecipitation-on-chip approach, we performed a genome-wide search for target genes of peroxisome proliferator-activated receptor γ (PPARγ) and its partner protein retinoid X receptor α during adipogenesis. We show that these two receptors target several genes that encode histone lysine methyltransferase SET domain proteins. The histone H4 Lys 20 (H4K20) monomethyltransferase PR-Set7/Setd8 gene is upregulated by PPARγ during adipogenesis, and the knockdown of PR-Set7/Setd8 suppressed adipogenesis. Intriguingly, monomethylated H4K20 (H4K20me1) levels are robustly increased toward the end of differentiation. PR-Set7/Setd8 positively regulates the expression of PPARγ and its targets through H4K20 monomethylation. Furthermore, the activation of PPARγ transcriptional activity leads to the induction of H4K20me1 modification of PPARγ and its targets and thereby promotes adipogenesis. We also show that PPARγ targets PPARγ2 and promotes its gene expression through H4K20 monomethylation. Our results connect transcriptional regulation and epigenetic chromatin modulation through H4K20 monomethylation during adipogenesis through a feedback loop.

COUP-TFII acts downstream of Wnt/β-catenin signal to silence PPARγ gene expression and repress adipogenesis

Wnt signaling through β-catenin and TCF maintains preadipocytes in an un-differentiated proliferative state; however, the molecular pathway has not been completely defined. By integrating gene expression microarray, chromatin immunoprecipitation-chip, and cell-based experimental approaches, we show that Wnt/β-catenin signaling activates the expression of COUP-TFII which recruits the SMRT corepressor complex to the first introns located downstream from the first exons of both PPARγ1 and γ2 mRNAs. This maintains the local chromatin in a hypoacetylated state and represses PPARγ gene expression to inhibit adipogenesis. Our experiments define the COUP-TFII/SMRT complex as a previously unappreciated component of the linear pathway that directly links Wnt/β-catenin signaling to repression of PPARγ gene expression and the inhibition of adipogenesis.

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type–specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI) transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA–mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our study demonstrates the utility of FAIRE-seq in providing a global view of cell type–specific regulatory elements in the genome and in identifying transcriptional regulators of adipocyte differentiation.

Modulation of Chlamydomonas reinhardtii flagellar motility by redox poise

Redox-based regulatory systems are essential for many cellular activities. Chlamydomonas reinhardtii exhibits alterations in motile behavior in response to different light conditions (photokinesis). We hypothesized that photokinesis is signaled by variations in cytoplasmic redox poise resulting from changes in chloroplast activity. We found that this effect requires photosystem I, which generates reduced NADPH. We also observed that photokinetic changes in beat frequency and duration of the photophobic response could be obtained by altering oxidative/reductive stress. Analysis of reactivated cell models revealed that this redox poise effect is mediated through the outer dynein arms (ODAs). Although the global redox state of the thioredoxin-related ODA light chains LC3 and LC5 and the redox-sensitive Ca2+-binding subunit of the docking complex DC3 did not change upon light/dark transitions, we did observe significant alterations in their interactions with other flagellar components via mixed disulfides. These data indicate that redox poise directly affects ODAs and suggest that it may act in the control of flagellar motility.

Ca2+-dependent waveform conversion in the flagellar axoneme of Chlamydomonas mutants lacking the central-pair/radial spoke system

Chlamydomonas flagella undergo a striking waveform conversion from an asymmetrical ciliary type to a symmetrical flagellar type when the cell is stimulated by intense light and the Ca2+ concentration within the flagellum is increased above approximately 10(-6) M. To see whether the central-pair/radial spoke system is needed for this conversion as suggested by previous studies, we examined the effect of Ca2+ on the reactivated axonemes of the mutants lacking the central pair (pf18) or the radial spokes (pf14). Although the flagella of these mutants are paralyzed in vivo, demembranated axonemes can be reactivated to beat under certain nucleotide conditions such as in the presence of low concentrations (< 100 microM) of ATP. We examined the waveform of the axonemes reactivated at 20 microM ATP in the presence of 10(-8)-10(-4) M Ca2+ and found that these axonemes, as well as the wild-type axonemes, undergo a waveform conversion over a Ca2+ concentration range of 10(-7)-10(-5) M: a highly asymmetrical waveform at <10(-6) M Ca2+ and a symmetrical waveform at >=10(-5) M Ca2+. Although the waveform is different between the mutants and the wild type, the Ca2+ concentration at which the waveform conversion occurred was similar. These results indicate that the central pair/radial spoke system is not essential for the waveform conversion.

The role of retrograde intraflagellar transport in flagellar assembly, maintenance, and function

An inducible dynein heavy chain 1b mutant reveals that robust retrograde intraflagellar transport is required for flagellar assembly and function but not the maintenance of flagellar length.

Reduction-oxidation poise regulates the sign of phototaxis in Chlamydomonas reinhardtii

In many phototrophic microorganisms and plants, chloroplasts change their positions relative to the incident light to achieve optimal photosynthesis. In the case of motile green algae, cells change their swimming direction by switching between positive and negative phototaxis, i.e., swimming toward or away from the light source, depending on environmental and internal conditions. However, little is known about the molecular signals that determine the phototactic direction. Using the green alga Chlamydomonas reinhardtii, we found that cellular reduction-oxidation (redox) poise plays a key role: Cells always exhibited positive phototaxis after treatment with reactive oxygen species (ROS) and always displayed negative phototaxis after treatment with ROS quenchers. The redox-dependent switching of the sign of phototaxis may contribute in turn to the maintenance of cellular redox homeostasis.

EXTRACHROMOSOMAL INHERITANCE OF OLIGOMYCIN RESISTANCE IN YEAST

Yeast mitochondria have several features in common with bacteria [l-3] including similar sensitivity of their protein synthesis to antibiotics [ 1,4] . These antibiotics inhibit the growth of yeast when non-fermentable carbon sources are used. Erythromycin resistant mutants were isolated by use of this property [S] . The resistance was inherited in non-Mendelian way and was linked to p [6,7] , in contrast to chromosomal inheritance of resistance to other drugs such as actidione [S-lo]. Chromosomal inheritance of oligomycin resistance was recently reported [ 111. We have isolated a mutant resistant to oligomycin using 2,6diaminopurine; this resistance was inherited cytoplasmically but was not removed by acriflavine nor by introduction of a nuclear gene which changed p+ to p-. Therefore the gene involved in this resistance was cytoplasmic but was not linked to p.

Calcium-dependent flagellar motility activation in Chlamydomonas reinhardtii in response to mechanical agitation.

Flagellar beating in Chlamydomonas was found to be activated by mechanical stimulation. Immediately after a wild-type cell suspension was vortexed, the average swimming velocity of cells increased from 130 mum/second to 150 mum/second, due to an elevation of flagellar beat frequency from approximately 60 Hz to approximately 70 Hz without detectable change in the flagellar waveforms. This response required outer arm dynein. Treatment with EGTA, Ca(2+)-channel blockers, or mechanosensitive-channel blockers inhibited it. In demembranated and reactivated cell models, a modest increase in Ca(2+) concentration elevated the axonemal beat frequency. These data indicate that the mechanical agitation increases beat frequency because it causes Ca(2+) influx into flagella, which then activates outer arm dynein.

Cooperative binding of the outer arm-docking complex underlies the regular arrangement of outer arm dynein in the axoneme

Significance In eukaryotic cilia and flagella, outer arm dyneins (OADs) are bound to axonemal doublet microtubules every 24 nm; however, how this regular arrangement is produced remains unknown. To approach this problem, we studied the properties of the OAD-docking complex (ODA-DC), a three-subunit complex that functions as the OAD-docking site on the doublet. Using recombinant ODA-DC, we found that the ODA-DC has an ∼24-nm-long ellipsoidal shape and cooperatively binds to the axoneme in an end-to-end manner. These and other results indicate that cooperative association of the ODA-DC underlies the periodic OAD arrangement at specific positions on the doublets. These findings provide insight into how the regular axonemal repeat structure is produced. Outer arm dynein (OAD) in cilia and flagella is bound to the outer doublet microtubules every 24 nm. Periodic binding of OADs at specific sites is important for efficient cilia/flagella beating; however, the molecular mechanism that specifies OAD arrangement remains elusive. Studies using the green alga Chlamydomonas reinhardtii have shown that the OAD-docking complex (ODA-DC), a heterotrimeric complex present at the OAD base, functions as the OAD docking site on the doublet. We find that the ODA–DC has an ellipsoidal shape ∼24 nm in length. In mutant axonemes that lack OAD but retain the ODA-DC, ODA-DC molecules are aligned in an end-to-end manner along the outer doublets. When flagella of a mutant lacking ODA-DCs are supplied with ODA-DCs upon gamete fusion, ODA-DC molecules first bind to the mutant axonemes in the proximal region, and the occupied region gradually extends toward the tip, followed by binding of OADs. This and other results indicate that a cooperative association of the ODA-DC underlies its function as the OAD-docking site and is the determinant of the 24-nm periodicity.