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USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function that shapes the transcriptional network in mouse embryonic stem cells (mESCs) remains poorly understood. We report that USP7 maintains mESC identity through both catalytic activity–dependent and –independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 levels and derepresses lineage differentiation genes thereby compromising mESC pluripotency. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant Polycomb repressive complex 1 and contributes to Polycomb chromatin–mediated repression of ME lineage genes in a catalytic activity–dependent manner. USP7 deficiency in its deubiquitination function is able to maintain RYBP binding to chromatin for repressing primitive endoderm–associated genes. Our study demonstrates that USP7 harbors both catalytic and noncatalytic activities to repress different lineage differentiation genes, thereby revealing a previously unrecognized role in controlling gene expression for maintaining mESC identity.

SUMMARYThe first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and an outer functional epithelium called trophectoderm (TE). The lineage specific transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4) by inhibiting OCT4 from promoting its own expression. However its downstream network in the developing early embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify components of the CDX2-regulated network in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells, derived from the TE. In addition, we examined the dynamics of gene expression changes using an inducible CDX2 embryonic stem (ES) cell system, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we were able to identify novel regulatory elements that are likely to repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells. In addition, we examined the dynamics of gene expression changes using inducible CDX2 embryonic stem (ES) cells, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we identify putative novel regulatory elements that repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

Photosynthetic activities and thylakoid membrane protein patterns as well as the ultrastructure of chloroplasts in flag leaves were investigated during the senescence processes in high-yield hybrid rice LYPJ under field condition. The earlier decrease of PS I activity than PS II in LYPJ was primarily due to the significant degradation of PS I chlorophyll–protein complex. The degradation rate for each chlorophyll–protein complex was different and the order for the stability of thylakoid membrane complexes during flag leaf senescence in rice LYPJ was: LHCII > OEC > PSII core antenna > PSII core > PSI core > LHCI, which was partly supported by the BN-PAGE gel combined with immunoblot analysis. A decrease in the chlorophyll a/b ratio at the senescence stage was observed to coincide with stability of the LHCII subunits. Ultrastructural investigations revealed that the chloroplasts have large loosen stacking grana without interconnecting stroma thylakoids during the senescence processes. It was hypothesized that the stability of grana thylakoids harboring the major LHCII under high radiation condition in summer might played a key role in the dissipation of excess light energy. This alternative strategy would protect photosynthetic apparatus from photodamage and might be causally related to the high yield of this rice cultivar.

The current study compares responses to open field and shade enclosure condition (plastic shading nets were used to imitate a natural shading rate) to test the possible benefit of shading in terms of physiological and growth characteristics in Ginkgo biloba L. during the reproductive stage in summer. Compared with the net shade treated plants (NS-plants), the open-field plants (O-plants) contained lower chlorophyll (Chl) a + b content and Chl a/b ratio, and exhibited a decreased ratio of Chl/Car. Results showed that the chlorophyll fluorescence characteristics including maximum PSII photochemical efficiency (F v /F m ), potential electron transport per excited leaf cross-section (ET0/CS0), potential electron transport per PSII reaction center (ET0/RC), dissipation per excited leaf cross-section (DI0/CS0), dissipation per PSII reaction center (DI0/RC), and overall performance index of PSII photochemistry on absorbtion basis (PIABS) were altered by the net shade treatment. It was observed that the grana were illegible and difficult to distinguish by transmission electron microscopy, especially, in the cells of O-plants in which phenols were observed in the vacuole. The phenomenon of photoinhibition induced by excessive irradiance was confirmed by the abnormally high levels of the reactive oxygen species. Moreover, antioxidant enzymes activities were induced by high irradiance in the ginkgo leaves. In addition, significant differences were observed in the fresh weight and dry weight of leaves and seeds. Comparison of the variation of underlying physiological and biochemical mechanisms suggested that there was a better efficiency of ginkgo plants under artificial net shade conditions. Therefore, ginkgo plant would be best grown at 30–35 % of natural irradiance in summer months to be more profitably harvested and then meet the increasing demand of leaves and seeds.

Cadmium contamination is a critical constraint to plant production in agricultural soils in some regions. Cerium is one of the rare earth elements, it plays a positive role in plant growth with a appropriate content. The present study was conducted to examine the role of cerium nutrition in the amelioration of effects on cadmium toxicity in rice (Oryza sativa L.) seedlings by a hydroponic experiment. Measurements included growth condition, photosynthesis related parameters, chloroplast ultra-structure and antioxidant enzymes content. Our results showed that the growth of rice seedlings was markedly inhibited by cadmium (100 μM), and the inhibition was significantly alleviated by cerium (10 μM). Fresh weight, single seedling height and chlorophyll content of rice plants in cerium treated groups were increased by 24.4, 18.2 and 32.05 % compared to those of plants cultivated in only cadmium-present condition. Additionally, in cadmium treated plants, the addition of cerium significantly increased the value of the maximum quantum yield of primary photochemistry (F v /F m ), indicator of PSII ‘structure and functioning’ (SFI ABS ) and the performance index on absorption basis (PI ABS ), elevated the activity of whole chain electron transport activity, enhanced photophosphorylation and its coupling factor Ca2+-ATPase activities. The result showed that the chloroplasts and thylakoid membrane of the rice seedlings leaves grown in cerium treatment developed better than that in cerium-absent group under cadmium toxicity. Moreover, addition with 10 μM cerium mitigated cadmium stress by inducing leaf enzyme activities for antioxidation like superoxide dismutase, peroxidase and catalase, dramatically depressed superoxide (O 2 ·− ), hydrogen peroxide and malondialdehyde accumulation. Results indicated that alleviation of cadmium toxicity by cerium application is partly related to improved light-use-efficiency, increased antioxidant enzymes, decreased oxidative stress in rice seedlings.

A proteomic analysis combining photosynthesis-related key enzymes measurement and mRNA level analysis was used to investigate the variations of proteins involved in the photosynthetic apparatus in flag leaves of high-yield rice LYPJ during senescence under field conditions. The stability of chlorophyll-protein complexes of thylakoid membranes was measured by BN-PAGE system. Our findings revealed that the LHCII complexes were more stable than F0F1-ATPase and Cyb 6 /f complexes. Thylakoid membranes proteins during the senescence stage were separated by two-dimensional gel electrophoresis. We identified 13 photosynthesis-related proteins (a fivefold or greater variation), including electron transport, Calvin–Benson cycle and chloroplast protease during senescence of flag leaves. Moreover, our data showed that Ca2+-ATPase was more stable during senescence of flag leaves in rice, compared to Mg2+-ATPase. In enzymes activities analyses, it was observed that a little increment of C4 photosynthetic enzymes activities at the beginning of flag leaves senescence might compensate, to some degree, for the larger reductions in Rubisco activity, confirmed by quantitative RT-PCR analysis.