Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana

PHYTOCHROME B and HISTONE DEACETYLASE 6 control light-induced chromatin compaction in Arabidopsis thaliana Tessadori, F.G.; van Zanten, M.; Pavlova, P.; Clifton, R.; Pontvianne, F.; Snoek, L.B.; Millenaar, F.F.; Schulkes, R.K.; van Driel, R.; Voesenek, L.A.C.J.; Spillane, C.; Pikaard, C.S.; Fransz, P.F.; Peeters, A.J.M. Published in: PLOS Genetics DOI: 10.1371/journal.pgen.1000638 Link to publication Citation for published version (APA): Tessadori, F., van Zanten, M., Pavlova, P., Clifton, R., Pontvianne, F., Snoek, L. B., ... Peeters, A. J. M. (2009). PHYTOCHROME B and HISTONE DEACETYLASE 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLOS Genetics, 5(9), e1000638. https://doi.org/10.1371/journal.pgen.1000638 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Abstract Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process

Studies on the Dissolution of Glucose in Ionic Liquids and Extraction Using the Antisolvent Method

International audienceBiomass, the fibrous material derived from plant cell walls, is a potentially clean and renewable nonfood feedstock for liquid fuel and chemical production in future biorefineries. The capability of ionic liquids to act as selective solvents and catalysts for biomass processing has already been proven. Thus, they are considered as an alternative to conventional solvents. Nevertheless, phase equilibria with biomass derived compounds is still lacking in the literature. To overcome the lack of experimental data on phase equilibria of biomass carbohydrates in ionic liquids, the solubility of D-glucose in four ionic liquids was measured within a temperature range from 283 to 373 K Solubility data were successfully correlated with local composition thermodynamic models such as NRTL and UNIQUAC. In this work, the possibility of extracting glucose from these ionic liquids using the antisolvent method has been also evaluated The parameters affecting the extraction process are the ionic liquid type, ethanol/ionic liquid ratio, temperature, water content, and time Results indicate that ethanol can be successfully used as an antisolvent to separate glucose from ionic liquids

Devenir obstétrical après transfusion in utero pour allo-immunisation fœto-maternelle

Objective: Erythrocyte allo-immunization's rate has decreased but without adapted treatment the prognosis is still poor. The aim of our study was to evaluate the fetal prognosis, the complication's rate and the risk factors of complications of the intrauterine transfusion. Methods: Retrospective study about 37 fetus and 86 intrauterine transfusions between 2001 and 2017. Our main criterion in judging was the occurrence of procedure related complications: premature membrane rupture or premature delivery within seven days from the procedure, chorioamnionitis, abnormal fetal heart rate indicating an emergency ceasarean section within the 24hours from the procedure, in utero death or neonatal death related to the procedure. Results: The survival rate was about 88.9% with a severe complication's rate of 5.8% per intrauterine transfusion and 13.5% per pregnancy. Intrauterine transfusions before 18 weeks of pregnancies was a complication risk factor: 50% of complications before 18 weeks vs. 1.3%, P=0.8×10-3. On the contrary, hydrops did not seem to be a complication risk factor (16.7% of complication with hydrops vs. 3.9%, P=0.27). The localisation of the needle insertion, intra-abdominal or placental insertion, had no effect on the fetal prognosis. Conclusion: Intrauterine transfusion complications are rare and it enhances the fetal prognosis. However, an early procedure is related to a higher rate of complications. Keywords: Allo-immunisation érythrocytaire; Anémie fœtale; Complications rate; Erythrocyte allo-immunization; Fetal anemia; Fetal prognosis; Intrauterine transfusion; Pronostic obstétrical; Taux de complications; Transfusion in utero

Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA

We report on the structural characterization of a functional U3 snoRNA ribonucleoprotein complex isolated from Brassica oleracea. The BoU3 snoRNP complex (formerly NF D) binds ribosomal DNA (rDNA), specifically cleaves pre-rRNA at the primary cleavage site in vitro and probably links transcription to early pre-rRNA processing in vivo. Using a proteomic approach we have identified 62 proteins in the purified BoU3 snoRNP fraction, including small RNA associated proteins (Fibrillarin, NOP5/Nop58p, Diskerin/Cbf5p, SUS2/PRP8 and CLO/GFA1/sn114p) and 40S ribosomal associated proteins (22 RPS and four ARCA-like proteins). Another major protein group is composed of chaperones/chaperonins (HSP81/TCP-1) and at least one proteasome subunit (RPN1a). Remarkably, RNA-dependent RNA polymerase (RdRP) and Tudor staphylococcal nuclease (TSN) proteins, which have RNA- and/or DNA-associated activities, were also revealed in the complex. Furthermore, three U3 snoRNA variants were identified in the BoU3 snoRNP fraction, notably an evolutionarily conserved and variable stem loop structure located just downstream from the C-box domain of the U3 sequence structures. We conclude that the BoU3 snoRNP complex is mainly required for 40S pre-ribosome synthesis. It is also expected that U3 snoRNA variants and interacting proteins might play a major role in BoU3 snoRNP complex assembly and/or function. This study provides a basis for further investigation of these novel ribonucleoprotein factors and their role in plant ribosome biogenesis

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes

Studies on the Dissolution of Glucose in Ionic Liquids and Extraction Using the Antisolvent Method

Biomass, the fibrous material derived from plant cell walls, is a potentially clean and renewable nonfood feedstock for liquid fuel and chemical production in future biorefineries. The capability of ionic liquids to act as selective solvents and catalysts for biomass processing has already been proven. Thus, they are considered as an alternative to conventional solvents. Nevertheless, phase equilibria with biomass derived compounds is still lacking in the literature. To overcome the lack of experimental data on phase equilibria of biomass carbohydrates in ionic liquids, the solubility of d-glucose in four ionic liquids was measured within a temperature range from 283 to 373 K. Solubility data were successfully correlated with local composition thermodynamic models such as NRTL and UNIQUAC. In this work, the possibility of extracting glucose from these ionic liquids using the antisolvent method has been also evaluated. The parameters affecting the extraction process are the ionic liquid type, ethanol/ionic liquid ratio, temperature, water content, and time. Results indicate that ethanol can be successfully used as an antisolvent to separate glucose from ionic liquids

Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana

Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process