Genetic identification of a novel locus, ACCELERATED FLOWERING 1 that controls chromatin modification associated with histone H3 lysine 27 trimethylation in Arabidopsis thaliana

Plant Science ◽  
2013 ◽  
Vol 208 ◽  
pp. 20-27 ◽  
Author(s):  
Sumin Lee ◽  
Kihye Shin ◽  
Inhye Lee ◽  
Hae-Ryong Song ◽  
Yoo-Sun Noh ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Genetic Identification

scholarly journals The Essential WD Repeat Protein Swd2 Has Dual Functions in RNA Polymerase II Transcription Termination and Lysine 4 Methylation of Histone H3

2004 ◽  
Vol 24 (7) ◽  
pp. 2932-2943 ◽  
Author(s):  
Hailing Cheng ◽  
Xiaoyuan He ◽  
Claire Moore
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Temperature Sensitive ◽  
Repeat Protein ◽  
Tightly Coupled ◽  
Cleavage And Polyadenylation ◽  
Wd Repeat

ABSTRACT Swd2, an essential WD repeat protein in Saccharomyces cerevisiae, is a component of two very different complexes: the cleavage and polyadenylation factor CPF and the Set1 methylase, which modifies lysine 4 of histone H3 (H3-K4). It was not known if Swd2 is important for the function of either of these entities. We show here that, in extract from cells depleted of Swd2, cleavage and polyadenylation of the mRNA precursor in vitro are completely normal. However, temperature-sensitive mutations or depletion of Swd2 causes termination defects in some genes transcribed by RNA polymerase II. Overexpression of Ref2, a protein previously implicated in snoRNA 3′ end formation and Swd2 recruitment to CPF, can rescue the growth and termination defects, indicating a functional interaction between the two proteins. Some swd2 mutations also significantly decrease global H3-K4 methylation and cause other phenotypes associated with loss of this chromatin modification, such as loss of telomere silencing, hydroxyurea sensitivity, and alterations in repression of INO1 transcription. Even though the two Swd2-containing complexes are both localized to actively transcribed genes, the allele specificities of swd2 defects suggest that the functions of Swd2 in mediating RNA polymerase II termination and H3-K4 methylation are not tightly coupled.

scholarly journals PDTB-10. INHIBITION OF RADIATION-INDUCED DNA DAMAGE REPAIR MEDIATED CHROMATIN MODIFICATION BY HISTONE H3 DEMETHYLASE INHIBITOR IN PEDIATRIC BRAINSTEM GLIOMA

2016 ◽  
Vol 18 (suppl_6) ◽  
pp. vi151-vi152
Author(s):  
Quanhong Ma ◽  
Andrea Plunti ◽  
Amanda Saratsis ◽  
Rishi Lulla ◽  
Jason R Fangusaro ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Repair ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Brainstem Glioma ◽  
Damage Repair ◽  
Radiation Induced

scholarly journals Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation

2018 ◽  
Author(s):  
Nadia Bouain ◽  
Arthur Korte ◽  
Santosh B. Satbhai ◽  
Seung Y. Rhee ◽  
Wolfgang Busch ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Root Growth ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Functional Module ◽  
Molecular Genetic ◽  
Chromatin Modification ◽  
Nutrient Deficiency ◽  
Mineral Nutrient ◽  
A Genome

AbstractThe molecular genetic mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using a panel of Arabidopsis thaliana natural accessions, we provide a comprehensive combinatorial analysis of RGR variation under macro- and micronutrient deficiency, namely phosphorus (P), iron (Fe), and zinc (Zn), which affect root growth in opposite directions. We found that while -P stimulates early RGR of most accessions, -Fe or -Zn reduces it. The combination of either -P-Fe or -P-Zn leads to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, Arabidopsis reference accession Columbia (Col-0) is not representative of the species under -P and -Zn. Using a genome wide association study, we identify candidate genes that control RGR under the assayed nutrient deficiency conditions. By using a network biology driven search using these candidate genes, we further identify a functional module enriched in regulation of cell cycle, DNA replication and chromatin modification that possibly underlies the suppression of root growth reduction in -P-Fe conditions. Collectively, our findings provide a framework for understanding the regulation of RGR under nutrient deficiency, and open new routes for the identification of both large effect genes and favorable allelic variations to improve root growth.

scholarly journals A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification

Blood ◽  
2007 ◽  
Vol 110 (13) ◽  
pp. 4445-4454 ◽  
Author(s):  
Dorothee Mueller ◽  
Christian Bach ◽  
Deniz Zeisig ◽  
Maria-Paz Garcia-Cuellar ◽  
Sara Monroe ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Elongation Factor ◽  
Polycomb Group ◽  
Fusion Partner ◽  
Transcriptional Elongation ◽  
Associated Proteins ◽  
Group Members

Chimeric proteins joining the histone methyltransferase MLL with various fusion partners trigger distinctive lymphoid and myeloid leukemias. Here, we immunopurified proteins associated with ENL, a protein commonly fused to MLL. Identification of these ENL-associated proteins (EAPs) by mass spectrometry revealed enzymes with a known role in transcriptional elongation (RNA polymerase II C-terminal domain kinase [RNAPolII CTD] positive transcription elongation factor b [pTEFb]), and in chromatin modification (histone-H3 methyltransferase DOT1L) as well as other frequent MLL partners (AF4, AF5q31, and LAF4), and polycomb group members (RING1, CBX8, and BCoR). The composition of EAP was further verified by coimmunoprecipitation, 2-hybrid analysis, pull-down, and colocalization experiments. Purified EAP showed a histone H3 lysine 79–specific methylase activity, displayed a robust RNAPolII CTD kinase function, and counteracted the effect of the pTEFb inhibitor 5,6-dichloro-benzimidazole-riboside. In vivo, an ENL knock-down diminished genome-wide as well as gene-specific H3K79 dimethylation, reduced global run-on elongation, and inhibited transient transcriptional reporter activity. According to structure-function data, DOT1L recruitment was important for transformation by the MLL-ENL fusion derivative. These results suggest a function of ENL in histone modification and transcriptional elongation.

scholarly journals Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana

2010 ◽  
Vol 10 (1) ◽  
pp. 238 ◽  
Author(s):  
Karin van Dijk ◽  
Yong Ding ◽  
Sridhar Malkaram ◽  
Jean-Jack M Riethoven ◽  
Rong Liu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Histone H3 ◽  
Dehydration Stress ◽  
Dynamic Changes ◽  
Genome Wide ◽  
Methylation Patterns

Defining the Leukemia Epigenome: Distinct Genome Wide Histone H3 Modification Patterns Exist in AML, ALL and Healthy Hematopoietic Progenitor Cells.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2124-2124
Author(s):  
Carsten Muller-Tidow ◽  
Claudia Homme ◽  
Hans-Ulrich Klein ◽  
Antje Hascher ◽  
Steffen Koschmieder ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Histone Modification ◽  
Progenitor Cells ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Support Vector ◽  
Acute Leukemias ◽  
Histone H3 Acetylation ◽  
H3 Acetylation ◽  
Histone Modification Patterns

Abstract Aberrant transcriptional regulation plays a crucial role in the pathogenesis of acute leukemias. Chromosomal translocations and other mutations frequently affect transcription and chromatin regulation-associated genes in these diseases. Based on these findings we hypothesized that distinct global chromatin modification patterns exist that can distinguish between progenitor cells (CD34+ HSC) and acute leukemia as well as its subtypes. We used high density oligonucleotide ChIP-Chip assays querying more than 31,000 genomic loci to analyze global Histone H3 acetylation (H3Ac) and Lysine 9 (H3K9me3) trimethylation patterns each in a large number of AML (n=115), ALL (n=30), CD34+ HSC (n= 21) and peripheral blood cell (N=18) specimens. Class comparisons and predictions as well as unsupervised analyses were performed. Bioinformatic analyses led to histone modification maps across the genome with Histone H3 acetylation levels peaking around the predicted transcriptional start sites. More than 1000 loci differed in H3 acetylation and H3K9me3 between AML and CD34+ specimens (5% FDR). Among the regulatory classes over-represented among the altered genes were those involved in oncogenesis and cellular proliferation/differentiation. Histone H3 acetylation and H3K9me3 patterns also differed at hundreds of loci between ALL and AML samples (5% FDR). Genes involved in transcriptional regulation were significantly altered between the two leukemia subtypes. Specific differences in global chromatin modifications allowed support vector machine-based classification of CD34+ progenitor cells, AML, and ALL, with about 90% sensitivity and specificity based on Histone H3 acetylation patterns. A similar classification power was observed for H3K9me3. Within the AML patients, several groups of patients were identified that clustered together in unsupervised hierarchical cluster analysis due to similar histone modification patterns. These patterns did not primarily depend on patients′ karyotypes,, indicating that it may be possible to define some, as yet unknown, different types of AML based on chromatin modification. On a global scale, acute leukemias are associated with specific histone modification patterns that distinguish AML from ALL and CD34+ hematopoietic progenitors. Taken together, these first data on the leukemia epigenome provide the basis for improved understanding of genes involved in leukemia pathogenesis.

scholarly journals Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings

2016 ◽  
Vol 57 (6) ◽  
pp. 646-654 ◽  
Author(s):  
Suvendu Mondal ◽  
Young Sam Go ◽  
Seung Sik Lee ◽  
Byung Yeoup Chung ◽  
Jin-Hong Kim
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gamma Irradiation ◽  
Histone Modifications ◽  
Gamma Rays ◽  
Regulation Of Gene Expression ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Marker Genes ◽  
Transcription Start Sites

Abstract Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.

scholarly journals Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana

2008 ◽  
Vol 49 (10) ◽  
pp. 1580-1588 ◽  
Author(s):  
Jong-Myong Kim ◽  
Taiko Kim To ◽  
Junko Ishida ◽  
Taeko Morosawa ◽  
Makiko Kawashima ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Histone H3 ◽  
Stress Conditions

scholarly journals Spreading of a Corepressor Linked to Action of Long-Range Repressor Hairy

2008 ◽  
Vol 28 (8) ◽  
pp. 2792-2802 ◽  
Author(s):  
Carlos A. Martinez ◽  
David N. Arnosti
Keyword(s):  
Long Range ◽  
Chromatin Immunoprecipitation ◽  
Histone Deacetylases ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Control Of Gene Expression ◽  
Repressor Proteins ◽  
Functional Classes ◽  
Order Complexes

ABSTRACT Transcriptional repressor proteins play key roles in the control of gene expression in development. For the Drosophila embryo, the following two functional classes of repressors have been described: short-range repressors such as Knirps that locally inhibit the activity of enhancers and long-range repressors such as Hairy that can dominantly inhibit distal elements. Several long-range repressors interact with Groucho, a conserved corepressor that is homologous to mammalian TLE proteins. Groucho interacts with histone deacetylases and histone proteins, suggesting that it may effect repression by means of chromatin modification; however, it is not known how long-range effects are mediated. Using embryo chromatin immunoprecipitation, we have analyzed a Hairy-repressible gene in the embryo during activation and repression. When inactivated, repressors, activators, and coactivators cooccupy the promoter, suggesting that repression is not accomplished by the displacement of activators or coactivators. Strikingly, the Groucho corepressor is found to be recruited to the transcribed region of the gene, contacting a region of several kilobases, concomitant with a loss of histone H3 and H4 acetylation. Groucho has been shown to form higher-order complexes in vitro; thus, our observations suggest that long-range effects may be mediated by a “spreading” mechanism, modifying chromatin over extensive regions to inhibit transcription.

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