scholarly journals SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Siju Zhang ◽  
Hongjiao Hao ◽  
Xiaonan Liu ◽  
Yingying Li ◽  
Xuan Ma ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Gene Expression Analysis ◽  
Regulatory Gene ◽  
Rhythmic Pattern ◽  
Biological Processes ◽  
Regulator Gene ◽  
Set Domain ◽  
Encoding Gene ◽  
Flowering Regulator ◽  
Functional Investigation

AbstractSET domain group (SDG) proteins have been identified to be involved in histone modification and participate in diverse biological processes. Rice contains 41 SDG genes, however, most of which have not been functionally characterized. Here, we report the identification and functional investigation of rice SDG712 gene. Phylogenic analysis revealed that SDG712 belongs to the H3K9-specific SDG subclade. SDG712 is highly expressed in leaves during reproductive growth stage with obvious circadian rhythmic pattern. Mutation of SDG712 promotes rice flowering, while overexpression of SDG712 delays rice flowering. Gene expression analysis suggested that SDG712 acts downstream of Hd1, while acts upstream of Ehd1, Hd3a and RFT1. Subcellular localization assay demonstrated that SDG712 is localized in the nucleus. Chromatin immunoprecipitation (ChIP) assay showed that the H3K9me2 levels at Hd3a and RFT1 loci were increased in SDG712 overexpression transgenic plants, indicating that SDG712 may mediate the H3K9 di-methylation on these loci to repress rice flowering. Taken together, our findings demonstrated that SDG712 is a negative flowering regulatory gene in rice, and it delays flowering through repressing key flowering regulator gene Ehd1 and the florigen genes Hd3a and RFT1.

Non-histone methylation of SET7/9 and its biological functions

2021 ◽  
Vol 16 ◽  
Author(s):  
Lili Gao ◽  
Weiping Yu ◽  
Peng Song ◽  
Qing Li
Keyword(s):  
Cancer Progression ◽  
Histone Methylation ◽  
Biological Processes ◽  
Biological Functions ◽  
Set Domain ◽  
Cell Cycle Protein ◽  
Cardiac Morphogenesis ◽  
Histone 3 ◽  
Development Methods ◽  
Human Carotid

Background: (su(var)-3-9,enhancer-of-zeste,trithorax) domain-containing protein 7/9 (SET7/9) is a member of the protein lysine methyltransferases (PLMTs or PKMTs) family. It contains a SET domain. Recent studies demonstrate that SET7/9 methylates both lysine 4 of histone 3 (H3-K4) and lysine(s) of non-histone proteins, including transcription factors, tumor suppressors, and membrane-associated receptors. Objective: This article mainly reviews the non-histone methylation effects of SET7/9 and its functions in tumorigenesis and development. Methods: PubMed was screened for this information. Results: SET7/9 plays a key regulatory role in various biological processes such as cell proliferation, transcription regulation, cell cycle, protein stability, cardiac morphogenesis, and development. In addition, SET7/9 is involved in the pathogenesis of hair loss, breast cancer progression, human carotid plaque atherosclerosis, chronic kidney disease, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and pulmonary fibrosis. Conclusion: SET7/9 is an important methyltransferase, which can catalyze the methylation of a variety of proteins. Its substrates are closely related to the occurrence and development of tumors.

scholarly journals Increased expression of SET domain-containing proteins and decreased expression of Rad51 in different classes of renal cell carcinoma

2016 ◽  
Vol 36 (3) ◽  
Author(s):  
Si Liu ◽  
Yiyang Li ◽  
Hongmei Xu ◽  
Kaichen Wang ◽  
Nan Li ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Chromatin Immunoprecipitation ◽  
Renal Cell ◽  
Specific Binding ◽  
Set Domain ◽  
Tissue Samples

Because of scant availability of tissue samples, we did not perform elaborate examination of chromatin immunoprecipitation and specific binding of SET domain-containing proteins to the promoters of Rad51. These remain avenues for future investigations.

scholarly journals Cross-Linking and Cell Harvesting v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Cell Harvesting ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Bioinformatics Analysis v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

2018 ◽  
Author(s):  
Noémie Vimont ◽  
Fu Xiang Quah ◽  
David Guillaume-Schöpfer ◽  
François Roudier ◽  
Elisabeth Dirlewanger ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Immunoprecipitation ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Prunus Avium ◽  
Rna Extraction ◽  
Biological Processes ◽  
Mads Box ◽  
Rna Seq ◽  
Chromatin Immunoprecipitation Sequencing

ABSTRACTChromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.

scholarly journals ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Noémie Vimont ◽  
Fu Xiang Quah ◽  
David Guillaume Schöepfer ◽  
François Roudier ◽  
Elisabeth Dirlewanger ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Immunoprecipitation ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Prunus Avium ◽  
Rna Extraction ◽  
Biological Processes ◽  
Mads Box ◽  
Rna Seq ◽  
Chromatin Immunoprecipitation Sequencing

AbstractChromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-BOX 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.

scholarly journals The Drosophila SET domain encoding gene dEset is essential for proper development

Hereditas ◽  
2006 ◽  
Vol 143 (2006) ◽  
pp. 177-188 ◽  
Author(s):  
Marianne Stabell ◽  
Mona Bjørkmo ◽  
Reidunn B. Aalen ◽  
Andrew Lambertsson
Keyword(s):  
Set Domain ◽  
Encoding Gene

scholarly journals Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals Immunoprecipitation, Decross-linking, and DNA Extraction v1

2020 ◽  
Author(s):  
Vasso Makrantoni ◽  
Daniel Robertson ◽  
Adele L. Marston
Keyword(s):  
Chromosome Segregation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Dna Recombination ◽  
Yeast Cells ◽  
Biological Processes ◽  
Technological Advancement ◽  
Entire Genome ◽  
Protein Dna Interactions ◽  
Generation Sequencing

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.

scholarly journals The Structure, Activity, and Function of the SETD3 Protein Histidine Methyltransferase

Life ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1040
Author(s):  
Apolonia Witecka ◽  
Sebastian Kwiatkowski ◽  
Takao Ishikawa ◽  
Jakub Drozak
Keyword(s):  
Protein S ◽  
Biological Processes ◽  
Set Domain ◽  
Hypoxic Conditions ◽  
Structure Activity ◽  
Mammalian Tissues ◽  
Bona Fide ◽  
And Function ◽  
Actin Protein ◽  
Cytoskeleton Integrity

SETD3 has been recently identified as a long sought, actin specific histidine methyltransferase that catalyzes the Nτ-methylation reaction of histidine 73 (H73) residue in human actin or its equivalent in other metazoans. Its homologs are widespread among multicellular eukaryotes and expressed in most mammalian tissues. SETD3 consists of a catalytic SET domain responsible for transferring the methyl group from S-adenosyl-L-methionine (AdoMet) to a protein substrate and a RuBisCO LSMT domain that recognizes and binds the methyl-accepting protein(s). The enzyme was initially identified as a methyltransferase that catalyzes the modification of histone H3 at K4 and K36 residues, but later studies revealed that the only bona fide substrate of SETD3 is H73, in the actin protein. The methylation of actin at H73 contributes to maintaining cytoskeleton integrity, which remains the only well characterized biological effect of SETD3. However, the discovery of numerous novel methyltransferase interactors suggests that SETD3 may regulate various biological processes, including cell cycle and apoptosis, carcinogenesis, response to hypoxic conditions, and enterovirus pathogenesis. This review summarizes the current advances in research on the SETD3 protein, its biological importance, and role in various diseases.

Sign in / Sign up

Export Citation Format

Share Document