The RNA-directed DNA Methylation (RdDM) is one type of epigenetic modification which was firstly discovered in plant. RdDM can directly cause DNA modifications of the genome through RNA-DNA interactions. In plant, both of RdDM and mRNA degradation induced by siRNA can silence sequence specific genes through RNA. They play very significant roles in chromosome rearrangement, defence of virus invasion, regulation of gene expression and many processes of plant development. However, the mechanisms of RdDM are still unclear. In this paper the basic characteristics of RdDM were briefly summarized and advances in studies on mechanisms of RdDM were reviewed. These include the kinds of DNA methyltransferases and their functional mechanisms in RdDM, the relationships between DNA methylation and chromatin modification, and important proteins involved in the RdDM process. In plants, RdDM may occur at both the transcriptional and post-transcriptionnal levels, both of which induce gene silencing. Methylation of the target gene promoter correlates with transcriptional gene silencing (TGS) whereas methylation of the coding sequence is associated with post-transcriptional gene silencing (PTGS). RdDM and RNAi all depend on the similar siRNA and enzymes, such as DCL3, RdR2, SDE4 and AGO4. There are at least three kinds of DNA methyltransferases, DRM1/2, MET1 and CMT3, in pants. They can interact with and modifies all cytidines within the DNA regions homologous to RNA sequence. Furthermore, methylation of lysine 9 in Histone H3 can affect the methylation of cytidines.
DNA Methylation ; DNA Modification Methylases ; metabolism ; Gene Silencing ; Plants ; genetics ; metabolism ; Protein Processing, Post-Translational ; RNA ; metabolism

Humans ; Oxidative Stress ; genetics ; Proteasome Endopeptidase Complex ; metabolism ; Protein Modification, Translational ; genetics ; Ubiquitination ; genetics

Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a role in targeting oxidized proteins and remove them. In this process, DSS1 (deleted in split hand/split foot 1), an evolutionally conserved small protein, is conjugated to proteins induced by oxidative stresses in vitro and in vivo, implying oxidized proteins are DSS1 clients. A subsequent ubiquitination targeting DSS1-protein adducts has been observed, suggesting the client proteins are degraded through the ubiquitin-proteasome pathway. The DSS1 attachment to its clients is evidenced to be an enzymatic process modulated by an unidentified ATPase. We name this novel protein modification as DSSylation, in which DSS1 plays as a modifier, whose attachment may render target proteins a signature leading to their subsequent ubiquitination, thereby recruits proteasome to degrade them.
Free Radicals ; metabolism ; HeLa Cells ; Humans ; Oxidation-Reduction ; Oxidative Stress ; genetics ; Proteasome Endopeptidase Complex ; genetics ; metabolism ; Protein Binding ; Protein Modification, Translational ; genetics ; Ubiquitin ; metabolism ; Ubiquitination ; genetics

Peroxisome proliferator-activated receptor gamma (PPARgamma) belongs to a nuclear receptor superfamily; members of which play key roles in the control of body metabolism principally by acting on adipose tissue. Ligands of PPARgamma, such as thiazolidinediones, are widely used in the treatment of metabolic syndromes and type 2 diabetes mellitus (T2DM). Although these drugs have potential benefits in the treatment of T2DM, they also cause unwanted side effects. Thus, understanding the molecular mechanisms governing the transcriptional activity of PPARgamma is of prime importance in the development of new selective drugs or drugs with fewer side effects. Recent advancements in molecular biology have made it possible to obtain a deeper understanding of the role of PPARgamma in body homeostasis. The transcriptional activity of PPARgamma is subject to regulation either by interacting proteins or by modification of the protein itself. New interacting partners of PPARgamma with new functions are being unveiled. In addition, post-translational modification by various cellular signals contributes to fine-tuning of the transcriptional activities of PPARgamma. In this review, we will summarize recent advancements in our understanding of the post-translational modifications of, and proteins interacting with, PPARgamma, both of which affect its transcriptional activities in relation to adipogenesis.
Gene Expression Regulation ; Homeostasis ; *Models, Genetic ; PPAR gamma/genetics/metabolism/*physiology ; *Protein Processing, Post-Translational ; Sumoylation ; Transcription Factors/metabolism/physiology ; Ubiquitination

The endoplasmic reticulum (ER) is a specialized organelle that plays a central role in biosynthesis, correct protein folding, and posttranslational modifications of secretory and membrane proteins. Loss of homeostasis in ER functions triggers the ER stress response, resulting in activation of unfolded protein response (UPR), a hallmark of many inflammatory diseases. These pathways have been reported as critical players in the pathogenesis of various pulmonary disorders, including pulmonary fibrosis, lung injury, and chronic airway disorders. More interestingly, ER stress and the related signaling networks are emerging as important modulators of inflammatory and immune responses in the development of allergen-induced bronchial asthma, especially severe asthma.
Asthma* ; Endoplasmic Reticulum ; Endoplasmic Reticulum Stress* ; Homeostasis ; Lung Injury ; Membrane Proteins ; Organelles ; Protein Folding ; Protein Processing, Post-Translational ; Pulmonary Fibrosis ; Unfolded Protein Response

OBJECTIVE: The incidence of colorectal carcinomas continues to rise in Korea due to the westernized life style. However, the precise colorectal carcinogenic mechanisms remain to be elucidated. The protein products of oncogenes and cancer suppressor genes play important roles in the carcinogenesis. The effects of the proteins are influenced by post-translational modifications as phosphorylation, acetylation, methylation, and ubiquitination. The aberrant sumoylation plays some roles in carcinogenesis. However, the expression pattern of small ubiquitin-related modifier (SUMO)-2/3 in the colorectal cancer has not been reported. We assessed the expression of SUMO-2/3 and evaluated the expression pattern in colorectal cancer. METHODS: The SUMO-2/3 expression was tested in one normal colon mucosal cell line and 5 colorectal cancer cell lines by Western blot. We collected 322 cases of colorectal cancer operated from January 2000 to December 2010 at Soonchunhyang University Cheonan Hospital. We fabricated the tissue microarray and the expression of SUMO-2/3 was evaluated by immunohistochemistry. The results were analyzed with clinicopathologic parameters. RESULTS: The SUMO-2/3 was not expressed in the normal colon mucosal cell line. However, it was expressed highly in all the 5 colorectal cancer cell lines as the beta-actin. The SUMO-2/3 was expressed in 68.3% of the colorectal cancers and its expression was correlated with the pathological tumor stage stage (odds ratio, 2.89; 95% confidence interval, 1.10 to 7.55; P=0.031). CONCLUSION: The SUMO-2/3 plays some roles in carcinogenesis and progression of the colorectal cancer.
Acetylation ; Actins ; Blotting, Western ; Cell Line ; Colon ; Colorectal Neoplasms ; Genes, Tumor Suppressor ; Immunohistochemistry ; Incidence ; Korea ; Life Style ; Methylation ; Oncogenes ; Phosphorylation ; Protein Processing, Post-Translational ; Proteins ; Sumoylation ; Tissue Array Analysis ; Ubiquitin ; Ubiquitination

Ubiquitination is a post-translational modification of proteins in eukaryotes, which mediates the specific degradation and signal transduction of proteins to regulate a variety of life processes and thus affects functions of the body. The disorder and imbalance of ubiquitination network is a major cause of serious human diseases. Ubiquitin molecules can form eight homogeneous ubiquitin chains with different topological structures, which vary greatly in abundance and function. At present, the classical ubiquitin chains K48 and K63 with high abundance and rich substrates have been intensively studied, while other atypical ubiquitin chains with low content remain to be studied. However, it has been proved that atypical ubiquitin chains play a key role in intracellular regulation. K6 is an important atypical ubiquitin chain, which is similar to K48 chain and has a tight spatial structure. It plays a role in DNA damage repair, mitochondrial quality control, the occurrence and development of tumor, and the pathogenesis of Parkinson's disease. Due to the lack of specific antibodies and effective enrichment methods for K6, little is known about its substrate and regulatory mechanism. This paper systematically reviews the structural characteristics, regulatory mechanism, biological functions, and relevant diseases of atypical K6 linkages, aiming to provide reference for the functional study of K6.
Humans ; Protein Processing, Post-Translational ; Signal Transduction ; Ubiquitin/chemistry* ; Ubiquitination

Gata4 is an important transcription factor in heart development. Gata4 post-transcriptional protein modification regulates transcriptional activity and DNA binding, which in turn affects expression of downstream genes and transcription factors, differentiation of embryonic stem cells and cardiogenesis. This article summarizes the effect of post-transcriptional protein modification on transcriptional activity of Gata4 and the relationship between this effect and congenital heart disease. It was shown that acetylation, phosphorylation and SUMOylation upregulate transcriptional activity, DNA binding, downstream gene expression and embryonic stem cell differentiation. On the other hand, methylation and deacetylation downregulate Gata4 transcriptional activity. Post-transcriptional protein modification of Gata4 is very important in clinical research on congenital and other heart diseases.
Acetylation ; Animals ; GATA4 Transcription Factor ; chemistry ; genetics ; metabolism ; Humans ; Methylation ; Phosphorylation ; Protein Processing, Post-Translational ; Sumoylation

The recent identification of the transactive response DNA binding protein with a molecular weight of 43 kDa (TDP-43) as the major pathological protein, in both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin positive inclusions (FTLD-U), provides the new insight into understanding disease processes. The pathogenesis of both diseases is unclear, although they are related by having some overlap of symptoms and now by the shared histopathology of TDP-43 deposition. The number of degenerative diseases associated with TDP-43 has increased, leading to the new designation "TDP-43 proteinopathy". TDP-43 is a highly conserved protein ubiquitously expressed in many tissues including the central nervous system where it is present in neuronal and glial nuclei and to a lesser extent in the cytoplasm. Currently, TDP-43 has been implicated in regulating gene transcription and alternative splicing, in addition to maintaining mRNA stability. However, we still need to investigate the effects of posttranslational modifications of TDP-43, including phosphorylation, ubiquitination, and cleavage, on its regulation of various cellular processes. We review recently published studies of TDP-43 and its relationship to human disease with a special focus on ALS and FTLD-U. We conclude that the TDP-43 proteinopathies represent a novel class of neurodegenerative disorders and both ALS and FTLD-U are closely related conditions linked to similar mechanism of neurodegeneration.
Alternative Splicing ; Amyotrophic Lateral Sclerosis ; Central Nervous System ; Cytoplasm ; DNA ; DNA-Binding Proteins ; Frontotemporal Dementia ; Frontotemporal Lobar Degeneration ; Humans ; Molecular Weight ; Neurodegenerative Diseases ; Neurons ; Phosphorylation ; Protein Processing, Post-Translational ; RNA Stability ; TDP-43 Proteinopathies ; Ubiquitin ; Ubiquitination

Proteins exert their roles in life activities via post-translational modifications(PTMs),which include phosphorylation,acetylation,ubiquitination,glycosylation,and methylation.These modifications can change the functions of proteins and play key roles in a variety of diseases.Endometriosis is a common disease in women of childbearing age,although its molecular mechanisms remain unclear.Recent studies have shown that PTMs may be involved in the pathogenesis of endometriosis.Here we review the roles of PTMs in the occurrence and development of endometriosis and the potential medical treatments.
Acetylation ; Endometriosis/pathology* ; Female ; Glycosylation ; Humans ; Phosphorylation ; Protein Processing, Post-Translational ; Ubiquitination