Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation relationship between dynamic histone modification and MtSERK1s expression during the processes of in vitro organogenesis, the expression of MtSERK1 was analyzed by qRT-PCR, and the modification status of H3K9me2, H3K4me3 and H3K9ac in the promoter region and different regions included in the gene body was analyzed by chromatin immunoprecipitation (ChIP). We found expression activation of MtSERK1 was related to the dynamic changes of histone H3K4me3 and H3K9ac in the 5' and 3' regions. This study will provide important theoretical guidance for understanding of the regulatory mechanism of MtSERK1 and also for establishing efficient genetic transformation system of Medicago truncatula.
Epigenesis, Genetic ; Gene Expression Regulation, Plant ; Genome, Plant ; Histone Code ; Medicago truncatula ; genetics ; growth & development ; Protein Kinases ; genetics ; Regeneration

Alteration of apoptosis is related with progression and recurrence of atypical meningiomas (AMs). However, no comprehensive study has been conducted regarding histone modification regulating apoptosis in AMs. This study aimed to determine the prognostic values of certain apoptosis-associated factors, and examine the role of histone modification on apoptosis in AMs. The medical records of 67 patients with AMs, as diagnosed during recent 13 yr, were reviewed retrospectively. Immunohistochemical staining was performed on archived paraffin-embedded tissues for pro-apoptotic factors (CASP3, IGFBP, TRAIL-R1, BAX, and XAF1), anti-apoptotic factors (survivin, ERK, RAF1, MDM2, and BCL2), and the histone modifying enzymes (MLL2, RIZ, EZH1, NSD2, KDM5c, JMJD2a, UTX, and JMJD5). Twenty-six (38.8%) patients recurred during the follow-up period (mean duration 47.7 months). In terms of time-to-recurrence (TTR), overexpression of CASP3, TRAIL-R1, and BAX had a longer TTR than low expression, and overexpression of survivin, MDM2, and BCL2 had a shorter TTR than low expression (P<0.05). Additionally, overexpression of MLL2, UTX, and JMJ5 had shorter TTRs than low expression, and overexpression of KDM5c had a longer TTR than low expression. However, in the multi-variate analysis of predicting factors for recurrence, low expression of CASP3 (P<0.001), and BAX (P<0.001), and overexpression of survivin (P=0.007), and MDM2 (P=0.037) were associated with recurrence independently, but any enzymes modifying histone were not associated with recurrence. Conclusively, this study suggests certain apoptosis-associated factors should be associated with recurrence of AMs, which may be regulated epigenetically by histone modifying enzymes.
Adult ; Aged ; Aged, 80 and over ; Apoptosis/*genetics ; Apoptosis Regulatory Proteins/genetics ; Epigenesis, Genetic/genetics ; Female ; Gene Expression Regulation, Neoplastic/genetics ; Histone Code/genetics ; Histone Demethylases/*genetics ; Histone-Lysine N-Methyltransferase/*genetics ; Humans ; Longitudinal Studies ; Male ; Meningeal Neoplasms/*genetics/pathology ; Meningioma/*genetics/pathology ; Middle Aged ; Neoplasm Recurrence, Local/*genetics

Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.
Acetylation ; Base Sequence ; Deoxyribonuclease I ; metabolism ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Genes, Plant ; Genomics ; methods ; Histone Code ; genetics ; Histones ; metabolism ; Models, Genetic ; Oryza ; genetics ; Promoter Regions, Genetic ; genetics ; Repetitive Sequences, Nucleic Acid ; genetics ; Sequence Analysis, DNA ; Transcription, Genetic

Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
Animals ; Chromatin Assembly and Disassembly ; DNA Methylation ; DNA Transposable Elements ; Embryo, Mammalian ; Embryonic Development/genetics* ; Epigenesis, Genetic ; Epigenome ; Female ; Fertilization/physiology* ; Gene Expression Regulation, Developmental ; Histone Code ; Histones/metabolism* ; Male ; Mice ; Oocytes/metabolism* ; Spermatozoa/metabolism*

OBJECTIVE: To evaluate therapeutic eff ect of siRNA-HDAC5 on non-obese diabetic (NOD) mice by using small interference RNA (siRNA) technique to knock down the expression of HDAC5 in spleen CD4+ T cells. METHODS: NOD mice, 12-weeks old, were randomly divided into 3 groups and were given normal saline, siRNA-Control or siRNA-HDAC5 through caudal vein injection. The spleens and other samples were collected at the 18th, 24th or 30th week. The blood glucose was tested by blood glucose meter. The urinary albumin and serum levels of IL-1, IL-6, IL-18, and TNF-α were detected by ELISA. The mRNA levels of CD11a, CCR5, and CX3CR1 in spleen CD4+ T cells were measured by quantitative Real-time PCR. The HDAC5 protein level in spleen CD4+ T cell was detected by Western blot. RESULTS: Compared with the control group, the siRNA-HDAC5 group showed a significant decrease in blood glucose, urine albumin excretion rate, serum cytokine and the mRNA levels of CD11a, CCR5, and CX3CR1, consist with the decrease in protein level of HDAC5. CONCLUSION Inhibition of HDAC5 expression in NOD mice could effectively alleviate the onset and development of kidney damage caused by diabetes.
Animals ; CD11a Antigen ; metabolism ; CD4-Positive T-Lymphocytes ; metabolism ; CX3C Chemokine Receptor 1 ; Cytokines ; blood ; Diabetes Mellitus, Experimental ; genetics ; therapy ; Enzyme-Linked Immunosorbent Assay ; Histone Code ; Histone Deacetylases ; genetics ; Mice ; Mice, Inbred NOD ; RNA, Messenger ; metabolism ; RNA, Small Interfering ; genetics ; therapeutic use ; Random Allocation ; Real-Time Polymerase Chain Reaction ; Receptors, CCR5 ; metabolism ; Receptors, Chemokine ; metabolism ; Spleen ; cytology