Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.
Animals ; Chromatin ; chemistry ; Computer Graphics ; Genome ; Genomics ; methods ; Humans ; Mice ; Software

Sperm DNA damage is recognized as an important biomarker of male infertility. To investigate this, sperm DNA damage was assessed by the sperm chromatin dispersion (SCD) test in semen and motile spermatozoa harvested by combined density gradient centrifugation (DGC) and swim-up in 161 couples undergoing in vitro fertilization (IVF). Semen analysis and sperm DNA damage results were compared between couples who did or did not achieve pregnancy. The sperm DNA damage level was significantly different between the two groups (P < 0.05) and was negatively correlated with IVF outcomes. Logistic regression analysis confirmed that it was an independent predictor for achieving clinical pregnancy. The effects of different levels of sperm DNA damage on IVF outcomes were also compared. There were significant differences in day 3 embryo quality, blastocyst formation rate, and implantation and pregnancy rates (P < 0.05), but not in the basic fertilization rate between the two groups. Thus, sperm DNA damage as measured by the SCD appears useful for predicting the clinical pregnancy rate following IVF.
Adult ; Chromatin/chemistry* ; DNA Damage ; Embryo Implantation ; Embryonic Development ; Female ; Fertilization in Vitro ; Humans ; Male ; Predictive Value of Tests ; Pregnancy ; Pregnancy Outcome ; Pregnancy Rate ; Semen Analysis ; Sperm Injections, Intracytoplasmic ; Sperm Motility ; Spermatozoa/ultrastructure*

SRT1720, a new discovered drug, was reported to activate silent information regulator 1 (SIRT1) and inhibit the chondrocyte apoptosis. However, the underlying mechanism remains elusive. In the present study, the chondrocytes were extracted from the cartilage tissues of New Zealand white rabbits, cultured in the presence of sodium nitroprusside (SNP) (2.5 mmol/L) and divided into five groups: 1, 5, 10, and 20 μmol/L SRT1720 groups and blank control group (0 μmol/L SRT1720). MTT assay was used to detect the chondrocyte viability and proliferation, and DAPI staining and flow cytometry to measure the chondrocyte apoptosis. The expression levels of SIRT1, p53, NF-κB/p65, Bax, and peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α) were detected by Western blotting and the expression levels of SIRT1, type II collagen, and aggrecan mRNA by RT-PCR. The results showed that in the SRT1720-treated groups, the nuclei of chondrocytes were morphologically intact and had uniform chromatin. In the blank control group, nuclear rupture into debris was observed in chondrocytes. With the SRT1720 concentration increasing, the chondrocyte viability increased, the apoptosis rate decreased, the protein expression levels of SIRT1 and PGC-1α and the mRNA expression levels of type II collagen and aggrecan increased ({ptP}<0.05), and the expression levels of p53, NF-κB and bax decreased (P<0.05). It was suggested that SRT1720 inhibits chondrocyte apoptosis by activating the expression of SIRT1 via p53/bax and NF-κB/PGC-1α pathways.
Aggrecans ; genetics ; metabolism ; Animals ; Apoptosis ; drug effects ; Cartilage, Articular ; cytology ; drug effects ; metabolism ; Cell Proliferation ; drug effects ; Cell Survival ; drug effects ; Chondrocytes ; cytology ; drug effects ; metabolism ; Chromatin ; chemistry ; drug effects ; metabolism ; Collagen Type II ; genetics ; metabolism ; Gene Expression Regulation ; Heterocyclic Compounds, 4 or More Rings ; pharmacology ; Nitroprusside ; toxicity ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; genetics ; metabolism ; Primary Cell Culture ; Rabbits ; Signal Transduction ; drug effects ; genetics ; Sirtuin 1 ; genetics ; metabolism ; Transcription Factor RelA ; genetics ; metabolism ; Tumor Suppressor Protein p53 ; genetics ; metabolism ; bcl-2-Associated X Protein ; genetics ; metabolism

Transposable elements (TEs) have no longer been totally considered as "junk DNA" for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 10(16); IMR90 fibroblasts: r = 0.94, P < 2.2 × 10(16)) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10(-4); IMR90: r = 0.934, P = 2 × 10(-2); Promoter: hESC: r = 0.995, P = 3.8 × 10(-4); IMR90: r = 0.996, P = 3.2 × 10(-4)). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.
Alu Elements ; genetics ; Base Composition ; Binding Sites ; Cell Line ; Chromatin ; chemistry ; genetics ; metabolism ; CpG Islands ; DNA ; metabolism ; Databases, Genetic ; Enhancer Elements, Genetic ; genetics ; Genome, Human ; Histones ; metabolism ; Humans ; Methylation

The detection of sperm DNA damage, as an important supplement to semen routine examination strategies, has been applied in some clinical andrology laboratories. What factors may lead to sperm DNA damage remains one of the concerns among many andrologists. Present studies show a variety of factors of sperm DNA damage, including age, environmental pollutants such as organophosphorus and organochloride pesticides, plasticizer, heavy metals such as lead, carcinogens such as polycyclic aromatic hydrocarbons (c-PAHs) and zearalenone (ZEA), male reproductive system diseases or systemic diseases such as varicocele, infection, tumor, spermatogenesis and maturation dysfunction, spinal cord injury and endocrine disorders, seasons and temperature, lifestyle, abstinence time, semen refrigeration, semen handling in vitro, and certain medications. Among them, spermatogenesis and sperm maturation dysfunction may be the most secretive factors, which are involved in the molecular mechanisms of sperm chromatin packaging and restructuring, such as the transformation of histone to protamine, single nucleotide polymorphism of genes, and the role of telomere, which may be one of the hotspots in the future studies of sperm DNA damage. Relevant researches in the future are expected to focus on the prevention of sperm DNA damage and clarification of its specific pathogenic mechanisms so as to provide some evidence for its treatment.
Age Factors ; Chromatin ; chemistry ; DNA Damage ; Environmental Pollutants ; toxicity ; Humans ; Male ; Protamines ; Semen ; drug effects ; Specimen Handling ; Spermatogenesis ; Spermatozoa ; drug effects ; Telomere ; physiology ; Varicocele ; complications

Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences. These alterations, namely epigenetic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.
Cell Death ; Cell Differentiation ; Cell Division ; Chromatin ; chemistry ; metabolism ; Chromatin Assembly and Disassembly ; DNA Methylation ; Epigenesis, Genetic ; Eukaryotic Cells ; cytology ; metabolism ; Histones ; genetics ; metabolism ; Humans ; Protein Processing, Post-Translational ; RNA, Untranslated ; genetics ; metabolism ; Transcription, Genetic

Although the molecular basis of flowering time control is well dissected in the long day (LD) plant Arabidopsis, it is still largely unknown in the short day (SD) plant rice. Rice flowering time (heading date) is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) are also epigenetically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.
Arabidopsis ; genetics ; growth & development ; metabolism ; Arabidopsis Proteins ; genetics ; metabolism ; Chromatin ; chemistry ; metabolism ; Epigenesis, Genetic ; Florigen ; metabolism ; Flowers ; genetics ; growth & development ; metabolism ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; MADS Domain Proteins ; genetics ; metabolism ; Oryza ; genetics ; growth & development ; metabolism ; Phenotype ; Time Factors

Murine gammaherpesvirus 68 (MHV-68), a member of the gammaherpesvirus family, replicates robustly in permissive cell lines and is able to infect laboratory mice. MHV-68 has emerged as a model for studying the basic aspects of viral replication and host-virus interactions of its human counterparts. Herpesvirus genome replication is mediated through a cis-element in the viral genome called the origin of lytic replication (oriLyt). A family of transcription factors, CCAAT/enhancer binding proteins (C/EBPs), assists in oriLyt-mediated DNA replication during gammaherpesvirus reactivation. In this study, we examined the role of C/EBPs in gammaherpesvirus DNA replication during de novo infection, using MHV-68 as a model. We found that C/EBP α and β bind to the CCAAT boxes in the MHV-68 oriLyt core region both in vitro and in vivo, as demonstrated by electrophoretic mobility shift assay and chromatin immunoprecipitation assay. A dominant negative form of C/EBPs significantly impaired the lytic replication efficiency of MHV-68 on both the plasmid and genome levels in a replication assay, indicating that functional C/EBPs are required for maximal MHV-68 genome DNA replication. Collectively, our data demonstrate that C/EBPs interact with the oriLyt core region and play an important role in MHV-68 lytic DNA replication during de novo infection.
Animals ; Base Sequence ; CCAAT-Enhancer-Binding Proteins ; genetics ; metabolism ; Cell Line ; Chromatin Immunoprecipitation ; Cricetinae ; DNA Replication ; DNA, Viral ; chemistry ; genetics ; metabolism ; Electrophoretic Mobility Shift Assay ; Genome, Viral ; Herpesviridae Infections ; genetics ; metabolism ; virology ; Humans ; Mice ; Molecular Sequence Data ; Plasmids ; Promoter Regions, Genetic ; Protein Isoforms ; genetics ; metabolism ; Replication Origin ; Rhadinovirus ; genetics ; metabolism ; Viral Proteins ; genetics ; metabolism ; Virus Latency ; genetics

OBJECTIVETo develop a real-time PCR-based chromatin immunoprecipitation (ChIP) assay for determining the effect of sodium butyrate on acetylation of histone in gamma-globin gene promoter regions in K562 cells.

METHODSK562 cells were grown in the presence or absence of 0.5 mmol/L sodium butyrate for 48 h, and 1=10(7) cells per group were used for real-time PCR-based ChIP with anti-acetylated histone H3 or H4 antibodies. The levels of acetylated histone H3 and H4 (acH3 and acH4) in Ggamma- and Agamma-globin gene promoter regions were measured.

RESULTSIn the K562 cells with sodium butyrate treatment or without any treatment, the levels of acH3 or acH4 in Ggamma- or Agamma-globin gene promoter were higher than that in the necdin gene (negative control). Compared with the untreated K562 cells, the cells treated with 0.5 mmol/L sodium butyrate showed a 3.1-fold or 2.6-fold increase in acH3 or acH4 in Ggamma-globin gene promoter region, with also a 3.7-fold or 3.2-fold increase in acH3 or acH4 in Agamma-globin gene promoter region, respectively (P<0.01).

CONCLUSIONWe have successfully developed a real-time PCR-based ChIP assay for analyzing the acetylation of histone H3 and H4 in gamma-globin gene promoter regions. Our results support the role of sodium butyrate in increasing the level of acetylated histone in gamma-globin gene promoter regions.

Acetylation ; Butyrates ; pharmacology ; Chromatin Immunoprecipitation ; methods ; Histones ; chemistry ; Humans ; K562 Cells ; Promoter Regions, Genetic ; genetics ; Real-Time Polymerase Chain Reaction ; methods ; gamma-Globins ; genetics

In eukaryotic cells, histones are packaged into octameric core particles with DNA wrapping around to form nucleosomes, which are the basic units of chromatin (Kornberg and Thomas, 1974). Multicellular organisms utilise chromatin marks to translate one single genome into hundreds of epigenomes for their corresponding cell types. Inheritance of epigenetic status is critical for the maintenance of gene expression profile during mitotic cell divisions (Allis et al., 2006). During S phase, canonical histones are deposited onto DNA in a replication-coupled manner (Allis et al., 2006). To understand how dividing cells overcome the dilution of epigenetic marks after chromatin duplication, DNA replication coupled (RC) nucleosome assembly has been of great interest. In this review, we focus on the potential influence of RC nucleosome assembly processes on the maintenance of epigenetic status.
Animals ; Chromatin Assembly and Disassembly ; genetics ; physiology ; DNA Replication ; Epigenesis, Genetic ; Histones ; chemistry ; physiology ; Humans ; Nucleosomes ; genetics ; physiology ; Protein Structure, Quaternary