Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus. Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA, such as DNA replication and DNA repair. Many factors, including histone variants, histone modification, DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities. Here, we review studies on the dynamics of chromatin higher order structure and its relationship with gene transcription.
Animals ; Chromatin ; chemistry ; metabolism ; Chromatin Assembly and Disassembly ; Eukaryotic Cells ; chemistry ; metabolism ; Gene Expression Regulation ; Humans ; Models, Molecular

The sperm DNA integrity is important for the success of natural or assisted fertilization, as well as normal development of the embryo, fetus and child. Some investigations have demonstrated that when the damaged spermatozoa DNA of the husband exceeds than 30%, the couple has very low potential of natural fertility. Several methods are available for the assessment of sperm DNA integrity, which is considered to be a better marker of male fertility potential than conventional semen parameters. Furthermore, monitering sperm DNA integrity may become an important part of the evaluation for couples seeking assisted reproductive techniques such as intracytoplasmic sperm injection (ICSI). Finally, the effects of cryopreservation and preparation techniques on sperm DNA integrity are summarized.
Chromatin ; chemistry ; Cryopreservation ; DNA Damage ; Humans ; Infertility, Male ; etiology ; genetics ; Male ; Reproductive Techniques ; Spermatozoa ; ultrastructure

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

OBJECTIVETo search for a simple, quick and accurate method for the sperm DNA integrity test by modifying the conventional sperm chromatin dispersion (SCD) test, and to investigate the reference value range of normal sperm DNA integrity by the improved SCD assay.

METHODSWe modified the conventional SCD test in its procedures, reagents preparing and utensils to be used, compared the improved method with the conventional one, and detected 293 normal semen samples for sperm DNA integrity by the modified SCD test.

RESULTSAn improved SCD test was established, and no statistical differences were found between the results of the modified and conventional methods. The reference value range was determined by the improved SCD assay for normal sperm DNA integrity, which was < 32.58% for abnormal sperm DNA integrity.

CONCLUSIONThe improved SCD test could detect sperm DNA integrity more quickly, and it reduced the cost in reagents.

Adult ; Chromatin ; ultrastructure ; DNA ; analysis ; Genetic Techniques ; Humans ; Male ; Reference Values ; Semen Analysis ; Sperm Motility ; genetics ; Spermatozoa ; chemistry

OBJECTIVESTo analysis the correlation between parameters of sperm chromatin structure assay(SCSA) and semen routine analysis, and to discuss the reliable methods of semen quality evaluation.

METHODSFive hundred and eleven semen samples were detected to analyse the mutiple-parameter correlation between results of SCSA (COMP alpha t) and semen routine analysis.

RESULTSThe parameters that have low-level positive correlation(r: 0.10-0.30) with denatured sperm percentage(COMP alpha t) were viscosity, ejaculation interval, abnormal sperm ratio, concentration of grade c sperm; those having low-level negative correlation(r: -0.30(-)-0.10) were VDL, VSL and VAP; those having mid-level positive correlation (r: 0.30-0.70) were sperm concentration, percentage of grade d sperm; those having mid-level negative correlation (r: -0.70(-)-0.30) were MAD, percentage of grade a sperm and survival rate.

CONCLUSIONSFlow cytometry can be used to evaluate the percentage of denatured or injured sperm rapidly, correctly and simply. The result (COMP alpha t) correlates partly with semen parameters, and it is not a conclusively parameter compared with routine semen analysis. It is important to use SCSA to evaluate productivity under the above situation.

Adult ; Chromatin ; chemistry ; DNA Damage ; Flow Cytometry ; Humans ; Hydrogen-Ion Concentration ; Male ; Semen ; Sperm Count ; Spermatozoa ; ultrastructure ; Viscosity

OBJECTIVETo investigate the effects on male reproductive function working under cold area.

METHODSAfter on site investigation, advanced molecular lab analysis-single-cell gel electrophoresis (SCGE) and sperm chromatin structure assay (SCSA) which are combined with semen routine analysis were used to evaluate semen quality and sperm sub-clinical injury.

RESULTSSemen routine analysis showed that the semen parameters of the males working in cold area were within normal range, but level I comet cell percentage in SCGE increased significantly, which was 4.4%, compared to the contrast group (1.9%) with significant difference. During sperm chromatin structure assay parameters, comp alpha t increased, with an average value of 22.26%. The two kinds of results both showed single and double strand breakages in sperm.

CONCLUSIONLong-term exposure to cold could induce sperm DNA injury, but not affect sperm quality. The results suggested that it was important to reinforce the reproductive care in males working in cold areas.

Adult ; Chromatin ; chemistry ; Cold Climate ; Comet Assay ; DNA Damage ; Fertility ; Humans ; Male ; Semen ; Sperm Count ; Spermatozoa ; cytology

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

Breast cancer susceptibility gene 1(BRCA1) plays an important role in breast cancer development and progression. BRCA1 encodes a 1863-amino acid protein with two BRCA1 C-terminal (BRCT) domains at its C-terminus, BRCT1 and BRCT2. Many cancer-predisposing mutations are located in the BRCT domains, which have been shown to induce chromatin unfolding by use of an approach that allows visualization of large-scale chromatin structure through lac repressor/lac operator recognition. To map the important region of BRCT domain (amino acid residues 1642-1736), six deletion mutant constructs were made. The chromatin structure assay showed that amino acid residues 1691-1721 are involved in the induction of chromatin unfolding. To further localize the critical amino acid residues, ten alanine scanning mutant constructs were made. The chromatin structure assay demonstrated that the 1707IAGGK1711 region is critical for the chromatin unfolding activity. Based on the mapped important region, Blast analysis identified a novel homologous protein. Mapping of the BRCT1 domain may aid in the presymptomatic risk assessment and provide a valuable tool for further study on the BRCT1 structure and function.
BRCA1 Protein ; chemistry ; physiology ; Base Sequence ; Chromatin ; chemistry ; Cloning, Molecular ; Female ; Genes, BRCA1 ; Humans ; Molecular Sequence Data ; Mutation ; Protein Folding ; Structure-Activity Relationship

The largest subunit of eukaryotic RNA polymerase II contains a unique domain at its carboxy-terminus, which is referred to as the carboxy-terminal domain (CTD). The CTD is made up of an evolutionarily conserved heptapeptide repeat (YSPTSPS). Over the past decade, there has been increasing attention on the role of the CTD in transcription regulation in the view of mRNA processing and chromatin remodeling. This paper provides a brief overview of the recent progress in the dynamic changes in CTD phosphorylation and its role in integrating multiple nuclear events.
Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Chromatin/*physiology ; Chromatin Assembly and Disassembly ; Conserved Sequence ; Histones/metabolism ; Humans ; Isomerism ; Phosphorylation ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/*physiology ; RNA, Messenger/metabolism ; Transcription, Genetic

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