Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability

Methylation of lysine residues of histones is associated with functionally distinct regions of chromatin, and, therefore, is an important epigenetic mark. Over the past few years, several enzymes that catalyze this covalent modification on different lysine residues of histones have been discovered. Intriguingly, histone lysine methylation has also been shown to be cross-regulated by histone ubiquitination or the enzymes that catalyze this modification. These covalent modifications and their cross-talks play important roles in regulation of gene expression, heterochromatin formation, genome stability, and cancer. Thus, there has been a very rapid progress within past several years towards elucidating the molecular basis of histone lysine methylation and ubiquitination, and their aberrations in human diseases. Here, we discuss these covalent modifications with their cross-regulation and roles in controlling gene expression and stability. Received 24 September 2008; received after revision 21 November 2008; accepted 28 November 2008     

Chromatin affinity-precipitation using a small metabolic molecule: its application to analysis of <Emphasis Type="Italic">O</Emphasis>-acetyl-ADP-ribose

In the cell, many small endogenous metabolic molecules are involved in distinct cellular functions such as modulation of chromatin structure and regulation of gene expression. O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability. Here, we developed a novel chromatin affinity-precipitation (ChAP) method to detect the chromatin fragments at which small molecules interact with binding partners. We used this method to demonstrate that AAR associated with heterochromatin. Moreover, we applied the ChAP method to whole genome tiling array chips to compare the association of AAR and Sir2. We found that AAR and Sir2 displayed similar genomic binding patterns. Furthermore, we identified 312 potential association cluster regions of AAR. The ChAP assay may therefore be a generally useful strategy to study the small molecule association with chromosomal regions. Our results further suggest that the small metabolic molecule AAR associates with silent chromatin regions in a Sir2-dependent manner and provide additional support for the role of AAR in assembly of silent chromatin.     

Differential giemsa staining of the holokinetic chromosomes of the two-spotted spider mite,Tetranychus urticae Koch (Acari,Tetranychidae)

Summary The chromosomes of the spider miteTetranychus urticae can be stained differentially with Giemsa-staining methods for G-bands. C-band patterns representing constitutive heterochromatin could not be detected. Their absence may be related to the holokinetic condition of the chromosomes.     

High resolution of heterochromatin of Drosophila melanogaster by distamycin A

A DNA-binding AT-specific antibiotic, distamycin A, was used as inhibitor of the condensation process of the heterochromatic regions in Drosophila melanogaster embryonic cells. By this treatment the structural organization of heterochromatin at interphase is preserved until metaphase. The different patterns observed are interpreted as chronological steps in the condensation process.     

Reelin is a platelet protein and functions as a positive regulator of platelet spreading on fibrinogen

Abnormalities of platelet functions have been linked to reelin-impaired neuronal disorders. However, little attention has been given to understanding the interplay between reelin and platelet. In this study, reelin was found to present in the human platelets and megakaryocyte-like leukemic cells. Reelin-binding assays revealed that extracellular reelin can interact with platelets through the receptor belonging to the low density lipoprotein receptor gene family. The reelin-to-platelet interactions enhance platelet spreading on fibrinogen concomitant with the augmentation of lamellipodia formation and F-actin bundling. In contrast, reelin has no effect on integrin αIIbβ3 activation and agonist-induced platelet aggregation. Molecular analysis revealed that the up-regulation of Rac1 activity and the inhibition of protein kinase C δ-Thr505 phosphorylation are important for reelin-mediated enhancement of platelet spreading on fibrinogen. These findings demonstrate for the first time that reelin is present in platelets and the reelin-to-platelet interactions play a novel role in platelet signaling and functions.     

SET domain proteins modulate chromatin domains in eu- and heterochromatin

The SET domain is a 130-amino acid, evolutionarily conserved sequence motif present in chromosomal proteins that function in modulating gene activities from yeast to mammals. Initially identified as members of the Polycomb- and trithorax-group (Pc-G and trx-G) gene families, which are required to maintain expression boundaries of homeotic selector (HOM-C) genes, SET domain proteins are also involved in position-effect-variegation (PEV), telomeric and centromeric gene silencing, and possibly in determining chromosome architecture. These observations implicate SET domain proteins as multifunctional chromatin regulators with activities in both eu- and heterochromatin – a role consistent with their modular structure, which combines the SET domain with additional sequence motifs of either a cysteine-rich region/zinc-finger type or the chromo domain. Multiple functions for chromatin regulators are not restricted to the SET protein family, since many trx-G (but only very few Pc-G) genes are also modifiers of PEV. Together, these data establish a model in which the modulation of chromatin domains is mechanistically linked with the regulation of key developmental loci (e.g. HOM-C).     

Chromosome banding patterns and the nucleolar organizer region of the eastern mole (Scalopus aquaticus)

Summary The C and G chromosome banding patterns and the AgAS positive sites (NOR regions) of cultured lung cells of the Eastern mole (Scalopus aquaticus) are presented. A distinctive secondary constriction is found on a pair of autosomes instead of on the X-chromosome as previously believed. The presence of a heterochromatic heteromorphism is noted and a large amount of constitutive heterochromatin is present in the karyotype.     

Influence of bacteria on epigenetic gene control

Cellular information is inherited by daughter cells through epigenetic routes in addition to genetic routes. Epigenetics, which is primarily mediated by inheritable DNA methylation and histone post-translational modifications, involves changes in the chromatin structure important for regulating gene expression. It is widely known that epigenetic control of gene expression plays an essential role in cell differentiation processes in vertebrates. Furthermore, because epigenetic changes can occur reversibly depending on environmental factors in differentiated cells, they have recently attracted considerable attention as targets for disease prevention and treatment. These environmental factors include diet, exposure to bacteria or viruses, and air pollution, of which this review focuses on the influence of bacteria on epigenetic gene control in a host. Host-bacterial interactions not only occur upon pathogenic bacterial infection but also continuously exist between commensal bacteria and the host. These bacterial stimuli play an essential role in various biological responses involving external stimuli and in maintaining physiological homeostasis by altering epigenetic markers and machinery.     

C-band differentiation between the chromosomes of two subspecies of the chironomid midge Chironomus thummi

The metaphase chromosomes of Chironomus th. thummi contain approximately 17% more pericentric C-band heterochromatin than the chromosomes of Chironomus th. piger with 11% heterochromatin. In Ch. th. thummi, the proportion of heterochromatin appeared to be much larger in metaphase chromosomes than in polytene chromosomes. This discrepancy is interpreted as being due to the specific chromosome organization and not as the result of an underreplication of heterochromatin during polytenization.     

Distribution of constitutive heterochromatin (C-bands) in the somatic chromosomes of an Indian bird,Chrysomma sinense (Gmelin)

Summary The localization of constitutive heterochromatin has been studied in a passerine bird,Chrysomma sinense (2n=±70). In all the 7 pairs of macrochromosomes pericentric heterochromatin has been observed as usual except in pairs Nos 2 and 4, in which both pericentric and non-centromeric heterochromatin have been recorded.The authors are grateful to Prof. B. K. Behura, Department of Zoology, Utkal University, for necessary laboratory and library facilities. T.S. is grateful to the CSIR for providing financial assistance under the JRF scheme.