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The orthologs have similar or even identical functions in different species, share the anological regulatory pathways, and play the close or even same role among species. Furthermore, the vast majority of the biological core functions were assumed to a considerable number of orthologous genes in organisms. Orthologs was the most reliable choices for functional annotation and analysis of genomic sequences, whose unique biological characteristics demonstrated that comparative genomics research based on orthologs will certainly provide clues for detecting the origin, expression, and loss of important functional genes during the biological evolution in different organisms. In this review, the fundamental characteristics of orthologous genes and the relationship between the orthologs and comparison genomics were recounted. The corresponding approaches and the current status in comparative genomic research based on the orthologs were summarized.

Investigation of DNA-protein interactions is fundamental to understand the mechanism underlying a variety of life processes. In this article, various types of biochemical methods in DNA-protein interaction study in vivo and in vitro at the level of DNA, protein, and the complex, respectively were briefly reviewed. Traditional assays including Nitrocellulose filter-binding assay, Footprinting, EMSA, and Southwestern blotting were summarized. In addition, chromatin immunoprecipitation techniques including nChIP, xChIP, and ChIP-on-chip, which were widely used in epigenetics, were particularly introduced.

A mispairing PCR-RFLP technique was applied in this study to determine the Insulin-like Growth Factor 2(IGF2) gene intron3 G3072A mutation in an outbred Landrace and Large White, and the gelded boars from Landrace x Large White cross. The difference of corresponding traits and the genetic effects of the boars inherited from parental A allele and inherited from parental G allele were analyzed. The results indicated that comparing with the boars inherited from parental G allele, the boars inherited from parental A allele increased significantly in the circumference 3.06% (P< 0.05) and index of body 3.01% (P< 0.05), respectively. The boars inherited from parental A allele had a significantly less average buttock fat thickness (15.31%, P< 0.01), thorax-waist fat thickness (23.74%, P< 0.01), skin thickness 9.38% (P< 0.01), fiber density (20.03%, P< 0.01) and had more less 6th-7th rib fat thickness (20.27%, P< 0.05), tendernce (17.32%, P< 0.05), and had more thick shoulder fat thickness (7.97%, P< 0.05), and had bigger the loin eye area (22.58%, P< 0.01) and fiber cross-sectional area (32.70%, P< 0.01) and fiber diameter (15.38%, P< 0.01) and lean meat (2.18%, P< 0.01) than the boars inherited from parental G allele. The results were suggested that the parental A allele has highly significant genetic effects in improving pig body development and carcass lean percent by increasing fiber diameter and the loin eye area, and decreasing the skin thickness and fat percent.

Lysine methylation is an important covalent modification of histone and has fundamental and divers roles in biological processes including regulation of chromatin structure dynamics and gene expression. Recently, a distinct class of histone lysine methyltransferase DOT1 was found to methylate histone H3 lysine79 (H3K79) residue, which is located on the accessible face of the core nucleosome. The DOT1 proteins do not contain a SET domain, a conserved sequence motif found in all previously characterized histone H3 lysine methyltransferases that act on the histone N-termianl tail. The characteristics of DOT1 proteins and H3K79 methylation suggest that they may have important and characteristic functions. Here, we summarize recent advances in specific structure of DOT1 protein, biological functions of DOT1 proteins and H3K79 methylation and trans-histone regulatory1 between histone H2B ubiquitination and H3K79 methylation.

In mouse, matured oocytes are arrested at metaphase- (M) after ovulation. If the M oocytes are not fertilized on time, they will increasingly become aged in the oviduct. The aging of oocytes can lead to abnormal development of embryos. So it is important to study the mechanism of oocyte aging. Herein, we studied the change of oocyte chromosome after ovulation into the oviduct in vivo. Results indicated that 65% of old oocytes (34 h post hCG) showed aberrant MII, with chromosome misalignment and dispersal, in contrast to the young oocytes (14 h post hCG). In addition, chromosome changes may be associated with the increase of acetylation of histone 3 and histone 4, at lysine 14 and lysine 16 (H3K14 and H4K16), respectively. On the other hand, the decrease of methylation of histone 3 at lysine 9 (H3K9) presumably facilitated aberrant chromosome formation.

RH (radiation hybrid) has proved to be an effective method in constructing human genome maps (including ESTs, STSs and microsatellites). In this study, based on the information of five human genes (FMR1, IDS, FATE, BGN, F8A) on the X chromosome, the linkage relationship of these five genes in pigs were analyzed by a panel of 96 radiation hybrid cell lines. The results showed that FMR1, IDS, FATE, BGN, F8A were in the same linkage group, when LOD was set at 4. When LOD was set at 5, FMR1 and IDS were in the one group, FATE and BGN in the other group, and F8A was in a group by itself.

Circumstantial studies indicated that incomplete or inappropriate epigenetic reprogramming of donor nuclei was likely to be the primary reason for failures in nuclear transfer. In this view, we discussed the roles of several epigenetic mechanisms, including DNA methylation, chromatin remodeling, imprinting and X chromosome inactivation, telomere maintenance, and epigenetic inheritance in the observed abnormalities in clones from different species. Understanding the mechanisms underlying epigenetic reprogramming control will help us resolve the inherent problems in nuclear transfer technology and make its applications promising.

In and out of the eukaryotic genomes, there exist many covalent modifications, of which are the methylation of DNA and histones, and they are both involved in genes silencing, in which the methylation of DNA and H3K9 are synergistic, but the methylation of H3K4 is antagonistic to them. The recent studies showed that these two methylations are correlated, that is, DNA methylation is dependent on the methylation of H3K9. However, the relationship of these two methylations is more complicated in mammals than in lower eukaryotons and plants.