Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA

An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization

Structure and compositions of cenozoic oils from the pannonian basin (Yugoslavia)

The average structural characteristics of oily and resinous components of nine crude oils of various types from different Miocene horizons of the Sirakovo and Bradarac-Maljurevac oil fields (Serbia), as well as the mass-spectrometrically established hydrocarbon-group composition of these oils, are described. The most abundant components of crudes from both oil fields are mono- and bicyclanes bearing long alkyl substituents. It was found that there is no universal trend in the chemical type of the oils with the occurrence depth of the producing zones in these fields, that is, oils are enriched in aliphatic hydrocarbons with depth in the Sirakovo oil field and in naphthene hydrocarbons in the Bradarac field. These trends cannot be explained by microbial degradation processes or by the catagenetic alteration of petroleum composition in the Earth's interior and indicate a low level of thermal maturity of the source organic matter that gave rise to the hydrocarbon systems in question. A certain parallelism of variation in the structural parameters of hydrocarbonaceous and heteroorganic (resinous) components of the oils depending on natural factors is noted

Structure and compositions of cenozoic oils from the pannonian basin (Yugoslavia)

The average structural characteristics of oily and resinous components of nine crude oils of various types from different Miocene horizons of the Sirakovo and Bradarac-Maljurevac oil fields (Serbia), as well as the mass-spectrometrically established hydrocarbon-group composition of these oils, are described. The most abundant components of crudes from both oil fields are mono- and bicyclanes bearing long alkyl substituents. It was found that there is no universal trend in the chemical type of the oils with the occurrence depth of the producing zones in these fields, that is, oils are enriched in aliphatic hydrocarbons with depth in the Sirakovo oil field and in naphthene hydrocarbons in the Bradarac field. These trends cannot be explained by microbial degradation processes or by the catagenetic alteration of petroleum composition in the Earth's interior and indicate a low level of thermal maturity of the source organic matter that gave rise to the hydrocarbon systems in question. A certain parallelism of variation in the structural parameters of hydrocarbonaceous and heteroorganic (resinous) components of the oils depending on natural factors is noted

Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming

Summary Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and cancer resistance. We observed that the reprogramming efficiency of NMR fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts. Expression of SV40 LargeT antigen (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that NMR chromatin may be refractory to reprogramming. Analysis of the global histone landscape revealed that NMR had higher levels of repressive H3K27 methylation marks and lower levels of activating H3K27 acetylation marks than mouse. ATAC-seq revealed that in NMR, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the NMR promoters. These results suggest that NMR displays a more stable epigenome that resists de-differentiation, contributing to the cancer resistance and longevity of this species