SINEs, evolution and genome structure in the opossum

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.     

SINEs: Short interspersed repeated elements of the eukaryotic genome

Much of the eukaryotic genome is composed of a variety of repetitive sequences. Amongst these, there are two kinds of retroposons (sequence elements derived from nonviral cellular RNA): SINEs (short interspersed elements) and LINEs (long interspersed elements). Amplification of SINEs occurs in a single germ cell, and the members of SINEs spread and become fixed in populations through genetic drift. SINEs can be regarded as phylogenetic landmarks: they are specific to one species, a few species, a genus or in some cases a family, indicating a specific time of amplification during evolution. Recent studies concerning the structure and origin of many SINEs revealed that retroposons are more widespread in animal genomes than was previously thought.     

Barriers to genome editing with CRISPR in bacteria

Journal of Industrial Microbiology & Biotechnology - Genome editing is essential for probing genotype–phenotype relationships and for enhancing chemical production and phenotypic...     

鉴定SINEs的方法及在鱼类基因组中的研究

在高等真核生物的基因组中,编码蛋白质的基因所占比例不到基因组的5%,大部分是无明显功能的、高度变异的中度和高度重复序列[1].     

DNA-guided genome editing tool

正Technologies for targeted modification of eukaryotic genomes are of great value for elucidating and manipulating gene functions in fundamental and applied biological research.In the past two decades,genome editing tools have evolved quickly from random DNA mutagenesis-inducing chemicals or ionizing radiation to programmable sequencespecific nucleases(SSNs)with the CRISPR/Cas technology as the most significant breakthrough(Gaj et al.,2013).     

艰难梭菌基因编辑技术研究进展

艰难梭菌Clostridioesdifficile是一种革兰氏阳性、产芽孢、专性厌氧细菌,是医院相关性腹泻的主要病原体。近年来,随着强毒株的出现(如核糖体027型),其流行性与致死率逐年上升,因此对艰难梭菌生理、生化特征及致病机制的研究受到广泛重视。艰难梭菌生理、生化特征及致病机制研究又以建立其稳定、高效的基因编辑方法为必要前提。借助基因编辑工具,研究者可以扰动艰难梭菌核心生物学过程,在分子水平研究其分子致病机制。如Clos Tron技术在艰难梭菌毒素A (Toxin A)和毒素B (Toxin B)与其致病力关系的研究中起到了关键作用。文中以时间为主线综述了艰难梭菌基因编辑技术的发展历程和最新进展,并对艰难梭菌基因编辑技术未来的研究方向进行展望。