Numerous potentially functional but non-genic conserved sequences on human chromosome 21

The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes.     

非编码RNA与表达调控作用

真核生物转录产生了大量的非编码RNA（ncRNA）,种类繁多？表达及调节模式复杂多样,且对细胞的生长是必须的,并非是转录的＂垃圾＂。根据功能,ncRNA可以大致分成＂持家RNA＂与＂调控RNA＂。ncRNA在遗传信息的载体（DNA和染色质）与表达产物（蛋白质）的相关生物过程中都有着极其重要的作用。     

染色质转座酶可及性测序及其在木本植物中的应用前景

染色质转座酶可及性测序 (assay for transposase-accessible chromatin with high-throughput sequencing, ATAC-seq)是2013年在人类免疫细胞中建立的用于研究表观遗传调控的重要技术。该技术已在人类及小鼠等模式动物的基因组调控元件鉴定、转录因子结合位点识别及转录调控机制的解析等研究领域发挥了重要作用。然而,ATAC-seq技术在植物领域中的研究应用还处于起步阶段,相关研究主要集中在拟南芥和水稻等模式植物中。笔者主要概述了ATAC-seq技术在植物中的应用,包括染色质可及性图谱绘制、抗逆机制解析、表观修饰鉴定及调控元件识别等领域的研究进展,并进一步阐述了ATAC-seq在木本植物中的应用潜力,以推动ATAC-seq技术在木本植物表观基因组学研究中的应用。     

Determinants of nucleosome organization in primary human cells

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.     

雷蒙德氏棉DNase Ⅰ高敏感位点(DHSs)文库构建方法

染色质DNA对DNase Ⅰ表现出高敏感性的位点(DNase Ⅰ hypersensitive sites,DHSs)多是顺式作用元件所在的位置,包括启动子、增强子、调节子和衰减子等.研究DHSs位点的数目及其动态变化是探明顺式作用元件功能、揭示基因表达调控机制,乃至进行基因编辑和创新遗传材料的重要辅助手段.本文借鉴水稻和拟南芥DHSs文库构建方法,通过优化设计,初步建立了二倍体雷蒙德氏棉(Gossypium raimondii D5)的DHSs文库,为深入进行棉花功能基因组研究奠定基础.     

Topological domains in mammalian genomes identified by analysis of chromatin interactions

The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.     

Sequencing and comparison of yeast species to identify genes and regulatory elements

Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.