Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas

In eukaryotes, accurate control of replication time is required for the efficient completion of S phase and maintenance of genome stability. We present a high-resolution genome-tiling array-based profile of replication timing for approximately 1% of the human genome studied by The ENCODE Project Consortium. Twenty percent of the investigated segments replicate asynchronously (pan-S). These areas are rich in genes and CpG islands, features they share with early-replicating loci. Interphase FISH showed that pan-S replication is a consequence of interallelic variation in replication time and is not an artifact derived from a specific cell cycle synchronization method or from aneuploidy. The interallelic variation in replication time is likely due to interallelic variation in chromatin environment, because while the early- or late-replicating areas were exclusively enriched in activating or repressing histone modifications, respectively, the pan-S areas had both types of histone modification. The replication profile of the chromosomes identified contiguous chromosomal segments of hundreds of kilobases separated by smaller segments where the replication time underwent an acute transition. Close examination of one such segment demonstrated that the delay of replication time was accompanied by a decrease in level of gene expression and appearance of repressive chromatin marks, suggesting that the transition segments are boundary elements separating chromosomal domains with different chromatin environments.     

SYD-1, a presynaptic protein with PDZ,C2 and rhoGAP-like domains,specifies axon identity in C. elegans

Axons are defined by the presence of presynaptic specializations at specific locations. We show here that loss-of-function mutations in the C. elegans gene syd-1 cause presynaptic specializations to form in the dendritic processes of GABA-expressing motor neurons during initial differentiation. At a later developmental stage, however, syd-1 is not required for the polarity respecification of a subset of these neurons. The SYD-1 protein contains PDZ, C2 and rho-GTPase activating protein (GAP)-like domains, and is localized to presynaptic terminals in mature neurons. A truncated SYD-1 that lacks the rhoGAP domain interferes with neurite outgrowth and guidance. Our data indicate that syd-1 may be involved in specifying axon identity during initial polarity acquisition.     

High-Throughput Expression of C. elegans Proteins

Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in a structural proteomics initiative because of the high quality of its genome sequence and the availability of its ORFeome, protein-encoding open reading frames (ORFs), in a flexible recombinational cloning format. We developed a robotic pipeline for recombinant protein expression, applying the Gateway cloning/expression technology and utilizing a stepwise automation strategy on an integrated robotic platform. Using the pipeline, we have carried out heterologous protein expression experiments on 10,167 ORFs of C. elegans. With one expression vector and one Escherichia coli strain, protein expression was observed for 4854 ORFs, and 1536 were soluble. Bioinformatics analysis of the data indicates that protein hydrophobicity is a key determining factor for an ORF to yield a soluble expression product. This protein expression effort has investigated the largest number of genes in any organism to date. The pipeline described here is applicable to high-throughput expression of recombinant proteins for other species, both prokaryotic and eukaryotic, provided that ORFeome resources become available.     

组蛋白修饰在自身免疫性疾病中的作用

组蛋白修饰是表观遗传修饰的重要方式,在基因表达的调控中扮演重要角色.常见的组蛋白修饰包括组蛋白乙酰化和甲基化.自身免疫性疾病是以机体对自身抗原发生免疫应答而导致自身组织损害为特点的一类疾病.有研究证实,组蛋白修饰参与了多种自身免疫性疾病的发生和发展,如系统性红斑狼疮、类风湿性关节炎、系统性硬化.因而阐明组蛋白修饰的机制可为自身免疫性疾病的治疗提供新的思路.     

Transgene-mediated cosuppression in the C. elegans germ line

Functional silencing of chromosomal loci can be induced by transgenes (cosuppression) or by introduction of double-stranded RNA (RNAi). Here, we demonstrate the generality of and define rules for a transgene-mediated cosuppression phenomenon in the Caenorhabditis elegans germ line. Functional repression is not a consequence of persistent physical association between transgenes and endogenous genes or of mutations in affected genes. The cosuppression mechanism likely involves an RNA mediator that defines its target specificity, reminiscent of RNAi. Cosuppression is strongly abrogated in rde-2 and mut-7 mutants, but is not blocked in an rde-1 mutant, indicating that cosuppression and RNAi have overlapping but distinct genetic requirements.     

Automated assays to study longevity in C. elegans

The nematode Caenorhabditis elegans is excellently suited as a model for studying the genetic and molecular genetic basis of aging, and to test chemical compounds that interfere with the aging process. Mutants of factors in both the insulin and target of rapamycin (TOR) signalling pathways have been shown to extend life span of the worm. Phenotypic similarities among those mutants suggested that, exploiting the corresponding phenotypes in a semiautomated way, may increase the speed of investigating life span and aging in C. elegans. Here, we discuss several methodological approaches to automate longevity assays in the nematode.     

Behavioral Plasticity in the C. elegans Mechanosensory Circuit

This review outlines research into the cellular and molecular mechanisms underlying a simple behavior in the soil-dwelling nematode, C. elegans. A tap administered to the side of a petri plate acts as a nonlocalized mechanical stimulus to the worms within. Most adult worms respond to this tap stimulus with backward locomotion, an action known as the tap-withdrawal response. This behavior has been thoroughly characterized and the neural circuit mediating it has been determined. The response habituates following repeated stimulation, and current work is aimed at elucidating the mechanism behind this simple form of nonassociative learning. Changes in cell excitability and the strength of glutamatergic synapses play key roles in mediating this plasticity.     

SUT-1 enables tau-induced neurotoxicity in C. elegans

We previously reported a transgenic Caenorhabditis elegans model for tauopathies in which expression of human tau in neurons caused insoluble phosphorylated tau accumulation, neurodegeneration and uncoordinated movement (Unc). To identify genes participating in tau neurotoxicity, we conducted a forward genetic screen for mutations that ameliorate tau-induced uncoordination. The recessive mutation sut-1(bk79) partially suppresses the Unc phenotype, tau aggregation and neurodegenerative changes caused by tau. We identified the sut-1 gene and found it encodes a novel protein. We conducted a yeast two hybrid screen to identify SUT-1 binding partners and found UNC-34, the C. elegans homolog of the cytoskeletal regulatory protein Enabled (ENA). In vitro protein binding assays and genetic studies validated the interaction between SUT-1 and UNC-34. The SUT-1/UNC-34 protein-protein interaction plays a role in both the normal function of UNC-34 and in the tau-induced phenotype. Thus, we have found a conserved molecular pathway participating in tau neurotoxicity in C. elegans.     

吞噬作用能促进线虫的程序性细胞死亡

在后生动物的发育中 ,程序性细胞死亡 (ＰＣＤ)在组织的塑型、神经元间的精细连接、多余细胞或损伤细胞的消除等诸多方面扮演重要角色。通过ＰＣＤ方式 ,正在死亡的细胞迅速被吞噬细胞包裹清除。在线虫体内 ,ＰＣＤ需要杀手基因 (ｋｉｌｌｅｒｇｅｎｅｓ)ｅｇｌ- 1、ｃｅｄ - 4和ｃｅｄ - 3等的协同作用 ,而正在死亡细胞的吞噬过程 (ｅｎｇｕｌｆｍｅｎｔ)则由ｃｅｄ - 1、ｃｅｄ -2、ｃｅｄ - 5、ｃｅｄ - 6、ｃｅｄ - 7、ｃｅｄ - 10、ｃｅｄ - 12等吞噬基因 (ｅｎｇｕｌｆｍｅｎｔｇｅｎｅｓ)协同完成。根据基因相互作用的基础 ,将线虫的…     

Natural variation in C. elegans short tandem repeats

Short tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1–6 bp in the reference genome of C. elegans. Of these STRs, 27,667 harbored polymorphisms across 540 wild strains and only 9691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared with the reference genome, the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed the lowest STR diversity and constrained STR mutations. STR diversity also showed similar genetic divergence and selection signatures among wild strains as in previous studies using SNVs. We further identified STR variation in two mutation accumulation line panels that were derived from two wild strains and found background-dependent and fitness-dependent STR mutations. We also performed the first genome-wide association analyses between natural variation in STRs and organismal phenotypic variation among wild C. elegans strains. Overall, our results delineate the first large-scale characterization of STR variation in wild C. elegans strains and highlight the effects of selection on STR mutations.

Short tandem repeats (STRs) are repetitive elements consisting of 1–6 bp DNA sequence motifs that provide a large source for genetic variation in both inherited and de novo mutations (Willems et al. 2016; Fotsing et al. 2019). The predominant mechanism of STR mutations is DNA replication slippage, which often causes expansion or contraction in the number of repeats (Mirkin 2007; Gemayel et al. 2010). Because of their intrinsically unstable nature, STRs have orders of magnitude higher mutation rates than other types of mutations, such as single nucleotide variants (SNVs) and short insertions or deletions (indels) (Lynch 2010; Sun et al. 2012; Willems et al. 2016; Gymrek et al. 2017). The precise mutation rates of STRs are highly variable across different loci and are affected by motif sequences and repeat lengths (Legendre et al. 2007). In humans, STRs are estimated to constitute about 3% of the genome and are associated with dozens of diseases (Mirkin 2007; Hannan 2018; Malik et al. 2021). Emerging studies have also revealed the role of STRs in regulation of gene expression and complex traits in humans and other organisms, which were suggested to facilitate adaptation and accelerate evolution (Fotsing et al. 2019; Jakubosky et al. 2020; Reinar et al. 2021).The free-living nematode Caenorhabditis elegans is a keystone model organism that has been found across the world (Brenner 1974; Kiontke et al. 2011; Andersen et al. 2012; Félix and Duveau 2012; Cook et al. 2017; Crombie et al. 2019, 2022; Lee et al. 2021). The C. elegans Natural Diversity Resource (CeNDR) catalogs and distributes thousands of wild strains, genome sequence data, and genome-wide variation data, including SNVs and short indels (Andersen et al. 2012; Cook et al. 2017; Evans et al. 2021a). Numerous C. elegans population genomics studies and genome-wide association (GWA) studies have leveraged CeNDR resources, such as the genetic variant data across wild strains and the GWA mapping pipeline (Snoek et al. 2020; Lee et al. 2021; Evans et al. 2021a; Gilbert et al. 2022; Widmayer et al. 2022; Zhang et al. 2022). However, the natural diversity in C. elegans STRs and their impacts on organism-level and molecular traits among wild strains remain unknown because of the lack of STR variation characterization. STRs are challenging to genotype because of their repetitive nature causing errors such as “PCR stutters” (Gymrek 2017). Recent advances provided opportunities to identify genome-wide STR variation accurately in large scales using high-throughput sequencing data (Willems et al. 2017).In this work, we focused on characterization of STRs with motif lengths of 1–6 bp in the reference genome of C. elegans and identified their natural variation across 540 genetically distinct wild strains. Using these data, we analyzed mutations, diversity, and how selection occurred in the STR loci. We also investigated the possible impacts of STR variation on phenotypic variation across wild C. elegans strains.     

组蛋白修饰在糖尿病发病中的作用

组蛋白修饰是表观遗传学的一个重要内容,在基因表达调控中发挥至关重要的作用。最新研究表明组蛋白修饰直接或间接参与糖尿病的发病,深入研究糖尿病组蛋白修饰情况,将为糖尿病的治疗或干预带来全新的方法。     

Generation and modulation of chemosensory behaviors in C. elegans

C. elegans recognizes and discriminates among hundreds of chemical cues using a relatively compact chemosensory nervous system. Chemosensory behaviors are also modulated by prior experience and contextual cues. Because of the facile genetics and genomics possible in this organism, C. elegans provides an excellent system in which to explore the generation of chemosensory behaviors from the level of a single gene to the motor output. This review summarizes the current knowledge on the molecular and neuronal substrates of chemosensory behaviors and chemosensory behavioral plasticity in C. elegans.     

Global histone modification of histone H3 in colorectal cancer and its precursor lesions

Chromatin remodeling through histone modification is an important mechanism of epigenetic gene dysregulation in human cancers. However, little is known about global alteration of histone status during tumorigenesis and cancer progression. Histone H3 status was examined in benign and malignant colorectal tumors by immunohistochemistry and Western blotting. For immunohistochemical evaluation, 4 anti-histone H3 antibodies, specific to dimethylation at lysine 4 (H3K4me2), acetylation at lysine 9 (H3K9ac), dimethylation at lysine 9 (H3K9me2), and trimethylation at lysine 27 (H3K27me3), were used. On immunohistochemistry, H3K4me2, H3K9ac, and H3K27me3 showed no significant changes between normal and colorectal tumors. On the other hand, the global level of H3K9me2 was distinctly higher in neoplastic cells (adenoma and adenocarcinoma) than in normal glandular cells. In addition, it was significantly higher in adenocarcinoma than in adenoma. Correspondingly, Western blotting confirmed that H3K9me2 expression was significantly higher in adenocarcinomas than in normal colorectal mucosa. No alteration of H3K9me2 was observed with tumor differentiation and with the histological subtypes of colorectal cancers. These results suggest that aberration of the global H3K9me2 level is an important epigenetic event in colorectal tumorigenesis and carcinogenesis involved with gene regulation in neoplastic cells through chromatin remodeling.