基于CRISPR/Cas9系统高通量筛选研究功能基因

利用功能缺失型(Loss-of-function)或者功能获得型(Gain-of-function) 策略高通量筛选功能基因,是研究人员快速寻找调控特定表型的重要或关键基因的主要方法。RNA干扰(RNA interference,RNAi)的遗传筛选方法因操作简单、成本相对较低等优势,尽管已经得到了广泛的应用,然而其抑制效果不完全、脱靶效应明显等劣势依然存在。近年来兴起的CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeat sequences/ CRISPR-associated protein 9)技术能快速、简便、准确地实现基因组敲除等编辑功能,因而成为一种强大的遗传筛选工具;在各种细胞系、人和小鼠及斑马鱼等多种模式动物中,大规模运用该方法筛选功能基因已经取得了巨大成功。本文总结了CRISPR/Cas9技术的特点,将其与传统基因工程方法进行了分析比较,回顾了近期相关的高通量功能基因筛选工作,最后探讨了该技术未来的发展趋势。     

CRISPR/Cas9技术在微生物研究中的应用进展

CRISPR(Clustered regularly interspaced short palindromic repeats)/Cas(CRISPR associated proteins)系统是在细菌和古生菌中发现的一种RNA指导的降解入侵病毒或质粒DNA的适应性免疫系统。由II型CRISPR/Cas系统改造而成的CRISPR/Cas9技术已经被开发成一种强大的基因组编辑和表达调控工具,并且广泛应用于基因功能研究、代谢工程和合成生物学等领域。本文从CRISPR/Cas9系统的发现过程、分类、作用原理、在微生物研究中的应用进展等方面进行总结,并展望了该技术的应用前景。     

CRISPR/Cas系统及其在昆虫基因功能研究中的应用

近年来在众多细菌和古细菌中发现一类成簇的、有规律间隔的短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)结构家族,通过对其及相关基因(CRISPR-associated genes,Cas gene)的系统研究得知,它是生物体长期进化形成的获得性免疫系统,由RNA介导,降解入侵病毒或者噬菌体DNA。众多研究者将CRISPR/Cas系统改造成第三代人工核酸酶,用于靶向编辑基因组,目前已广泛应用于人类细胞、小鼠、大鼠、斑马鱼、细菌、果蝇、酵母、线虫等。综述了此系统的基本结构、原理及在昆虫上的应用、展望前景,为今后开展昆虫基因功能研究提供一定的技术参考。     

CRISPR/Cas9基因编辑技术在食用菌中的应用现状

CRISPR/Cas9基因编辑系统是一项通用的基因修饰技术,是植物、动物、真菌以及微生物的功能基因和遗传育种研究的重要技术。本文介绍了该技术在食用真菌的基因研究和遗传育种中的应用现状,包括Cas9和sgRNA的递送和表达策略、遗传转化方法、突变体筛选以及DNA双链断裂后的靶位点的修复策略。同时总结了该技术在食用菌中应用所面临的主要问题及其优化策略,并结合个人研究背景展望了其未来在食用菌研究中的应用价值。     

CRISPR/Cas9基因编辑技术在丝状真菌中的应用

随着对丝状真菌基因水平研究的不断深入,CRISPR/Cas9技术作为先进的基因编辑技术,已被广泛应用于丝状真菌的基因编辑。探究了CRISPR/Cas9系统在不同丝状真菌中的应用情况,主要从sgRNA的构建与表达、Cas9蛋白的改造与表达、不同的DNA双链断裂修复（DNA double-strand break,DSB）方式等方面进行概述,并对编辑效率、脱靶效应进行总结,旨在为今后丝状真菌中CRISPR/Cas9系统的构建及改良提供思路。     

CRISPR/Cas基因编辑技术及其在微藻研究中的应用

微藻由于在医药、食品、可再生燃料和化学原料等方面的潜力,受到了研究者越来越多的关注和青睐。然而,合适基因编辑方法和转化工具的缺乏,使得微藻基因工程的进展还相对比较缓慢。随着分子生物和基因编辑技术的发展,CRISPR 技术凭借简便、特异和高效的优势,逐渐成为探讨基因功能、提高植物育种和增加代谢物产物等研究的有力手段。基于此,本文综述了CRISPR/Cas 的2 种主要类型,重点论述了其在微藻领域中的应用进展,并总结了CRISPR 技术在微藻应用中所存在的问题,期望为以后的研究提供启发和参考。     

CRISPR/Cas9系统在昆虫中的应用

CRISPR/Cas9(clustered regularly interspaced short palindromic repeat/CRISPR-associated nuclease 9)技术是一种RNA引导的基因组靶向编辑技术,能对基因组序列进行精确编辑,在探究基因功能、修复受损基因、沉默有害基因、改良品质性状等方面具有广阔的应用前景。近年来,随着对CRISPR/Cas9系统研究的不断深入和改造,该系统以其操作简易、省时、高效等优点在生物学研究的众多领域中得以推广和应用,特别是在果蝇(Bombyx mori)、家蚕(silkworm)、埃及伊蚊(Aedes aegypti)和蝴蝶(butterfly)等多种昆虫中。本文概述了CRISPR/Cas9的结构、作用原理及发展优化,总结了CRISPR/Cas9导入昆虫的策略和在昆虫中的应用,以及对CRISPR/Cas9系统产生脱靶问题的应对策略,以期对经济昆虫和有益昆虫的分子育种、害虫的生物技术防控等研究提供参考。     

CRISPR/Cas9在丝状真菌基因组编辑中的应用

丝状真菌(filamentous fungi)通常指那些菌丝体较发达且不产生大型肉质子实体结构的真核微生物。丝状真菌不仅在自然界物质循环中发挥着重要作用,还与人类健康和工农业生产有着紧密的联系。然而,对丝状真菌进行遗传操作相对困难,极大地妨碍了丝状真菌的遗传学研究。成簇的规律间隔的短回文重复序列及其相关系统(clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9, CRISPR/Cas9)是近年来发现的一种存在于细菌和古菌中保守的获得性免疫防御机制。最近,CRISPR/Cas9被开发成为了一种方便灵活的基因组编辑技术。目前,该技术已经广泛应用在不同物种的基因组编辑中。本文概述了CRISPR/Cas9在丝状真菌基因组编辑中的应用进展,旨在为开展该领域的研究工作提供参考。     

转录因子ZnF-706在鳞翅目昆虫中的进化格局及在家蚕中的功能

【目的】探讨家蚕Bombyx mori的潜在驯化基因——转录因子ZnF-706在鳞翅目(Lepidoptera)昆虫进化过程及家蚕驯化过程中的分子进化格局;并基于CRISPR/Cas9家蚕基因组编辑平台,探讨ZnF-706基因在家蚕中的功能。【方法】首先分析了家蚕ZnF-706序列特征,并利用已发表芯片数据调研该基因在家蚕幼虫组织中的表达格局;利用Phylogenetic Analysis byMaximum Likelihood (PAML)分支检验方法,分析该基因在鳞翅目不同类群中的分子进化格局。基于已发表的家蚕-野桑蚕Bombyx mandarina群体基因组多态性数据,对ZnF-706进行基因区域人工选择信号分析;对ZnF-706基因上游2 kb的调控区域进行单核苷酸多态性位点频率检测,发掘在家蚕群体中固定下来的突变位点;针对突变位点所在区域进行转录因子结合活性预测。利用CRISPR/Cas9基因编辑技术敲除ZnF-706基因,获得纯和突变体;以野生型家蚕为对照,检测突变体的茧重及蛹重变化。【结果】家蚕ZnF-706的编码蛋白具有典型的锌指蛋白结构域。ZnF-706在家蚕5龄第3天幼虫各组织中广泛表达,尤其表皮、脂肪体和生殖腺中有很高的表达量;该基因在鳞翅目、蚕蛾总科(Bombycoidea)及天蚕Antherea yamamai 3个分支中均呈现快速进化信号,在家蚕中有强烈的人工选择信号。该基因所在基因组区域的家蚕-野桑蚕种群分歧度参数Fst明显升高,家蚕群体中的群体多样性π明显降低,表明它位于一个选择扫荡区域内;该基因在家蚕-野桑蚕中的9个SNP位点存在于上游调控区,并位于转录因子结合活性区域内。该基因的纯合家蚕突变体ΔZn F-706生存力减弱,并且茧重以及蛹重与野生型家蚕相比都显著降低。但与黑腹果蝇Drosophila melanogaster中不同的是,家蚕中该基因的突变并不致死。【结论】ZnF-706可能在鳞翅目尤其是泌丝昆虫中进化,并在家蚕驯化过程中受到选择压力,提示其对于特征性状茧丝的变异可能发挥作用。该基因可能通过对丝蛋白基因的直接调控,或通过影响家蚕的生长发育而间接地影响茧丝性状。本研究不仅为探究家养动物人工选择机制提供了来自昆虫类材料的独有证据,也为后续深入开展家蚕重要经济性状的转录调控研究提供线索。     

Serial analysis of gene expression in the silkworm, Bombyx mori

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.     

Ecdysteroid-induced programmed cell death and cell proliferation during pupal wing development of the silkworm, Bombyx mori

The wing margin of adult wings of Lepidoptera is defined by the position of a "bordering lacuna"(BL). During adult wing development, cell proliferation and scale formation proximal to this lacuna and programmed cell death distal to the lacuna are generally observed. To determine the effect of 20-hydroxyecdysone (20E) on these events, we cultured the silkworm pupal wings with or without 20E and analyzed regional specificity for cell death by the TUNEL method and cell proliferation by 5-bromodeoxyuridine labeling. Programmed cell death was induced by 20E after 5 days of culture and was detected only in the region distal to BL. Cell proliferation after 1 day of culture and scale formation after 5 days of culture were also inducible by 20E and detected in the region proximal to BL. These results suggest that two types of pupal wing cells, which are divided by the position of the BL, respond to ecdysteroid in different manners. Higher concentrations of 20E (more than 1,000 ng/ml) repressed the scale formation, while such repression could not be observed in the peripheral cell death even with 5,000 ng/ml 20E. The ecdysteroid may work both as a trigger to make the wing margin and scales and as a developmental timer to arrange these cellular responses.     

Functional analysis of Ultrabithorax in the silkworm, Bombyx mori, using RNAi

The formation of abdominal appendages in insects is suppressed by the Hox genes Ultrabithorax (Ubx) and abdominal-A (abd-A), but mechanisms of the suppression can differ among species. As the function of Ubx and abd-A has been described in only a few species, more data from various insects are necessary to elucidate the evolutionary transition of regulation on abdominal appendages. We examined the function of Ubx in the silkworm Bombyx mori (Bm-Ubx) by embryonic RNA interference (RNAi). This is the first case in which functional analysis for Ubx is performed in lepidopteran insects. Larvae treated with Bm-Ubx dsRNA displayed an additional pair of thoracic leg-like protuberances in A1, whereas the other abdominal segments had no transformation. Our results suggest that Bm-Ubx is a suppressor of leg development in A1.     

Gene expression profiling in the silkworm, Bombyx mori, during early embryonic development

We prepared a cDNA library for a microarray from eggs of the silkworm, Bombyx mori, at the germ-band formation (24 hours after fertilization) stage. Using a microarray constructed with 2,445 ESTs, we screened gene expression profiles during germ-band formation at six specific time points in the early embryonic stages (from the unfertilized egg to the formation of abdominal leg appendages), and determined 241 of these cDNAs to represent genes that were expressed differentially during the germ-band formation stage. These differentially expressed genes grouped into two clusters. In the early and late clusters, 203 and 38 genes were upregulated, respectively. In the upregulated clusters, we isolated several genes that were associated with development and cell communication, including egalitarian, RAD23b, innexin 2, and senescence-associated protein. Northern blot hybridization revealed that the expression patterns of 14 genes had changed in each of the stages. In this study, we assessed changes in the levels of gene expression in relation to the germ-band formation stages in whole Bombyx embryos.     

Synthesis and phosphorylation of ecdysteroids during ovarian development in the silkworm, Bombyx mori

In the silkworm, Bombyx mori, it has been demonstrated that most free ecdysteroids in the ovary are converted to physiologically inactive ecdysteroid 22-phosphates, which are then transformed back to free ecdysteroids during early embryonic development. Two specific enzymes involved in the reciprocal conversion of ecdysteroids, namely, ecdysteroid 22-kinase (EcKinase) and ecdysteroid-phosphate phosphatase, have been isolated and characterized. In this study, we first attempted a phylogenetic analysis of EcKinase. The resulting phylogenetic tree showed that many proteins homologous to B. mori EcKinase are found not only in ecdysozoa, including insects and nematodes, but also in teleosts, fungi, and bacteria. We then investigated the sites where free ecdysteroids are synthesized and phosphorylated in the ovary. We found that (1) the mRNAs of two P450 enzymes involved in ecdysteroidogenesis, CYP306a1 (25-hydroxylase) and CYP314a1 (20-hydroxylase), are expressed mainly in follicle cells, (2) EcKinase mRNA localizes in the oocyte and nurse cells, and (3) EcKinase immunoreactivity localizes mainly in the external region of the oocyte, not in nurse cells or follicle cells. From these results, we suggest that ecdysteroids in the B. mori ovary are synthesized in follicle cells and transferred into the oocyte, where they are phosphorylated by EcKinase, whose mRNA originates from nurse cells and the oocyte itself.     

DNA replication events during larval silk gland development in the silkworm, Bombyx mori

The silk gland is an important organ in silkworm as it synthesizes silk proteins and is critical to spinning. The genomic DNA content of silk gland cells dramatically increases 200-400 thousand times for the larval life span through the process of endomitosis. Using in vitro culture, DNA synthesis was measured using BrdU labeling during the larval molt and intermolt periods. We found that the cell cycle of endomitosis was activated during the intermolt and was inhibited during the molt phase. The anterior silk gland, middle silk gland, and posterior silk gland cells asynchronously exit the endomitotic cycle after day 6 in 5th instar larvae, which correlated with the reduced expression of the cell cycle-related cdt1, pcna, cyclin E, cdk2 and cdk1 mRNAs in the wandering phase. Additional starvation had no effect on the initiation of silk gland DNA synthesis of the freshly ecdysed larvae.     

Hormonal control of ovarian development in the silkworm,Bombyx mori

Hormonal control of ovarian development was examined in Bombyx mori. The weight of the ovary increased suddenly by 3 days after pupal ecdysis, and vitellogenin could be immunologically detected in the ovary at that time. The ecdysteroid titers during pupal-adult development, quantified by radioimmunoassay, increased from day 0 to day 2. Ovarian development was arrested for a long period in brainless pupae and isolated pupal abdomens. Injection of 20-hydroxyecdysone into such preparations stimulated development of the ovaries, and vitellogenin could be detected in ovaries 2 days after injection. The results suggest that 20-hydroxyecdysone acts by stimulating the growth of ovary.     

Functional analysis of a survivin-like gene in Bombyx mori

The survivin (svv) gene is a newly discovered member of the inhibitors of apoptosis gene family. In recent years, svv has been confirmed to have an anti-apoptosis function and to play a critical role in cell division. We identified a survivin-like gene in the silkworm, Bombyx mori (Bm-svv). In this study, to gain insight into its function, a baculovirus expression system was used to express the Bm-svv gene in insect cell lines. The recombinant viruses were then used as a vector to transform insect cells, and cell activity was determined using the Cell Counting Kit-8 (CCK-8), which is usually employed for detecting mammalian cell number. The results indicated that the Bm-svv gene plays a role in the cell growth arrest or apoptosis induced by viruses. Furthermore, the CCK-8 kit is effective in determining the activity of insect cells.