鸡长链非编码RNA发掘及组织特异性表达分析

长链非编码RNA(Long non-coding RNA,lnc RNA)是一类长度大于200个核苷酸、缺少蛋白编码功能的RNA。lnc RNA可从多层面调控基因表达,影响表型性状。鸡作为重要经济动物和模式生物,lnc RNA研究相对滞后。为加快鸡lnc RNA研究进展,利用公共数据库(如NCBI-SRA等)中鸡高通量转录组测序(RNA-seq)数据,通过生物信息学方法发掘8 040条鸡lnc RNA,发现大量组织特异性表达lnc RNA,为鸡lnc RNA功能研究奠定基础。     

基于转录组分析ABA促进葡萄花青苷积累相关基因

【目的】分析参与调控ABA促进葡萄着色的相关基因,探讨ABA促进葡萄果实花青苷积累的分子机制。【方法】以‘红巴拉多’葡萄为试材,在转色前期（约花后6周）使用300 mg∙L^-1 ABA对果穗进行浸果处理,以清水处理为对照。观察表型,并利用超高液相色谱质谱联用仪（UPLC-MS）测定花青苷组分及含量,再利用转录组测序技术从分子水平对ABA促进花青苷积累的机制进行生物信息学分析。【结果】外源ABA处理3 d后,葡萄果实着色明显加深,花青苷种类和含量增多,其中芍药素3-O-葡萄糖苷、锦葵色素3-O-葡萄糖苷两种单体花青苷含量增加最为显著。分析ABA处理18 h和3 d后葡萄果实转录水平的差异,并通过KEGG富集分析发现了11个ABA信号通路基因以及52个与花青苷生物合成和转运相关的基因差异表达,它们均在外源ABA处理后表达上调。通过将差异基因与葡萄转录因子库进行比对,共发现297个转录因子差异表达。进一步分析差异转录因子表达模式,筛选与VvMYBA1表达模式相近的转录因子,发现15个MYB、bHLH、bZIP、NAC、Dof、HD-ZIP等家族的转录因子,其可能参与调控花青苷生物合成。启动子顺式作用元件分析表明,大部分筛选到的差异基因启动子中含有ABRE元件,说明这些差异表达基因的启动子可能为ABA诱导型启动子。对部分候选基因的表达模式进行实时荧光定量（qRT-PCR）分析,证实了RNA-seq的准确性。【结论】ABA促进葡萄花青苷积累涉及11个ABA信号转导、52个花青苷合成和转运相关基因,15个转录因子可能参与调控了这一生物过程。研究结果为揭示ABA促进葡萄花青苷积累的分子机制提供了一定基础。     

基于转录组测序的枣黑顶病发病机理初探

为进一步诠释枣黑顶病发病机理,本研究使用Illumina高通量测序技术对自然发病枣果(ZJINF)、氢氧化钙处理枣果(ZJPRE)及健康枣果(ZJCON)进行分析,拟从转录组水平探明枣果黑顶病发生的分子机理。基因功能注释(GO)分析结果表明,ZJINF vs ZJCON中的差异表达基因主要体现在钙离子结合、钙依赖磷脂结合、金属离子体内平衡、防御反应等生物学功能上,导致枣果对外界不良环境的抗性减弱。代谢通路(KEGG)富集分析显示:植物-病原体互作、内质网蛋白质加工、吞噬体等代谢通路富集程度较高。ZJINF vs ZJCON中,CALR、CRT被抑制低表达;而喷施氢氧化钙之后,枣果的CALR、CRT两种钙蛋白表达水平均与健康枣果无显著差异。表明CALR、CRT在黑顶病的抗病过程中可能有着重要的作用。     

重度冷应激下民猪背最长肌应答分子调控网络分析

为解析家猪在重度冷应激下骨骼肌应答反应的分子机制,本研究利用民猪的重度冷应激模型结合RNA-seq测序技术,对遭受重度冷应激后民猪背最长肌的基因和lncRNA的表达变化、功能注释以及两者间的调控关系进行了分析。结果表明:1)民猪在遭受3 d的重度冷应激(-17 ℃~-26 ℃)后,背最长肌的53个基因发生了显著上调表达,35个基因发生了显著下调表达;53个lncRNA发生了显著上调,38个lncRNA发生了显著下调。差异表达基因中有多个与炎症反应相关的基因,如AREG、HAS1、MMP25和SLC11A1等基因发生了显著上调表达;与低温胁迫相关的TREH和与应激反应相关的TRIB3、与碳水化合物、葡萄糖和脂质代谢相关的HGFAC等基因也发生了显著上调表达。2)差异表达基因所参与的生物过程主要集中在胶原代谢、伤口愈合表皮细胞扩散和肌肉肥大调节过程等,且多位于细胞外区间;差异表达基因显著富集的生物学通路仅1个MAPK通路。3)存在显著表达差异的91个lncRNA顺式调控129个基因,反式调控750个基因,lncRNA与靶基因间的互作关系复杂。预测到的靶基因显著富集到MAPK和TNF 2个生物学通路。综上,重度冷应激导致民猪背最长肌出现了炎症反应,改变了部分与炎症、低温胁迫、应激反应和营养物质代谢相关基因的表达及部分lncRNA的表达,MAPK和TNF信号通路被激活。     

甘蓝型油菜角果数突变体基因的定位及候选基因分析

角果数是油菜单株产量重要的构成因子之一,其优异等位基因的发掘和利用对产量的提高至关重要。油菜中已定位到上百个角果数QTL,但大多数效应不大且不稳定,难以进行精细定位或克隆。本研究前期发掘到一个油菜突变体(No.7931),其花序顶端在分化出约十朵花后即停止生长,因而成熟期角果极少。利用该少角果突变体和多角果品系No.73290构建F2分离群体,从中挑选角果数极端单株各30株进行BSA-seq,在C02染色体检测到3个关联区间:0～1.1 Mb、4.7～6.2 Mb、11.5～12.4 Mb。该候选区间在油菜参考基因组DarmorV8.1中有522个注释基因,存在SNP或Indel差异且有同源注释的基因235个。在花芽分化初期,选取两亲本(No.73290和No.7931)的茎尖分生组织进行RNA-seq,总共鉴定到8958个差异表达基因(DEGs)。这些DEGs显著富集于20个生物学通路,包括碳代谢、翻译、氨基酸代谢(和花芽分化高度相关)等,其中99个位于关联区间。结合基因功能注释以及序列和表达差异分析确定了9个候选基因(BnaC02g00490.1D2、BnaC02g01030.1D...     

Transcriptome sequencing reveals two subtypes of cortisol-secreting adrenocortical tumours in dogs and identifies CYP26B1 as a potential new therapeutic target

Cushing's syndrome (CS) is a serious endocrine disorder that is relatively common in dogs, but rare in humans. In ~15%–20% of cases, CS is caused by a cortisol-secreting adrenocortical tumour (csACT). To identify differentially expressed genes that can improve prognostic predictions after surgery and represent novel treatment targets, we performed RNA sequencing on csACTs (n = 48) and normal adrenal cortices (NACs; n = 10) of dogs. A gene was declared differentially expressed when the adjusted p-value was <.05 and the log₂ fold change was >2 or < −2. Between NACs and csACTs, 98 genes were differentially expressed. Based on the principal component analysis (PCA) the csACTs were separated in two groups, of which Group 1 had significantly better survival after adrenalectomy (p = .002) than Group 2. Between csACT Group G1 and Group 2, 77 genes were differentially expressed. One of these, cytochrome P450 26B1 (CYP26B1), was significantly associated with survival in both our canine csACTs and in a publicly available data set of 33 human cortisol-secreting adrenocortical carcinomas. In the validation cohort, CYP26B1 was also expressed significantly higher (p = .012) in canine csACTs compared with NACs. In future studies it would be interesting to determine whether CYP26B1 inhibitors could inhibit csACT growth in both dogs and humans.     

Molecular phenotyping of malignant canine mammary tumours: Detection of high-risk group and its relationship with clinicomolecular characteristics

Canine mammary gland tumours (CMTs) constitute the most common cancer in female dogs and comprise approximately 50% of all canine cancers. With the advent of high-throughput technologies such as microarray and next-generation sequencing, the molecular phenotyping (classification) of various cancers has been extensively developed. The present study used a canine RNA-sequencing dataset, namely GSE119810, to classify 113 malignant CMTs and 64 matched normal samples via an unsupervised hierarchical algorithm with a view to evaluating the association between the resulting subtypes (clusters) (n = 4) and clinical and molecular characteristics. Finally, a molecular classifier was developed, and it detected 1 high-risk molecular subtype in the training dataset (GSE119810) and 2 independent validation datasets (GSE20718 and GSE22516). Our results revealed four molecular subtypes (C2–C5) in malignant CMTs. Furthermore, the normal samples constituted a distinct group in the clustering analysis. Marked significant associations were observed between the molecular subtypes (especially C5) and clinical/molecular features, including positive lymphatic invasion, high tumour grades, histopathology diagnoses, short survival and high TP53 mutation rates (ps <.05). The high-risk subtype (C5) was further characterized through the development of a cell cycle-based gene signature, which comprised 37 proliferation-related genes according to the support vector machine algorithm. This signature identified the high-risk group in both training and validation datasets (ps <.001). In the validation analysis, our potential classifier robustly predicted patients with positive lymphatic invasion, metastases and short survival.     

基于RNA-seq对猪瘟病毒感染宿主的转录组学研究进展

对转录组测序(RNA-seq)的技术特点及其发展进行概述，对该技术在猪瘟感染研究中的应用进行详细综述，并对其存在的问题及未来发展做了进一步展望，以期为猪瘟的相关研究提供参考。