检索结果-内蒙古大学图书馆

Long-read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities

引用

AMERICAN JOURNAL OF MEDICAL GENETICS PART A 2024年第12期194卷 e63818页

作者： Sund, Kristen L. Liu, Jie Lee, Joyce Garbe, John Abdelhamed, Zakia Maag, Chelsey Hallinan, Barbara Wu, Steven W. Sperry, Ethan Deshpande, Archana Stottmann, Rolf Smolarek, Teresa A. Dyer, Lisa M. Hestand, Matthew S. Cincinnati Childrens Hosp Med Ctr Div Human Genet Cincinnati OH 45229 USA Univ Cincinnati Dept Pediat Cincinnati OH USA Bionano Genom San Diego CA USA Univ Minnesota Genom Ctr Minneapolis MN USA Cincinnati Childrens Hosp Med Ctr Div Neurol Cincinnati OH USA Yale Univ Sch Med New Haven CT USA Ohio State Univ Dept Pediat Columbus OH USA Nationwide Childrens Hosp Inst Genom Med Columbus OH USA Gene Dx Gaithersburg MD USA Pacific Biosci Menlo Pk CA USA

Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long-read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease-causing genes with relevant neurologic phenotypes (MBD5, NKX2-1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.

关键词： chromosome analysis long read neurologic disease noncoding optical genome mapping structural variation

来源：评论

学校读者我要写书评

暂无评论

Regulatory noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

引用

MSYSTEMS 2020年第1期5卷 e00584-19页

作者： Gelsinger, Diego R. Uritskiy, Gherman Reddy, Rahul Munn, Adam Farney, Katie DiRuggiero, Jocelyne Johns Hopkins Univ Dept Biol Baltimore MD 21218 USA

Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environment. In this study, we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed in an extremophilic microbial community inhabiting halite nodules (salt rocks) in the Atacama Desert. For this, we built SnapT, a new sRNA annotation pipeline that can be applied to any microbial community. We found asRNAs with expression levels negatively correlated with that of their overlapping putative target and itsRNAs that were conserved and significantly differentially expressed between 2 sampling time points. We demonstrated that we could perform target prediction and correlate expression levels between sRNAs and predicted target mRNAs at the community level. Functions of putative mRNA targets reflected the environmental challenges members of the halite communities were subjected to, including osmotic adjustments to a major rain event and competition for nutrients. IMPORTANCE Microorganisms in the natural world are found in communities, communicating and interacting with each other;therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through noncoding RNA-mediated gene regulation.

关键词： RNA extremophiles gene regulation metagenomics metatranscriptomics microbial communities microbiome noncoding

来源：评论

学校读者我要写书评

暂无评论

Evaluating noncoding nucleotide repeat expansions in amyotrophic lateral sclerosis

引用

NEUROBIOLOGY OF AGING 2014年第4期35卷 936.e1-936.e4页

作者： Figley, Matthew D. Thomas, Anna Gitler, Aaron D. Stanford Univ Sch Med Dept Genet Stanford CA USA Stanford Univ Sch Med Stanford Neurosci Grad Program Stanford CA 94305 USA Presentat High Sch San Jose CA USA

Intermediate-length polyglutamine expansions in ataxin 2 are a risk factor for amyotrophic lateral sclerosis (ALS). The polyglutamine tract is encoded by a trinucleotide repeat in a coding region of the ataxin 2 gene (ATXN2). noncoding nucleotide repeat expansions in several genes are also associated with neurodegenerative and neuromuscular diseases. For example, hexanucleotide repeat expansions located in a noncoding region of C9ORF72 are the most common cause of ALS. We sought to assess a potential larger role of noncoding nucleotide repeat expansions in ALS. We analyzed the nucleotide repeat lengths of 6 genes (ATXN8, ATXN10, PPP2R2B, NOP56, DMPK, and JPH3) that have previously been associated with neurologic or neuromuscular disorders, in several hundred sporadic patients with ALS and healthy control subjects. We report no association between ALS and repeat length in any of these genes, suggesting that variation in the noncoding repetitive regions in these genes does not contribute to ALS. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Ataxin polyQ noncoding Nucleotide repeat expansion ALS

来源：评论

学校读者我要写书评

暂无评论

Long noncoding RNA-H19promotes proliferation and Epithelial-Mesenchymal transition through a myc-related feedback loop during liver regeneration in mice

Long noncoding RNA-H19promotes proliferation and Epithelial-...

引用

中华医学会2012年医学遗传学年会暨全国第十一次医学遗传学学术会议

作者：王芳杨富徐丹袁继行张铃孙树汉第二军医大学医学遗传学教研室上海200433

Liver regeneration driven by hepatocyte proliferation is necessary for tissue repair and survival after acute liver injury,liver transplantation,and chronic hepatic *** a partial hepatectomy(PHx)in mice,a rapid induction of proliferative factors activates quiescent hepatocytes and primes their subsequent *** this process,many transcription factors are activated and up-regulate a large number of proliferation-related target genes to repair the liver.c-Myc is a central transcription factor and is essential for total liver *** up-regulation of c-myc mRNA occurs 30 minutes after PHx and sharply increases after several ***,the mechanism of the fast up-regulation of c-myc in early liver regeneration remains *** this study,we reported for the first time that a c-myc-related positive feedback loop contributed to this phenomenon.A long noncoding RNA(lncRNA),H19,stabilized the c-myc mRNA by forming a H19-hnRNP U-myc complex and was transcriptionally up-regulated by c-myc in liver *** many microRNAs,which are a type of noncoding RNA,have been reported to control liver regeneration,H19 is the first lncRNA that is involved in liver *** also found that H19 promotes an epithelial-to-mesenchymal transition(EMT)in liver cells during ***:lncRNA-H19 promotes hepatocyte proliferation and EMT by stabilizing c-myc mRNA in early liver ***,the existence of a c-myc-related positive feedback loop augmented the effect of c-myc for a short time period during early liver regeneration.

关键词： long noncoding RNA hnRNP U partial hepatectomy RNA-protein complex epithelial-mesenchymal transition

来源：评论

学校读者我要写书评

暂无评论

Discovering Transcription Factor noncoding RNA Targets Using ChIP-Seq Analysis

Discovering Transcription Factor Noncoding RNA Targets Using...

引用

作者： Vitalay Fomin Carol Prives

Next generation sequencing enables large-scale analysis of mRNA expression (RNA-seq), genome variance (whole genome or exome), and transcription factor binding (ChIP-seq). Here we describe a method that allows the ide... 详细信息

关键词： ChIP-seq Next Generation Sequencing Bowtie Peak Calling Genomics p53 Transcription factor noncoding

来源：评论

学校读者我要写书评

暂无评论

Combining eQTL and SNP Annotation Data to Identify Functional noncoding SNPs in GWAS Trait-Associated Regions

Combining eQTL and SNP Annotation Data to Identify Functiona...

引用

作者： Stephen A. Ramsey Zheng Liu Yao Yao Benjamin Weeder

We describe a statistical method for prioritizing candidate causal noncoding single nucleotide polymorphisms (SNPs) in regions of the genome that are detected as trait-associated in a population-based genome-wide association study (GWAS). Our method’s key step is to combine, within a naïve Bayes-like framework, three quantities for each SNP: (1) the p-value for the association test between the SNP’s genotype and the trait; (2) the p-value for the SNP’s cis-expression quantitative trait locus (cis-eQTL) association test; and (3) a model-based prediction score for the SNP’s potential to be a regulatory SNP (rSNP). The method is flexible with respect to the source of the model-based rSNP prediction score; we demonstrate the method using scores obtained using the previously published machine-learning-based rSNP prediction method, CERENKOV2. Because it requires only the GWAS trait association test p-value for each SNP and not full genotype information, our method is applicable for GWAS secondary analysis in the common situation where only summary data (and not full genotype data) are readily available. We illustrate how the method works in step-by-step fashion. less

关键词： SNP Annotation Statistical Calculation Genome-Wide Association Study Bioinformatics SNP eQTL GWAS noncoding Computational rSNP Likelihood

来源：评论

学校读者我要写书评

暂无评论

The long noncoding RNA lnc-ob1 facilitates bone formation by upregulating Osterix in osteoblasts

引用

Science Foundation in China 2019年第2期27卷 38-38页

With the support by the National Natural Science Foundation of China,the research team directed by *** XiaoGang(王晓刚)at the Beijing Advanced Innovation Center for Big Data-Based Precision Medicine,Beihang University,recently reported that lncRNA regulates osteoblast activity and bone formation in mice by up-regulating the osteogenic transcription factor Osterix,which was published in Nature Metabolism(2019,1:485—496).

关键词： The long noncoding RNA lnc-ob1 facilitates bone formation by upregulating Osterix in osteoblasts RNA

来源：评论

学校读者我要写书评

暂无评论

Rare germline genetic variation in PAX8 transcription factor binding sites and susceptibility to epithelial ovarian cancer

引用

AMERICAN JOURNAL OF EPIDEMIOLOGY 2025年第4期194卷 1023-1031页

作者： Ezquina, Suzana A. M. Jones, Michelle Dicks, Ed de Vries, Amber Peng, Pei-Chen Lawrenson, Kate Corona, Rosario, I Tyrer, Jonathan Hazelett, Dennis Brenton, James Antoniou, Antonis Gayther, Simon A. Pharoah, Paul D. P. Univ Cambridge Ctr Canc Genet Epidemiol Dept Publ Hlth & Primary Care Cambridge CB2 0SR England Cedars Sinai Med Ctr Ctr Bioinformat & Funct Genom Dept Biomed Sci Los Angeles CA 90048 USA Cedars Sinai Med Ctr Dept Computat Biomed Los Angeles CA 90048 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90024 USA Univ Cambridge Ctr Canc Genet Epidemiol Dept Oncol Cambridge CB1 8RN England Univ Cambridge Dept Oncol Cambridge CB2 0RE England

Common genetic variation throughout the genome and rare coding variants identified to date explain about half of the inherited genetic component of epithelial ovarian cancer risk. It is likely that rare variation in the noncoding genome will explain some of the unexplained heritability, but identifying such variants is challenging. The primary problem is a lack of statistical power to identify individual risk variants by association, as power is a function of sample size, effect size, and allele frequency. Power can be increased by using burden tests, which test for the association of carriers of any variant in a specified genomic region. This has the effect of increasing the putative effect allele frequency. PAX8 is a transcription factor that plays a critical role in tumor progression, migration, and invasion. Furthermore, regulatory elements proximal to target genes of PAX8 are enriched for common ovarian cancer risk variants. We hypothesized that rare variation in PAX8 binding sites is also associated with ovarian cancer risk but unlikely to be associated with risk of breast, colorectal, or endometrial cancer. We have used publicly available, whole-genome sequencing data from the UK 100,000 Genomes Project to evaluate the burden of rare variation in PAX8 binding sites across the genome. Data were available for 522 ovarian cancers, 2984 breast cancers, 2696 colorectal cancers, 836 endometrial cancers, and 2253 noncancer controls. Active binding sites were defined using data from multiple PAX8 and H3K27 chromatin immunoprecipitation sequencing experiments. We found no association between the burden of rare variation in PAX8 binding sites (defined in several ways) and risk of ovarian, breast, or endometrial cancer. An apparent association with colorectal cancer was likely to be a technical artifact as a similar association was also detected for rare variation in random regions of the genome. Despite the null result, this study provides a proof-of-principle for usin

关键词： cancer ovarian transcription factor PAX8 noncoding rare variants whole genome burden test

来源：评论

学校读者我要写书评

暂无评论

Phenotypic Plasticity in Locusts: Trade-Off Between Migration and Reproduction

引用

ANNUAL REVIEW OF ENTOMOLOGY 2025年第1期70卷 23-44页

作者： Guo, Xiaojiao Kang, Le Chinese Acad Sci Inst Zool State Key Lab Integrated Management Pest Insects & Beijing Peoples R China Hebei Univ Inst Life Sci & Green Dev Coll Life Sci Baoding Peoples R China

Locusts exhibit phenotypic plasticity in response to population density changes, with distinct phenotypes in the solitary and gregarious phases. In the past decade, many studies have revealed the molecular mechanisms underlying phase changes, which include the change of body coloration, pheromones, behavior, flight, fecundity, immunity, and aging. Our understanding of the molecular mechanisms related to these phenotypic differences has expanded in breadth and depth with the decoding of the locust genome, involving transcriptional, post-transcriptional, translational, and epigenetic regulation. Large-scale regulation networks composed of genes and noncoding RNAs reflect the systematic modifications of the locust phase transition in response to environmental changes. Gene manipulation techniques have verified the functions of specific genes and related pathways in phase changes. This review highlights the latest advances in studies of locust phase changes and suggests that the divergence of energy and metabolism allocation in gregarious and solitary locusts is an adaptive strategy for long-distance migration and local reproduction, respectively. Finally, we propose future research directions and discuss emerging questions in the area of phenotypic plasticity of locusts.

关键词： phase change behavior pheromone dopamine phenylalanine noncoding RNAs

来源：评论

学校读者我要写书评

暂无评论

Qualitative, quantitative and structural analysis of non-coding regions of classical swine fever virus genome

引用

Chinese Science Bulletin 2001年第15期46卷 1251-1258页

作者： XIAO Ming ZHU Zhizhan ZHANG Chuyu Institute of Virology College of Life SciencesWuhan UniversityWuhan 430072China Department of Physics Wuhan UniversityWuhan 430072China

Classical swine fever virus (CSFV) is the pathogen of the swine fever. Understanding of the replication and expression of its genome is the basis for research of the pathogenicity for CSFV and development of antiviral drug. The noncoding regions (NCRs) of CSFV are the main regulatory regions for replication and expression. Qualitative, quantitative and structural analysis of 3’ NCRs and 5’ NCRs was done in order to locate the regulatory region in the NCRs and to character the NCRs. The sites, conserved sequences and structural elements related to the initiation of replication and expression were extracted from 17 3’ NCRs and 56 5’ NCRs. Those cis-elements may be initial recognition sites for replication, binding sites for transcription factors of host cell and interacting sites for initiation of protein synthesis, based on which a mechanism for the replication and expression of CSFV was brought forth. This research offers the direction for further experiment and lays down a basis for the research on

关键词： classical swine fever virus noncoding regions RNA replication information content pestivirus plus-strand RNA virus.

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：