检索结果-内蒙古大学图书馆

Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy

PLANT JOURNAL 2023年第6期116卷 1804-1824页

作者： Xu, Yu Bush, Stephen J. Yang, Xinyi Xu, Linfeng Wang, Bo Ye, Kai Xi An Jiao Tong Univ Sch Life Sci & Technol Xian Shaanxi Peoples R China Xi An Jiao Tong Univ Sch Automat Sci & Engn Fac Elect & Informat Engn Xian Shaanxi Peoples R China Xi An Jiao Tong Univ Fac Elect & Informat Engn MOE Key Lab Intelligent Networks & Networks Secur Xian Shaanxi Peoples R China Xi An Jiao Tong Univ Affiliated Hosp 1 Genome Inst Xian Shaanxi Peoples R China

Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.

关键词： conserved non-coding elements transcriptomic evolution whole-genome duplication fractionation BIA gene cluster

来源：评论

学校读者我要写书评

暂无评论

Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators

引用

SCIENTIFIC REPORTS 2024年第1期14卷 1-9页

作者： Nakayama, Daiki Makino, Takashi Tohoku Univ Fac Sci Dept Biol 6-3 Aramaki Aza AobaAoba Ku Sendai 9808578 Japan Tohoku Univ Grad Sch Life Sci 6-3 Aramaki Aza AobaAoba Ku Sendai 9808578 Japan

Mammals maintain their body temperature, yet hibernators can temporarily lower their metabolic rate as an energy-saving strategy. It has been proposed that hibernators evolved independently from homeotherms, and it is possible that the convergent evolution of hibernation involved common genomic changes among hibernator-lineages. Since hibernation is a seasonal trait, the evolution of gene regulatory regions in response to changes in season may have been important for the acquisition of hibernation traits. High-frequency accumulation of mutations in conserved non-coding elements (CNEs) could, in principle, alter the expression of neighboring genes and thereby contribute to the acquisition of new traits. To address this possibility, we performed a comparative genomic analysis of mammals to identify accelerated CNEs commonly associated with hibernation. We found that accelerated CNEs are common to hibernator-lineages and could be involved with hibernation. We also found that common factors of genes that located near accelerated CNEs and are differentially expressed between normal and hibernation periods related to gene regulation and cell-fate determination. It suggests that the molecular mechanisms controlling hibernation have undergone convergent evolution. These results help broaden our understanding of the genetic adaptations that facilitated hibernation in mammals and may offer insights pertaining to stress responses and energy conservation.

关键词： Hibernation Accelerated evolution conserved non-coding elements

来源：评论

学校读者我要写书评

暂无评论

The Partial Order Kernel And Its Application To Understanding The Regulatory Grammar Of conserved non-coding elements

The Partial Order Kernel And Its Application To Understandin...

引用

作者： Maryam Abdollahyan Queen Mary University of London

学位级别：博士

conserved non-coding elements (CNEs) are regions of non-coding DNA which have remained evolutionarily conserved across various species over millions of years and are found to cluster near genes involved in early embryonic development, suggesting that they play an important role as regulatory elements. Indeed, many CNEs have been shown to act as enhancers; however, not all regulatory elements are conserved and in some cases, deletion of CNEs did not result in any notable phenotypes. These opposing ndings indicate that the functions of CNEs are still poorly understood and further research on these elements is needed to uncover the reasons for their extreme conservation. The aim of this thesis is to investigate the use and development of algorithms for decoding the regulatory grammar of CNEs. Initially, an assessment of several methods for functional classi cation of CNEs is provided. The results obtained using these methods are validated by functional assays and their limitations in capturing the grammar of CNEs are discussed. Motivated by these limitations, a partial order graph representation of the sequence of transcription factor binding sites (TFBSs) in a CNE that allows e cient handling of the overlapping sites is introduced. A dynamic programming-based method for aligning two such graphs and identifying regulatory signatures composed of co-occurring TFBSs is proposed and evaluated. The results demonstrate the predictive ability of this method, which can be used to prioritise regions for experimental validation. Building on this method, the partial order kernel (POKer) for comparison of strings containing alternative substrings and represented by partial order graphs is introduced. The POKer is evaluated in di erent sequence comparison tasks, including visual localisation. An approach using the POKer for functional classi cation of CNEs is introduced and its e ectiveness in capturing the grammar of CNEs is demonstrated. Finally, the implications of the results p

关键词： conserved non-coding elements non-coding DNA transcription factor binding sites partial order kernel

来源：评论

学校读者我要写书评

暂无评论

The Partial Order Kernel and its Application to Understanding the Regulatory Grammar of conserved non-coding elements

The Partial Order Kernel and its Application to Understandin...

引用

作者： Abdollahyan, M Queen Mary University of London Queen Mary University of London

学位级别：博士

关键词： conserved non-coding elements non-coding DNA transcription factor binding sites partial order kernel

来源：评论

学校读者我要写书评

暂无评论

Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals

引用

BMC EVOLUTIONARY BIOLOGY 2014年第1期14卷 1-19页

作者： Davies, Kalina T. J. Tsagkogeorga, Georgia Rossiter, Stephen J. Queen Mary Univ London Sch Biol & Chem Sci London E1 4NS England

Background: The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. conserved non-coding elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and similar to 82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Results: Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of ech

关键词： Bats conserved non-coding elements Ear development Hearing/deafness

来源：评论

学校读者我要写书评

暂无评论

Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas

引用

Science China(Life Sciences) 2024年第9期67卷 2003-2015页

作者： Simin Chai Yujie Chong Daiqing Yin Qiang Qiu Shixia Xu Guang Yang Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou 511458China Jiangsu Key Laboratory for Biodiversity and Biotechnology School of Life SciencesNanjing Normal UniversityNanjing 210023China School of Ecology and Environment Northwestern Polytechnical UniversityXi’an 710072China

Jerboas is a lineage of small rodents displaying atypical mouse-like morphology with elongated strong hindlimbs and short *** have evolved obligate bipedal saltation and acute senses,and been well-adapted to vast desert-like *** a newly sequenced chromosome-scale genome of the Mongolian five-toed jerboa(Orientallactaga sibirica),our comparative genomic analyses and in vitro functional assays showed that the genetic innovations in both protein-coding and non-coding regions played an important role in jerboa morphological and physiological ***-specific amino acid substitutions,and segment insertions/deletions(indels)in conserved non-coding elements(CNEs)were found in components of proteoglycan biosynthesis pathway(XYLT1 and CHSY1),which plays an important role in limb ***,we found specific evolutionary changes functionally associated with energy or water metabolism(e.g.,specific amino acid substitutions in ND5 and indels in CNEs physically near ROR2)and senses(e.g.,expansion of vomeronasal receptors and the FAM136A gene family)in *** dual-luciferase reporter assay verified that some of the CNEs with jerboa-specific segment indels exerted a significantly different influence on luciferase activity,suggesting changes in their regulatory function in *** results revealed the potential molecular mechanisms underlying jerboa adaptation since the divergence from the Eocene-Oligocene transition,and provided more resources and new insights to enhance our understanding of the molecular basis underlying the phenotypic diversity and the environmental adaptation of mammals.

关键词： jerboa adaptive evolution comparative genomics conserved non-coding elements bipedal saltation

来源：评论

学校读者我要写书评

暂无评论

Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis

引用

Plant Communications 2024年第1期5卷 130-147页

作者： Yu Zhang Yuan Fu Wenfei Xian Xiuli Li Yong Feng Fengjiao Bu Yan Shi Shiyu Chen Robin van Velzen Kai Battenberg Alison M.Berry Marco G.Salgado Hui Liu Tingshuang Yi Pascale Fournier Nicole Alloisio Petar Pujic Hasna Boubakri M.Eric Schranz Pierre-Marc Delaux Gane Ka-Shu Wong Valerie Hocher Sergio Svistoonoff Hassen Gherbi Ertao Wang Wouter Kohlen Luis G.Wall Martin Parniske Katharina Pawlowski Philippe Normand Jeffrey J.Doyle Shifeng Cheng Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Biosystematics Group Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Department of Plant Sciences University of CaliforniaDavisDavisCA 95616USA Department of Ecology Environment and Plant SciencesStockholm University10691 StockholmSweden Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Universite´de Lyon Universite´Lyon 1CNRSUMR5557Ecologie MicrobienneINRAUMR 141843 bd du 11 novembre 191869622 VilleurbanneFrance Laboratoire de Recherche en Sciences Ve´ge´tales(LRSV) Universite´de ToulouseCNRSUPS24 chemin de Borde RougeAuzevilleBP4261731326 Castanet TolosanFrance Department of Biological Sciences University of AlbertaEdmontonAB T6G 2E9Canada French National Research Institute for Sustainable Development(IRD) UMR LSTM(IRD/CIRAD/INRAe/Montpellier University/Supagro)-Campus International BaillarguetTA A-82/J34398 Montpellier Cedex 5France National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologySIBSChinese Academy of SciencesShanghaiChina Laboratory of Molecular Biology Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Laboratory of Biochemistry Microbiology and Soil Biological InteractionsDepartment of Science and TechnologyNational University of QuilmesCONICETBernalArgentina Faculty of Biology GeneticsLMU MunichGroßhaderner Strasse 2-482152 MartinsriedGermany School of Integrative Plant Science Sections of Plant Biology and Plant Breeding&GeneticsCornell UniversityIthacaNY 14853USA State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Univer

Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume *** species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time ***,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the ***,much remains to be learned about nodulation,especially outside of ***,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of *** phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the *** transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response *** 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage *** study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC ***-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in ***,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

关键词： nitrogen-fixing root-nodule symbiosis two competing hypotheses phylogenomics phylotranscrip-tomics conserved non-coding elements convergence deep homology

来源：评论

学校读者我要写书评

暂无评论

Assessing candidate DLX-regulated genes in the first pharyngeal arch of chick embryos

引用

DEVELOPMENTAL DYNAMICS 2025年第0期 2025 Jan 15页

作者： Sohail, Afshan Nicoll, Olivia Bendall, Andrew J. Univ Guelph Dept Mol & Cellular Biol 50 Stone Rd E Guelph ON N1G 2W1 Canada

BackgroundInsights into the development and evolution of asymmetrical jaws will require an understanding of the gene regulatory networks that underpin the differential morphogenesis of the maxillary and mandibular domains of the first pharyngeal arch in a variety of gnathostomes. While a robust relationship has been demonstrated between jaw patterning and the Endothelin-Dlx gene axis, much less is known of the next level of genes in the jaw patterning *** genes, whose expression depends on Dlx5 and/or Dlx6, have been identified in mice. Here, we examined the expression patterns of the chick orthologues of some of those genes, namely GSC, PITX1, HAND2, and GBX2, and tested their dependence on endothelin signaling to assess whether there is a conserved regulatory relationship between those genes in the chick embryo. To further validate these genes as direct DLX targets, we identified conserved non-coding sequences containing candidate DLX binding motifs and demonstrated DLX-responsiveness in *** evidence presented in this study combines to support the hypothesis that these four genes are direct targets of DLX transcription factors in the lower jaw-forming tissue.

关键词： chick embryo conserved non-coding elements endothelin signaling expression patterns jaw patterning transcription factors

来源：评论

学校读者我要写书评

暂无评论

Cis-regulation and conserved non-coding elements in amphioxus

引用

BRIEFINGS IN FUNCTIONAL GENOMICS 2012年第2期11卷 118-130页

作者： Beaster-Jones, Laura Univ Calif San Diego Scripps Inst Oceanog La Jolla CA 92093 USA

The origin of the vertebrates was a major event in the evolution of morphological diversity and the genetic mechanisms responsible for this diversity, once purely theoretical, can now be approached experimentally in the genome era. With a prototypical chordate genome, vertebrate-like development and simple morphology, amphioxus provides the appropriate model for investigating the origin of the vertebrates. Comparative genomics is revealing that both conservation and divergence of genes and cis-regulatory elements involved in developmental regulatory networks are required to shape different animal body plans. This article reviews the cis-regulatory studies performed in amphioxus, the discovery of conserved non-coding elements (CNEs) across the metazoans and the examination of amphioxus CNEs. Emerging ideas on the evolution of CNEs after large-scale genome duplication events and the state of cephalochordate genomics are also discussed.

关键词： amphioxus conserved non-coding elements evolution comparative genomics cis-regulation

来源：评论

学校读者我要写书评

暂无评论

Deciphering enhancers of hearing loss genes for efficient and targeted gene therapy of hereditary deafness

引用

Neuron 2025年第10期113卷 1579.0-159600000.0页

作者： Zhao, Simeng Yang, Qiuxiang Yu, Zehua Chu, Cenfeng Dai, Shengqi Li, Hongli Diao, Min Feng, Lingyue Ke, Junzi Xue, Yilin Zhou, Qifang Liu, Yan Ma, Hanhui Lin, Chao-Po Yao, Yong-Gang Zhong, Guisheng iHuman Institute ShanghaiTech University Shanghai 201210 China School of Life Science and Technology ShanghaiTech University Shanghai 201210 China State Key Laboratory of Genetic Evolution and Animal Models Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms Yunnan Engineering Center on Brain Disease Models KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of Zoology Chinese Academy of Sciences Yunnan Kunming 650204 China Shanghai Clinical Research and Trial Center Shanghai 201210 China Shanghai Key Laboratory of High-Resolution Electron Microscopy ShanghaiTech University Shanghai 201210 China National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility) and National Resource Center for Non-Human Primates Kunming Institute of Zoology Chinese Academy of Sciences Yunnan Kunming 650107 China Kunming College of Life Science University of Chinese Academy of Sciences Yunnan Kunming 650204 China Shanghai Key Laboratory of Gene Editing and Cell Therapy for Rare Diseases Fudan University Shanghai 20031 China

Hereditary hearing loss accounts for about 60% of congenital deafness. Although adeno-associated virus (AAV)-mediated gene therapy shows substantial potential for treating genetic hearing impairments, there remain significant concerns regarding the specificity and safety of AAV vectors. The sophisticated nature of the cochlea further complicates the challenge of precisely targeting gene delivery. Here, we introduced an AAV-reporter-based in vivo transcriptional enhancer reconstruction (ARBITER) workflow, enabling efficient and reliable dissection of enhancers. With ARBITER, we successfully demonstrated that the conserved non-coding elements (CNEs) within the gene locus collaboratively regulate the expression of Slc26a5, which was further validated using knockout mouse models. We also assessed the potential of identified enhancers to treat hereditary hearing loss by conducting gene therapy in Slc26a5 mutant mice. Based on the original Slc26a5 enhancer with limited efficiency, we engineered a highly efficient and outer hair cell (OHC)-specific enhancer, B8, which successfully restored hearing of Slc26a5 knockout mice. © 2025 Elsevier Inc.

关键词： AAVs adeno-associated viruses CNEs conserved non-coding elements gene therapy hereditary hearing loss OHC outer hair cell Slc26a5 transcriptional enhancer

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：