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cis regulatory element

Shuai Li, Yanhua Ding, Dajian Zhang, Xutong Wang, Xuemin Tang, Deyan Dai, Hanqi Jin, Suk-Ha Lee, Chunmei Cai, Jianxin Ma
Stem growth habit is a key plant architecture trait determining yield potential in grain legumes, and phenotypic changes from indeterminate stem growth habit of wild mungbeans (Vigna radiata) to determinate stem growth habit of cultivated mungbeans is a critical domestication transition. Here we show that indeterminate stem in wild mungbean is modulated by a single gene VrDet1, which encodes a signaling protein of shoot apical meristems. The transition from indeterminate to determinate stem growth habit was achieved by selection of two linked point mutations in two putative cis-regulatory elements, resulting in significant reduction in gene expression...
August 15, 2018: Plant Journal: for Cell and Molecular Biology
Lain Guio, Cristina Vieira, Josefa González
Transposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. However, few studies have dissected the role of specific transposable element insertions on epigenetic gene regulation. Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. In this work, we integrated publicly available ChIP-seq and piRNA data with chromatin immunoprecipitation experiments to get a more comprehensive picture of Bari-Jheh molecular effects...
August 15, 2018: Scientific Reports
Wen Wang, Xiao Guo, Yan-Mei Li, Xiao-Yin Wang, Xian-Jun Yang, Yan-Fang Wang, Tian-Yun Wang
Transgene expression in eukaryotic cells suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. The use of epigenetic regulators is a promising approach to alleviating such unwanted effects. we investigated the effect of the strong human EF1-α promoter combined with six cis-acting elements on transgene expression in transfected Chinese hamster ovary (CHO) cells. The six elements included the human cytomegalovirus immediate early core promoter element (hCPE), three synthetic enhancer element (SEE1, SEE2, Syn1), human cytomegalovirus immediate early enhancer (hCMV-IEE), and a regulatory element isolated from CHO-K1 genomic DNA (E77)...
August 12, 2018: European Journal of Pharmaceutical Sciences
Chang-Qing Ding, Sophia Ng, Lu Wang, Yu-Chun Wang, Na-Na Li, Xin-Yuan Hao, Jian-Ming Zeng, Xin-Chao Wang, Ya-Jun Yang
Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L...
August 10, 2018: Planta
Muhammad Waseem, Fiaz Ahmad, Sidra Habib, Yanqiag Gao, Zhengguo Li
FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated...
August 7, 2018: Gene
Sarah K Whitley, Anand Balasubramani, Carlene Zindl, Ranjan Sen, Yoichiro Shibata, Gregory E Crawford, Nathaniel M Weathington, Robin D Hatton, Casey T Weaver
IL-1β plays a critical role in IL-6- and TGFβ- initiated Th17 differentiation and induction of Th17-mediated autoimmunity. However, the means by which IL-1 regulates various aspects of Th17 development remains poorly understood. We recently reported that IL-1β enhances STAT3 phosphorylation via NF-kB-mediated repression of SOCS3 to facilitate Il17 transcription and Th17 differentiation, identifying an effect of IL-1 signaling on proximal events of STAT3 signaling. Here we show that IL-1β promotes STAT3 binding to key cis-elements that control IL-17 expression...
August 9, 2018: Journal of Biological Chemistry
Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne de Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit
Cis-regulation plays an essential role in the control of gene expression, and is particularly complex and poorly understood for developmental genes, which are subject to multiple levels of modulation. In this study, we performed a global analysis of the cis-acting elements involved in the control of the zebrafish developmental gene krox20. krox20 encodes a transcription factor required for hindbrain segmentation and patterning, a morphogenetic process highly conserved during vertebrate evolution. Chromatin accessibility analysis reveals a cis-regulatory landscape that includes 6 elements participating in the control of initiation and autoregulatory aspects of krox20 hindbrain expression...
August 6, 2018: PLoS Genetics
Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina, Andrew C Adey, Frank J Steemers, Jay Shendure, Cole Trapnell
Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of "chromatin hubs"-they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression...
July 23, 2018: Molecular Cell
Papri Basak, Shiny Sangma, Abhishek Mukherjee, Tanushree Agarwal, Sonali Sengupta, Sudipta Ray, Arun Lahiri Majumder
The promoter deletion mutants from second isoform of INO1 (gene-encoding MIPS) from Porteresia coarctata of 932 bp (pPcINO1.2.932) and 793 bp (pPcINO1.2.793) prove to be very efficient as salt/drought stress-inducible promoters, while pPcINO1.2.932 is found to be responsive to cold stress as well. The promoters of the two identified myo-inositol-1-phosphate synthase (INO1) isoforms from salt-tolerant wild rice, Porteresia coarctata (PcINO1.1 and PcINO1.2) have been compared bioinformatically with their counterparts present in the salt-sensitive rice, Oryza sativa...
July 31, 2018: Planta
Lan-Hsin Wang, Nicholas E Baker
Growth and patterning are coordinated during development to define organ size and shape. The growth, proliferation and differentiation of Drosophila wings are regulated by several conserved signaling pathways. Here, we show that the Salvador-Warts-Hippo (SWH) and Notch pathways converge on an enhancer in the expanded (ex) gene, which also responds to levels of the bHLH transcription factor Daughterless (Da). Separate cis-regulatory elements respond to Salvador-Warts-Hippo (SWH) and Notch pathways, to bHLH proteins, and to unidentified factors that repress ex transcription in the wing pouch and in the proneural region at the anterior wing margin...
2018: PloS One
Si-Jin Cheng, Shuai Jiang, Fang-Yuan Shi, Yang Ding, Ge Gao
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites (TFBSs) are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential "interference" among multiple variants within the same TFBS. In this study, we presented COPE-TFBS (Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site), a novel method that considers sequence context to accurately predict variant effects on TFBSs...
July 7, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Sundaravelpandian Kalaipandian, Gang-Ping Xue
Specific interaction between transcription factor (TF) and cis-regulatory elements in the context of chromatin is the key to determining gene expression. Thus, it is important to measure DNA-binding specificity and identify cis-elements of TFs of your interest. In this chapter, we described a microwell-based assay to determine DNA-binding specificity by using translational fusion of a TF with a highly active cellulase (CELD), which hydrolyzes 4-methylumbelliferyl β-D-cellobioside to a fluorescent 4-methylumbelliferone product...
2018: Methods in Molecular Biology
María Katherine Mejia-Guerra, Wei Li, Andrea I Doseff, Erich Grotewold
Regulation of gene expression is a fundamental biological process that relies on transcription factors (TF) recognizing specific cis motifs in the regulatory regions of the genes that they control. In most eukaryotic organisms, cis-regulatory elements are significantly enriched around the transcription start site (TSS). However, different from other genic features, TSSs need to be experimentally determined, becoming then important components of genome annotations. One of the methods for experimentally determining TSSs at the genome-wide level is CAGE (cap analysis of gene expression)...
2018: Methods in Molecular Biology
Felix Wolter, Holger Puchta
The recent emergence of the CRISPR/Cas system as a genome editing tool enables simple, fast, and efficient induction of DNA double-strand breaks at precise positions in the genome. This has proven extremely useful for analysis and modification of protein-coding sequences. Regulatory sequences have received much less attention, but can now be quickly and easily disrupted as well. Editing of cis-regulatory elements (CRE) offers considerable potential for crop improvement via fine-tuning of gene expression that cannot be achieved by simple KO mutations, but its widespread application is still hampered by a lack of precise knowledge about functional motifs in CRE...
2018: Methods in Molecular Biology
Anu P Minhas, Rakesh Tuli, Sanjeev Puri
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC , on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains...
2018: Frontiers in Plant Science
Marina Telonis-Scott, Ary A Hoffmann
The molecular underpinnings of pigmentation diversity in Drosophila have recently emerged as a model for understanding how the evolution of different cis -regulatory variants results in common adaptive phenotypes within species. We compared sequence variation in a 5' regulatory region harboring a modular enhancer containing a ∼0.7-kb core element contributing to abdominal melanisation in African, and a ∼0.5-kb core element contributing to thoracic pigmentation in D. melanogaster from Japan, to tropical and temperate populations from eastern Australia previously shown to be divergent in thoracic pigmentation and ebony expression...
2018: Frontiers in Physiology
Hansol Lim, Seung-Ho Paek, Seung-Eun Oh
INTRODUCTION: Cellulose microfibril is a major cell wall polymer that plays an important role in the growth and development of plants. The gene cellulose synthase A (CesA), encoding cellulose synthases, is involved in the synthesis of cellulose microfibrils. However, the regulatory mechanism of CesA gene expression is not well understood, especially during the early developmental stages. OBJECTIVE: To identify factor(s) that regulate the expression of CesA genes and ultimately control seedling growth and development...
July 21, 2018: Genes & Genomics
Wenjie Yue, Xiaojun Nie, Licao Cui, Yongqiang Zhi, Ting Zhang, Xianghong Du, Weining Song
Autophagy, a highly conserved intracellular degradation system, is regarded to be responsible for self-defense and protect cells from abiotic stress. Extensive studies have demonstrated that autophagy plays a crucial role in regulating plant growth and development as well as in response to diverse stresses. However, little is known about autophagy-associated genes (ATGs) in wheat, especially those involved in the regulatory network of stress processes. In this study, a total of 108 putative wheat ATGs (TaATG) were obtained based on a genome-wide search approach...
July 11, 2018: Journal of Plant Physiology
Yaolai Wang, Tengfei Ni, Wei Wang, Feng Liu
There is accumulating evidence that, from bacteria to mammalian cells, messenger RNAs (mRNAs) are produced in intermittent bursts - a much 'noisier' process than traditionally thought. Based on quantitative measurements at individual promoters, diverse phenomenological models have been proposed for transcriptional bursting. Nevertheless, the underlying molecular mechanisms and significance for cellular signalling remain elusive. Here, we review recent progress, address the above issues and illuminate our viewpoints with simulation results...
July 19, 2018: Biological Reviews of the Cambridge Philosophical Society
Shuai Liu, Chao Xue, Yuan Fang, Gang Chen, Xiaojun Peng, Yong Zhou, Chen Chen, Guanqing Liu, Minghong Gu, Kai Wang, Wenli Zhang, Yufeng Wu, Zhiyun Gong
Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice ( Oryza sativa L. japonica ) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins...
July 18, 2018: Molecular & Cellular Proteomics: MCP
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