keyword
MENU ▼
Read by QxMD icon Read
search

cis-regulatory elements

keyword
https://www.readbyqxmd.com/read/28339724/three-cis-regulatory-motifs-auxre-mycrs1-and-mycrs2-are-required-for-modulating-the-auxin-and-mycorrhiza-responsive-expression-of-a-tomato-gh3-gene
#1
Xiao Chen, Dehua Liao, Xiaofeng Yang, Minjie Ji, Shuangshuang Wang, Mian Gu, Aiqun Chen, Guohua Xu
Auxin is well known to be a key regulator that acts in almost all physiological processes during plant growth, and in interactions between plants and microbes. However, to date, the regulatory mechanisms underlying auxin-mediated plant-arbuscular mycorrhizal (AM) fungi symbiosis have not been well deciphered. Previously we identified a GH3 gene, SlGH3.4, strongly responsive to both auxin induction and mycorrhizal symbiosis. Here, we reported a refined dissection of the SlGH3.4 promoter activity using the β-glucuronidase (GUS) reporter...
February 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28338822/gene-expression-atlas-of-pigeonpea-and-its-application-to-gain-insights-into-genes-associated-with-pollen-fertility-implicated-in-seed-formation
#2
Lekha T Pazhamala, Shilp Purohit, Rachit K Saxena, Vanika Garg, L Krishnamurthy, Jerome Verdier, Rajeev K Varshney
Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To link the genome sequence information with agronomic traits resulting from specific developmental processes, a Cajanus cajan gene expression atlas (CcGEA) was developed using the Asha genotype. Thirty tissues/organs representing developmental stages from germination to senescence were used to generate 590.84 million paired-end RNA-Seq data. The CcGEA revealed a compendium of 28 793 genes with differential, specific, spatio-temporal and constitutive expression during various stages of development in different tissues...
February 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338820/evolutionary-dynamics-of-regulatory-changes-underlying-gene-expression-divergence-among-saccharomyces-species
#3
Brian P H Metzger, Patricia J Wittkopp, Joseph D Coolon
Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. While previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#4
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28332981/global-reorganisation-of-cis-regulatory-units-upon-lineage-commitment-of-human-embryonic-stem-cells
#5
Paula Freire-Pritchett, Stefan Schoenfelder, Csilla Várnai, Steven W Wingett, Jonathan Cairns, Amanda J Collier, Raquel García-Vílchez, Mayra Furlan-Magaril, Cameron S Osborne, Peter J Fraser, Peter J Rugg-Gunn, Mikhail Spivakov
Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements...
March 23, 2017: ELife
https://www.readbyqxmd.com/read/28332702/the-mtp1-promoters-from-arabidopsis-halleri-reveal-cis-regulating-elements-for-the-evolution-of-metal-tolerance
#6
Elisa Fasani, Giovanni DalCorso, Claudio Varotto, Mingai Li, Giovanna Visioli, Monica Mattarozzi, Antonella Furini
In the hyperaccumulator Arabidopsis halleri, the zinc (Zn) vacuolar transporter MTP1 is a key component of hypertolerance. Because protein sequences and functions are highly conserved between A. halleri and Arabidopsis thaliana, Zn tolerance in A. halleri may reflect the constitutively higher MTP1 expression compared with A. thaliana, based on copy number expansion and different cis regulation. Three MTP1 promoters were characterized in A. halleri ecotype I16. The comparison with the A. thaliana MTP1 promoter revealed different expression profiles correlated with specific cis-acting regulatory elements...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28331962/sex-combs-reduced-scr-regulatory-region-of-drosophila-revisited
#7
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region...
March 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28330144/upcot-an-integrated-pipeline-tool-for-clustering-upstream-dna-sequences-of-orthologous-genes-in-prokaryotic-genomes
#8
P V Parvati Sai Arun, Jogadhenu S S Prakash
UpCoT is a pipeline tool developed by automating the series of steps involved in prediction of cis-regulatory elements. UpCoT generates orthologs for each gene in target genome using bi-directional best blast hit against the reference genomes, then identifies potential orthologous transcriptional units using intergenic distance. Finally it generates the FASTA files containing upstream sequences of orthologous transcriptional units of each gene in target genome. The inputs of UpCoT are protein sequence files (*...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329684/cis-regulatory-circuits-regulating-nek6-kinase-overexpression-in-transformed-b-cells-are-super-enhancer-independent
#9
Yue Huang, Olivia I Koues, Jiang-Yang Zhao, Regina Liu, Sarah C Pyfrom, Jacqueline E Payton, Eugene M Oltz
Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28320880/rna-mediated-cis-regulation-in-acinetobacter-baumannii-modulates-stress-induced-phenotypic-variation
#10
Carly Ching, Kevin Gozzi, Björn Heinemann, Yunrong Chai, Veronica G Godoy
In the nosocomial opportunistic pathogen Acinetobacter baumannii, RecA-dependent mutagenesis, which causes antibiotic resistance acquisition, is linked to the DNA damage response (DDR). Notably, unlike the Escherichia coli paradigm, recA and DDR gene expression in A. baumannii are bimodal. Namely, there is phenotypic variation upon DNA damage, which may provide a bet-hedging strategy for survival. Thus, understanding recA gene regulation is key to elucidate the yet unknown DDR regulation in A. baumannii Here, we identify a structured 5' Untranslated Region (5' UTR) in the recA transcript which serves as a cis-regulatory element...
March 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28299656/roles-of-the-runx1-enhancer-in-normal-hematopoiesis-and-leukemogenesis
#11
Wei-Siang Liau, Phuong Cao Thi Ngoc, Takaomi Sanda
Enhancers are regulatory elements in genomic DNA that contain specific sequence motifs that are bound by DNA-binding transcription factors. The activity of enhancers is tightly regulated in an integrated and combinatorial manner, thus yielding complex patterns of transcription in different tissues. Identifying enhancers is crucial to understanding the physiological and pathogenic roles of their target genes. The RUNX1 intronic enhancer, eR1, acts in cis to regulate RUNX1 gene expression in hematopoietic stem cells (HSCs) and hemogenic endothelial cells...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28298474/tumor-protein-d52-expression-is-post-transcriptionally-regulated-by-t-cell-intercellular-antigen-tia-1-and-tia-related-protein-via-mrna-stability
#12
Hiromi Motohashi, Yoshiki Mukudai, Chihiro Ito, Kosuke Kato, Toshikazu Shimane, Seiji Kondo, Tatsuo Shirota
Although tumor protein D52 (TPD) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than TPD53 and 54. We subsequently focused on the 3'-untranslated region (3'-UTR) of TPD52 as a cis -acting element in post-transcriptional gene regulation...
March 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28295817/plasticity-and-innovation-of-regulatory-mechanisms-underlying-seed-oil-content-mediated-by-duplicated-genes-in-the-palaeopolyploid-soybean
#13
Dajian Zhang, Meixia Zhao, Shuai Li, Lianjun Sun, Weidong Wang, Chunmei Cai, Emily C Dierking, Jianxin Ma
Many plants have undergone whole genome duplication (WGD). However, how regulatory networks underlying a particular trait are reshaped in polyploids has not been experimentally investigated. Here we show that the regulatory pathways modulating seed oil content, which involve WRINKLED1 (WRI1), (LEAFY COTYLEDON1) LEC1, and LEC2 in Arabidopsis, have been modified in the palaeopolyploid soybean. Such modifications include functional reduction of GmWRI1b of the GmWRI1a/GmWRI1b homoeologous pair relevant to WRI1, complementary non-allelic dosage effects of the GmLEC1a/GmLEC1b homoeologous pair relevant to LEC1, pseudogenization of the singleton GmLEC2 relevant to LEC2, and the rise of the LEC2-like function of GmABI3b, contrasting to its homoeolog GmABI3a, which maintains the ABSCISIC ACID INSENSITIVE 3 (ABI3)-like function in modulating seed maturation and dormancy...
March 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28294971/exploring-the-functions-of-9-lipoxygenase-dklox3-in-ultrastructural-changes-and-hormonal-stress-response-during-persimmon-fruit-storage
#14
Kun Meng, Yali Hou, Ye Han, Qiuyan Ban, Yiheng He, Jiangtao Suo, Jingping Rao
Lipoxygenase (LOX) initiates the hydroperoxidation of polyunsaturated fatty acids and is involved in multiple physiological processes. In this study, investigation of various microscopic techniques showed that the fruit peel cellular microstructure of the two persimmon cultivars differed after 12 days of storage, resulting in fruit weight loss and an increased number and depth of microcracks. Analysis of subcellular localization revealed that greater amounts of DkLOX3-immunolabelled gold particles accumulated in "Fupingjianshi" than in "Ganmaokui" during storage...
March 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28293543/the-tudor-staphylococcal-nuclease-protein-of-entamoeba-histolytica-participates-in-transcription-regulation-and-stress-response
#15
Javier Cázares-Apátiga, Christian Medina-Gómez, Bibiana Chávez-Munguía, Mercedes Calixto-Gálvez, Esther Orozco, Carlos Vázquez-Calzada, Aarón Martínez-Higuera, Mario A Rodríguez
Entamoeba histolytica is the protozoa parasite responsible of human amoebiasis, disease that causes from 40,000 to 100,000 deaths annually worldwide. However, few are known about the expression regulation of molecules involved in its pathogenicity. Transcription of some virulence-related genes is positively controlled by the cis-regulatory element named URE1. Previously we identified the transcription factor that binds to URE1, which displayed a nuclear and cytoplasmic localization. This protein belongs to the Tudor Staphyococcal nuclease (TSN) family, which in other systems participates in virtually all pathways of gene expression, suggesting that this amoebic transcription factor (EhTSN; former EhURE1BP) could also play multiple functions in E...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28289196/osmolality-salinity-responsive-enhancers-osres-control-induction-of-osmoprotective-genes-in-euryhaline-fish
#16
Xiaodan Wang, Dietmar Kültz
Fish respond to salinity stress by transcriptional induction of many genes, but the mechanism of their osmotic regulation is unknown. We developed a reporter assay using cells derived from the brain of the tilapia Oreochromis mossambicus (OmB cells) to identify osmolality/salinity-responsive enhancers (OSREs) in the genes of Omossambicus Genomic DNA comprising the regulatory regions of two strongly salinity-induced genes, inositol monophosphatase 1 (IMPA1.1) and myo-inositol phosphate synthase (MIPS), was isolated and analyzed with dual luciferase enhancer trap reporter assays...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28288969/visualizing-endoderm-cell-populations-and-their-dynamics-in-the-mouse-embryo-with-a-hex-tdtomato-reporter
#17
Tao Wu, Anna-Katerina Hadjantonakis, Sonja Nowotschin
Live imaging is the requisite tool for studying cell behaviors driving embryonic development and tissue formation. Genetically-encoded reporters expressed under cell type-specific cis-regulatory elements that drive fluorescent protein expression at sufficient levels for visualization in living specimens have become indispensable for these studies. Increasingly dual-color (red-green) imaging is used for studying the coordinate behaviors if two cell populations of interest, identifying and characterizing subsets of within broader cell populations or subcellular features...
March 13, 2017: Biology Open
https://www.readbyqxmd.com/read/28277973/an-ancient-transcriptional-regulatory-module-for-tip-growth-has-been-conserved-throughout-the-vascular-plant-lineage
#18
Hyung-Taeg Cho
The root hair development of vascular plants can be divided into two major processes, fate determination and hair morphogenesis, and the latter should be governed by the former so as to express the morphogenetic toolkits in a root hair-specific manner. Vascular plants, depending on taxa, show different fate-determining mechanisms for hair cell/non-hair cell fates, which leads to a question whether the downstream mophogenetic regulatory module is diverged accordingly to the upstream fate determiners or not. Our study demonstrates that the module of a transcription factor and a root hair-specific cis-element (RHE) for root hair-specific expression of morphogenetic toolkit genes is conserved in spite of different fate-determing mechanisms...
February 17, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28275002/high-constitutive-activity-of-a-broad-panel-of-housekeeping-and-tissue-specific-cis-regulatory-elements-depends-on-a-subset-of-ets-proteins
#19
Alessia Curina, Alberto Termanini, Iros Barozzi, Elena Prosperini, Marta Simonatto, Sara Polletti, Alessio Silvola, Monica Soldi, Liv Austenaa, Tiziana Bonaldi, Serena Ghisletti, Gioacchino Natoli
Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes...
March 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28272518/sumoylation-stabilizes-rack1b-and-enhance-its-interaction-with-rap2-6-in-the-abscisic-acid-response
#20
Rongkai Guo, Weining Sun
The highly conserved eukaryotic WD40 repeat protein, Receptor for Activated C Kinase 1 (RACK1), is involved in the abscisic acid (ABA) response in Arabidopsis. However, the regulation of RACK1 and the proteins with which it interacts are poorly understood. Here, we show that RACK1B is sumoylated at four residues, Lys50, Lys276, Lys281 and Lys291. Sumoylation increases RACK1B stability and its tolerance to ubiquitination-mediated degradation in ABA response. As a result, sumoylation leads to enhanced interaction between RACK1B and RAP2...
March 8, 2017: Scientific Reports
keyword
keyword
68261
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"