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cis-regulatory elements

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https://www.readbyqxmd.com/read/29775961/antioxidant-response-elements-discovery-classes-regulation-and-potential-applications
#1
REVIEW
Azhwar Raghunath, Kiruthika Sundarraj, Raju Nagarajan, Frank Arfuso, Jinsong Bian, Alan P Kumar, Gautam Sethi, Ekambaram Perumal
Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer protection against oxidative stress. This articulated universal mechanism is regulated through the cis-acting elements in an array of Nrf2 target genes called antioxidant response elements (AREs), which play a critical role in redox homeostasis. Though the Keap1/Nrf2/ARE system involves many players, AREs hold the key in transcriptional regulation of cytoprotective genes...
May 7, 2018: Redox Biology
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#2
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29772251/advances-of-dnase-seq-for-mapping-active-gene-regulatory-elements-across-the-genome-in-animals
#3
REVIEW
Ailing Chen, Daozhen Chen, Ying Chen
Expression of the eukaryotic genome is a highly complex and tightly regulated process, and its regulation depends on interactions among cis-acting elements and transcription factors. Identification of active gene regulatory elements is key to understanding transcriptional control of biological processes including differentiation, development, proliferation, cell-type specificity, and responses to the environment. DNase I hypersensitive sites (DHSs) are markers of open chromatin that provide a very effective method of targeting all types of cis-regulatory elements (CREs) including enhancers, promoters, insulators, silencers, and locus control regions...
May 14, 2018: Gene
https://www.readbyqxmd.com/read/29769331/temporal-transcriptional-logic-of-dynamic-regulatory-networks-underlying-nitrogen-signaling-and-use-in-plants
#4
Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D Brooks, Angelo V Pasquino, Sophie Léran, Shipra Mittal, Tara M Rock, Molly B Edwards, Grace J Kim, Sandrine Ruffel, W Richard McCombie, Dennis Shasha, Gloria M Coruzzi
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our "just-in-time" analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to "prune" the network to 155 TFs and 608 targets...
May 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29767704/gene-regulation-in-the-3d-genome
#5
Yun Li, Ming Hu, Yin Shen
The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In this review, we provide an overview of lessons learned from studying the chromatin structure and their implications in communications between gene promoters and distal cis-regulatory elements, such as enhancers. We first review the current knowledge of general genome organization, followed by the importance of chromatin folding in gene regulation...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29767663/cox-2-gene-expression-and-methylation-profile-in-sapajus-apella-as-an-experimental-model-for-gastric-adenocarcinoma
#6
Danilo do Rosário Pinheiro, Maria Lucia Harada, Rommel Mario Rodriguez Burbano, Barbara do Nascimento Borges
Gastric cancer (GC) remains one of the main causes of cancer-related death worldwide. There are two distinct histological types of GC: diffuse and intestinal. The latter is characterized by the presence of pre-neoplastic lesions. One of the most frequently altered enzymes in intestinal GC is COX-2, an important lesion marker. This work aimed to study COX-2 methylation and expression in N-methyl-N-Nitrosurea (MNU)-induced intestinal GC in six Sapajus apella animals. The partial promoter sequence of S. apella COX-2 gene was obtained and used to identify transcription factors and cis-regulatory element binding sites...
May 14, 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29764390/delineation-of-condition-specific-cis-and-trans-acting-elements-in-plant-promoters-under-various-endo-and-exogenous-stimuli
#7
Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, Tzong-Yi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou, Wen-Chi Chang
BACKGROUND: Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS: Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29759817/enhancer-logic-and-mechanics-in-development-and-disease
#8
REVIEW
Ryan Rickels, Ali Shilatifard
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health...
May 11, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29757404/analysis-of-pcc13-62-promoters-predicts-a-link-between-cis-element-variations-and-desiccation-tolerance-in-linderniaceae
#9
Valentino Giarola, Niklas Udo Jung, Aishwarya Singh, Pooja Satpathy, Dorothea Bartels
Reproductive structures of plants (e.g. seeds) and vegetative tissues of resurrection plants can tolerate desiccation. Many genes encoding desiccation-related proteins (DRP) have been identified in the resurrection plant Craterostigma plantagineum, but the function of these genes remains mainly hypothetical. Here the importance of the DRP gene pcC13-62 for desiccation tolerance is evaluated by analysing the expression of this gene in C. plantagineum and in the closely related desiccation tolerant species Lindernia brevidens and desiccation sensitive species Lindernia subracemosa...
May 11, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29752293/the-cis-regulatory-derare-element-regulates-leukemogenesis
#10
(no author information available yet)
DERARE methylation suppresses HOXB gene expression and leukemogenesis to maintain normal hematopoiesis.
May 11, 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29744943/the-floral-homeotic-protein-sepallata3-recognizes-target-dna-sequences-by-shape-readout-involving-a-conserved-arginine-residue-in-the-mads-domain
#11
Sandra Käppel, Rainer Melzer, Florian Rümpler, Christian Gafert, Günter Theißen
SEPALLATA3 of Arabidopsis thaliana is a MADS-domain transcription factor and a key regulator of flower development. MADS-domain proteins bind to sequences termed 'CArG-boxes' (consensus 5'-CC(A/T)6 GG-3'). Since only a fraction of the CArG-boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG-boxes into genuine recognition sites. Here, we investigate to which extent the shape of the DNA is involved in a 'shape readout' that contributes to the binding of SEPALLATA3...
May 9, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29743358/the-chromatin-remodeling-factor-spoc1-acts-as-a-cellular-restriction-factor-against-human-cytomegalovirus-by-repressing-the-major-immediate-early-promoter
#12
Anna Reichel, Anne-Charlotte Stilp, Myriam Scherer, Nina Reuter, Sören Lukassen, Bahram Kasmapour, Sabrina Schreiner, Luka Cicin-Sain, Andreas Winterpacht, Thomas Stamminger
The cellular protein SPOC1 (survival time-associated PHD finger protein in ovarian cancer 1) acts as a regulator of chromatin structure and DNA damage response. It binds H3K4me2/3 containing chromatin and promotes DNA condensation by recruiting corepressors such as KAP-1 and H3K9 methyltransferases. Previous studies identified SPOC1 as a restriction factor against human adenovirus (HAdV) infection that is antagonized by E1B-55K/E4orf6-dependent proteasomal degradation. Here, we demonstrate that, in contrast to HAdV-infected cells, SPOC1 is transiently upregulated during the early phase of HCMV replication...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29743197/regulatory-divergence-in-wound-responsive-gene-expression-between-domesticated-and-wild-tomato
#13
Ming-Jung Liu, Koichi Sugimoto, Sahra Uygun, Nicholas Panchy, Michael S Campbell, Mark Yandell, Gregg A Howe, Shin-Han Shiu
The evolution of transcriptional regulatory mechanisms is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis-regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated spe-cies. By profiling wound-responsive gene transcriptomes in wild Solanum pennellii and do-mesticated S. lycopersicum, we found extensive wound-response divergence and identified 493 S...
May 9, 2018: Plant Cell
https://www.readbyqxmd.com/read/29739903/identification-of-the-intragenomic-promoter-controlling-hepatitis-e-virus-subgenomic-rna-transcription
#14
Qiang Ding, Ila Nimgaonkar, Nicholas F Archer, Yaron Bram, Brigitte Heller, Robert E Schwartz, Alexander Ploss
Approximately 20 million hepatitis E virus (HEV) infections occur annually in both developing and industrialized countries. Most infections are self-limiting, but they can lead to chronic infections and cirrhosis in immunocompromised patients, and death in pregnant women. The mechanisms of HEV replication remain incompletely understood due to scarcity of adequate experimental platforms. HEV undergoes asymmetric genome replication, but it produces an additional subgenomic (SG) RNA encoding the viral capsid and a viroporin in partially overlapping open reading frames...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29734387/high-throughput-evaluation-of-t7-promoter-variants-using-biased-randomization-and-dna-barcoding
#15
Ryo Komura, Wataru Aoki, Keisuke Motone, Atsushi Satomura, Mitsuyoshi Ueda
Cis-regulatory elements (CREs) are one of the important factors in controlling gene expression and elucidation of their roles has been attracting great interest. We have developed an improved method for analyzing a large variety of mutant CRE sequences in a simple and high-throughput manner. In our approach, mutant CREs with unique barcode sequences were obtained by biased randomization in a single PCR amplification. The original T7 promoter sequence was randomized by biased randomization, and the target number of base substitutions was set to be within the range of 0 to 5...
2018: PloS One
https://www.readbyqxmd.com/read/29733395/towards-a-map-of-cis-regulatory-sequences-in-the-human-genome
#16
Meng Niu, Ehsan Tabari, Pengyu Ni, Zhengchang Su
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs...
May 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29730250/efficient-computation-of-co-transcriptional-rna-ligand-interaction-dynamics
#17
Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker
Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics...
May 3, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29727682/retinoid-sensitive-epigenetic-regulation-of-the-hoxb-cluster-maintains-normal-hematopoiesis-and-inhibits-leukemogenesis
#18
Pengxu Qian, Bony De Kumar, Xi C He, Christof Nolte, Madelaine Gogol, Youngwook Ahn, Shiyuan Chen, Zhenrui Li, Hanzhang Xu, John M Perry, Deqing Hu, Fang Tao, Meng Zhao, Yingli Han, Kate Hall, Allison Peak, Ariel Paulson, Chongbei Zhao, Aparna Venkatraman, Andrew Box, Anoja Perera, Jeffrey S Haug, Tari Parmely, Hua Li, Robb Krumlauf, Linheng Li
Hox genes modulate the properties of hematopoietic stem cells (HSCs) and reacquired Hox expression in progenitors contributes to leukemogenesis. Here, our transcriptome and DNA methylome analyses revealed that Hoxb cluster and retinoid signaling genes are predominantly enriched in LT-HSCs, and this coordinate regulation of Hoxb expression is mediated by a retinoid-dependent cis-regulatory element, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression, resulting in changes to many downstream signaling pathways (e...
May 3, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29722874/rsat-2018-regulatory-sequence-analysis-tools-20th-anniversary
#19
Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera, Morgane Thomas-Chollier
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara)...
May 2, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29720993/the-soybean-gmnark-affects-aba-and-salt-responses-in-transgenic-arabidopsis-thaliana
#20
Chunhong Cheng, Changman Li, Diandong Wang, Lifeng Zhai, Zhaoming Cai
GmNARK ( Glycine max nodule autoregulation receptor kinase) is the homolog of Arabidopsis thaliana CLAVATA1 ( CLV1 ) and one of the most important regulators in the process of AON (Autoregulation of Nodulation), a process that restricts excessive nodule numbers in soybean. However, except for the function in AON, little is known about this gene. Here, we report that GmNARK plays important roles in process of plant response to abiotic stresses. Bioinformatic analysis and subcellular localization experiment results showed that GmNARK was a putative receptor like kinase and located at membrane...
2018: Frontiers in Plant Science
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