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cis-regulatory elements

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https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#1
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28438336/distinct-cis-acting-regions-control-six6-expression-during-eye-field-and-optic-cup-stages-of-eye-formation
#2
Kelley L Ledford, Reyna I Martinez-De Luna, Matthew A Theisen, Karisa D Rawlins, Andrea S Viczian, Michael E Zuber
The eye field transcription factor, Six6, is essential for both the early (specification and proliferative growth) phase of eye formation, as well as for normal retinal progenitor cell differentiation. While genomic regions driving six6 optic cup expression have been described, the sequences controlling eye field and optic vesicle expression are unknown. Two evolutionary conserved regions 5' and a third 3' to the six6 coding region were identified, and together they faithfully replicate the endogenous X. laevis six6 expression pattern...
April 21, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28422315/regulation-of-the-alternative-splicing-and-function-of-cyclin-t1-by-the-serine-arginine-rich-protein-asf-sf2
#3
Jieqiong Zhou, Guozhen Gao, Panpan Hou, Chun-Mei Li, Deyin Guo
Positive transcription elongation factor-b (P-TEFb) is required for the release of RNA polymerase II (RNAPII) from its pause near the gene promoters and thus for efficient proceeding to the transcription elongation. It consists of two core subunits - CDK9 and one of T-typed or K-typed cyclin, of which, cyclin T1/CDK9 is the major and most studied combination. We have previously identified a novel splice variant of cyclin T1, cyclin T1b, which negatively regulates the transcription elongation of HIV-1 genes as well as several host genes...
April 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28417999/a-tiling-deletion-based-genetic-screen-for-cis-regulatory-element-identification-in-mammalian-cells
#4
Yarui Diao, Rongxin Fang, Bin Li, Zhipeng Meng, Juntao Yu, Yunjiang Qiu, Kimberly C Lin, Hui Huang, Tristin Liu, Ryan J Marina, Inkyung Jung, Yin Shen, Kun-Liang Guan, Bing Ren
Millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce. Here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (CREST-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in the genome. We used it to interrogate the 2-Mb POU5F1 locus in human embryonic stem cells, and identified 45 cis-regulatory elements. A majority of these elements have active chromatin marks, DNase hypersensitivity, and occupancy by multiple transcription factors, which confirms the utility of chromatin signatures in cis-element mapping...
April 17, 2017: Nature Methods
https://www.readbyqxmd.com/read/28413451/differential-dna-methylation-at-conserved-non-genic-elements-and-evidence-for-transgenerational-inheritance-following-developmental-exposure-to-mono-2-ethylhexyl-phthalate-and-5-azacytidine-in-zebrafish
#5
Jorke H Kamstra, Liana Bastos Sales, Peter Aleström, Juliette Legler
BACKGROUND: Exposure to environmental stressors during development may lead to latent and transgenerational adverse health effects. To understand the role of DNA methylation in these effects, we used zebrafish as a vertebrate model to investigate heritable changes in DNA methylation following chemical-induced stress during early development. We exposed zebrafish embryos to non-embryotoxic concentrations of the biologically active phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP, 30 µM) and the DNA methyltransferase 1 inhibitor 5-azacytidine (5AC, 10 µM)...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28411839/the-molecular-revolution-in-cutaneous-biology-edc-and-locus-control
#6
REVIEW
Inez Y Oh, Cristina de Guzman Strong
The epidermal differentiation complex (EDC) locus consists of a cluster of genes important for the terminal differentiation of the epidermis. While early studies identified the functional importance of individual EDC genes, the recognition of the EDC genes as a cluster with its shared biology, homology, and physical linkage was pivotal to later studies that investigated the transcriptional regulation of the locus. Evolutionary conservation of the EDC and the transcriptional activation during epidermal differentiation suggested a cis-regulatory mechanism via conserved noncoding elements or enhancers...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411083/overexpression-of-gma-mir1510a-b-suppresses-the-expression-of-a-nb-lrr-domain-gene-and-reduces-resistance-to-phytophthora-sojae
#7
Xiaoxia Cui, Qiang Yan, Shuping Gan, Dong Xue, Daolong Dou, Na Guo, Han Xing
MicroRNAs (miRNAs) are universal regulators that repress target gene expression in eukaryotes and play essential roles in plant immune responses. miRNAs were recently found to be involved in soybean and Phytophthora sojae interactions. Here, we screened miR1510, which was repressed in soybean during infection with P. sojae, indicating that it might be involved in soybean response to pathogens. To further uncover the roles of miRNAs in soybean, gma-miR1510a/b was overexpressed in the hairy roots of soybean using an Arabidopsis miR319a precursor as the backbone...
April 11, 2017: Gene
https://www.readbyqxmd.com/read/28408915/tomato-transcription-factor-slwus-plays-an-important-role-in-tomato-flower-and-locule-development
#8
Hui Li, Mingfang Qi, Meihua Sun, Ying Liu, Yudong Liu, Tao Xu, Yanbing Li, Tianlai Li
Tomato is a model species for fleshy fruit development. The shapes and sizes of tomato (Solanum lycopersicum L.) are mainly controlled by several loci, including locule number (lc). Two single nucleotide polymorphisms were found downstream of WUSCHEL (SlWUS) in a putative tomato CArG cis-regulatory element. The lc mutation may affect the binding of AGAMOUS(AG), cause the up-regulation of SlWUS and result in increased locule numbers. In this study, tissue expression levels showed that SlWUS is expressed in young floral buds and shoot apexes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28407294/altered-tert-promoter-and-other-genomic-regulatory-elements-occurrence-and-impact
#9
Barbara Heidenreich, Rajiv Kumar
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome...
April 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28407113/a-new-promoter-element-associated-with-daily-time-keeping-in-drosophila
#10
Brandi Sharp, Eric Paquet, Felix Naef, Akanksha Bafna, Herman Wijnen
Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. To date, relatively few clock-associated promoter elements have been identified and characterized. In an unbiased search of core clock gene promoters from 12 species of Drosophila, we discovered a 29-bp consensus sequence that we designated as the Clock-Associated Transcriptional Activation Cassette or 'CATAC'...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28390952/hypothyroidism-decreases-jak-stat-signaling-pathway-in-lactating-rat-mammary-gland
#11
Fiorella Campo Verde Arboccó, Fabio Andres Persia, María Belén Hapon, Graciela A Jahn
Thyroid pathologies have deleterious effects on lactation. Especially hypothyroidism (HypoT) induces premature mammary involution at the end of lactation and decreases milk production and quality in mid lactation. Milk synthesis is controlled by JAK2/STAT5 signaling pathway and prolactin (PRL), which activates the pathway. In this work we analyzed the effect of chronic 6-propyl-2- thiouracil (PTU)-induced HypoT on PRL signaling pathway on mammary glands from rats on lactation (L) days 2, 7 and 14. HypoT decreased prolactin receptor expression, and expression and activation of Stat5a/b protein...
April 5, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28389698/evolution-of-the-duplicated-intracellular-lipid-binding-protein-genes-of-teleost-fishes
#12
REVIEW
Ananda B Venkatachalam, Manoj B Parmar, Jonathan M Wright
Increasing organismal complexity during the evolution of life has been attributed to the duplication of genes and entire genomes. More recently, theoretical models have been proposed that postulate the fate of duplicated genes, among them the duplication-degeneration-complementation (DDC) model. In the DDC model, the common fate of a duplicated gene is lost from the genome owing to nonfunctionalization. Duplicated genes are retained in the genome either by subfunctionalization, where the functions of the ancestral gene are sub-divided between the sister duplicate genes, or by neofunctionalization, where one of the duplicate genes acquires a new function...
April 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28382035/heritable-gene-regulation-in-the-cd4-cd8-t-cell-lineage-choice
#13
REVIEW
Priya D A Issuree, Charles P Ng, Dan R Littman
The adaptive immune system is dependent on functionally distinct lineages of T cell antigen receptor αβ-expressing T cells that differentiate from a common progenitor in the thymus. CD4(+)CD8(+) progenitor thymocytes undergo selection following interaction with MHC class I and class II molecules bearing peptide self-antigens, giving rise to CD8(+) cytotoxic and CD4(+) helper or regulatory T cell lineages, respectively. The strict correspondence of CD4 and CD8 expression with distinct cellular phenotypes has made their genes useful surrogates for investigating molecular mechanisms of lineage commitment...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28381411/dual-functionality-of-cis-regulatory-elements-as-developmental-enhancers-and-polycomb-response-elements
#14
Jelena Erceg, Tibor Pakozdi, Raquel Marco-Ferreres, Yad Ghavi-Helm, Charles Girardot, Adrian P Bracken, Eileen E M Furlong
Developmental gene expression is tightly regulated through enhancer elements, which initiate dynamic spatio-temporal expression, and Polycomb response elements (PREs), which maintain stable gene silencing. These two cis-regulatory functions are thought to operate through distinct dedicated elements. By examining the occupancy of the Drosophila pleiohomeotic repressive complex (PhoRC) during embryogenesis, we revealed extensive co-occupancy at developmental enhancers. Using an established in vivo assay for PRE activity, we demonstrated that a subset of characterized developmental enhancers can function as PREs, silencing transcription in a Polycomb-dependent manner...
March 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28379136/la-related-protein-1-larp1-binds-the-mrna-cap-blocking-eif4f-assembly-on-top-mrnas
#15
Roni M Lahr, Bruno D Fonseca, Gabrielle E Ciotti, Hiba A Al-Ashtal, Jian-Jun Jia, Marius R Niklaus, Sarah P Blagden, Tommy Alain, Andrea J Berman
The 5'terminal oligopyrimidine (5'TOP) motif is a cis-regulatory RNA element located immediately downstream of the 7-methyl-guanosine [m7G] cap of TOP mRNAs, which encode ribosomal proteins and translation factors. In eukaryotes, this motif coordinates the synchronous and stoichiometric expression of the protein components of the translation machinery. La-related protein 1 (LARP1) binds TOP mRNAs, regulating their stability and translation. We present crystal structures of the human LARP1 DM15 region in complex with a 5'TOP motif, a cap analog (m7GTP), and a capped cytosine (m(7)GpppC) resolved to 2...
April 5, 2017: ELife
https://www.readbyqxmd.com/read/28373393/predictive-models-of-spatial-transcriptional-response-to-high-salinity
#16
Sahra Uygun, Alexander E Seddon, Christina B Azodi, Shin-Han Shiu
Plants are exposed to a variety of environmental conditions, and their ability to respond to environment variation depends on the proper regulation of gene expression in an organ, tissue, and cell type specific manner. Although our knowledge is accumulating on how stress responses are regulated, a genome-wide model of how plant transcription factors (TFs) and cis-regulatory elements (CREs) control spatially specific stress response has yet to emerge. Using Arabidopsis thaliana as a model, we identified a set of 1,894 putative CREs (pCREs) that are associated with high salinity (salt) up-regulated genes in the root or the shoot...
April 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28373291/dual-mechanism-of-rag-gene-repression-by-c-myb-during-pre-b-cell-proliferation
#17
Greg A Timblin, Liangqi Xie, Robert Tjian, Mark S Schlissel
Developing B lymphocytes undergo clonal expansion following successful immunoglobulin heavy chain gene rearrangement. During this proliferative burst, expression of the Rag genes is transiently repressed to prevent the generation of dsDNA breaks in cycling large pre-B cells. The Rag genes are then re-expressed in small resting pre-B cells for immunoglobulin light chain gene rearrangement. We previously identified c-Myb as a repressor of Rag transcription during clonal expansion using Abelson murine leukemia virus-transformed B cells...
April 3, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28369649/functional-anatomy-of-the-immunoglobulin-heavy-chain-3%C3%AE-super-enhancer-needs-not-only-core-enhancer-elements-but-also-their-unique-dna-context
#18
Sandrine Le Noir, François Boyer, Sandrine Lecardeur, Mylène Brousse, Zeliha Oruc, Jeanne Cook-Moreau, Yves Denizot, Michel Cogné
Cis-regulatory elements feature clustered sites for transcription factors, defining core enhancers and have inter-species homology. The mouse IgH 3΄ regulatory region (3'RR), a major B-cell super-enhancer, consists of four of such core enhancers, scattered throughout more than 25 kb of packaging 'junk DNA', the sequence of which is not conserved but follows a unique palindromic architecture which is conserved in all mammalian species. The 3'RR promotes long-range interactions and potential IgH loops with upstream promoters, controlling class switch recombination (CSR) and somatic hypermutation (SHM)...
March 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369570/functional-characterization-of-bnhsfa4a-as-a-heat-shock-transcription-factor-in-controlling-the-re-establishment-of-desiccation-tolerance-in-seeds
#19
Sirui Lang, Xiaoxia Liu, Hua Xue, Xu Li, Xiaofeng Wang
Desiccation tolerance (DT) is the crucial ability of seeds to resist desiccation. However, the regulatory mechanisms of seed DT are not fully understood. In this study, two heat shock cis-elements (HSEs) were identified in the Brassica napus galactinol synthase (BnGolS1) promoter and shown to bind the heat shock transcription factor A4a (BnHSFA4a). Transcriptional expression of BnHSFA4a was induced at the early stage of DT acquisition, prior to increased BnGolS1 activity and galactinol production. Ectopic overexpression of BnHSFA4a (oxBnHSFA4a) in Arabidopsis enhanced DT, particularly during DT re-establishment...
March 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28369503/populus-simonii-%C3%A3-populus-nigra-wrky70-is-involved-in-salt-stress-and-leaf-blight-disease-responses
#20
Hui Zhao, Jing Jiang, Kailong Li, Guifeng Liu, Chung-Jui Tsai
WRKY transcription factors (TFs) are important regulators in the complex stress response signaling networks in plants, but the detailed mechanisms underlying these regulatory networks have not been fully characterized. In the present study, we identified a Group III WRKY gene (PsnWRKY70, Potri.016G137900) from Populussimonii × Populusnigra and explored its function under salt and pathogen stresses. The promoter sequence that is located 2471-bp upstream from the start codon (SC) of PsnWRKY70 contained many stress-responsive cis-elements...
March 22, 2017: Tree Physiology
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