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https://www.readbyqxmd.com/read/28717181/discovery-of-novel-human-gene-regulatory-modules-from-gene-co-expression-and-promoter-motif-analysis
#1
Shisong Ma, Michael Snyder, Savithramma P Dinesh-Kumar
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28707656/-regulation-of-heat-shock-gene-expression-in-response-to-stress
#2
D G Garbuz
Heat shock (HS) genes, or stress genes, code for a number of proteins that collectively form the most ancient and universal stress defense system. The system determines the cell capability of adaptation to various adverse factors and performs a variety of auxiliary functions in normal physiological conditions. Common stress factors, such as higher temperatures, hypoxia, heavy metals, and others, suppress transcription and translation for the majority of genes, while HS genes are upregulated. Transcription of HS genes is controlled by transcription factors of the HS factor (HSF) family...
May 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28702326/rev-erb-co-regulates-muscle-regeneration-via-tethered-interaction-with-the-nf-y-cistrome
#3
Ryan D Welch, Chun Guo, Monideepa Sengupta, Katherine J Carpenter, Natalie A Stephens, Stacy A Arnett, Marvin J Meyers, Lauren M Sparks, Steven R Smith, Jinsong Zhang, Thomas P Burris, Colin A Flaveny
OBJECTIVE: The loss of skeletal muscle mass and strength are a central feature of traumatic injury and degenerative myopathies. Unfortunately, pharmacological interventions typically fail to stem the long-term decline in quality of life. Reduced Rev-Erb-mediated gene suppression in cultured C2C12 myoblasts has been shown to stimulate myoblast differentiation. Yet the mechanisms that allow Rev-Erb to pleiotropically inhibit muscle differentiation are not well understood. In this study, we sought to elucidate the role of Rev-Erb in the regulation of muscle differentiation and regeneration in vivo...
July 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28693226/screening-of-potentially-crucial-genes-and-regulatory-factors-involved-in-epithelial-ovarian-cancer-using-microarray-analysis
#4
Can Shi, Zhenyu Zhang
The present study aimed to screen potential genes implicated in epithelial ovarian cancer (EOC) and to further understand the molecular pathogenesis of EOC. In order to do this, datasets GSE14407 (containing 12 human ovarian cancer epithelia samples and 12 normal epithelia samples) and GSE29220 (containing 11 salivary transcriptomes from ovarian cancer patients with serous papillary adenocarcinoma and 11 matched controls) were obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) within these datasets were screened using the Linear Models for Microarray Data package, and potential gene functions were predicted by functional and pathway enrichment analyses...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28554693/overexpression-of-stnf-yb3-1-reduces-photosynthetic-capacity-and-tuber-production-and-promotes-aba-mediated-stomatal-closure-in-potato-solanum-tuberosum-l
#5
Guochao Xuanyuan, Congming Lu, Ruofang Zhang, Jiming Jiang
Nuclear factor Y (NF-Y) is one of the most ubiquitous transcription factors (TFs), comprising NF-YA, NF-YB and NF-YC subunits, and has been identified and reported in various aspects of development for plants and animals. In this work, StNF-YB3.1, a putative potato NF-YB subunit encoding gene, was isolated from Solanum tuberosum by rapid amplification of cDNA ends (RACE). Overexpression of StNF-YB3.1 in potato (cv. Atlantic) resulted in accelerated onset of flowering, and significant increase in leaf chlorophyll content in field trials...
August 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28526714/constans-imparts-dna-sequence-specificity-to-the-histone-fold-nf-yb-nf-yc-dimer
#6
Nerina Gnesutta, Roderick W Kumimoto, Swadhin Swain, Matteo Chiara, Chamindika Siriwardana, David S Horner, Ben F Holt, Roberto Mantovani
Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter...
June 2017: Plant Cell
https://www.readbyqxmd.com/read/28446918/microrna-and-transcription-factor-key-players-in-plant-regulatory-network
#7
REVIEW
Abdul F A Samad, Muhammad Sajad, Nazaruddin Nazaruddin, Izzat A Fauzi, Abdul M A Murad, Zamri Zainal, Ismanizan Ismail
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439015/mutant-p53-perturbs-dna-replication-checkpoint-control-through-topbp1-and-treslin
#8
Kang Liu, Fang-Tsyr Lin, Joshua D Graves, Yu-Ju Lee, Weei-Chin Lin
Accumulating evidence supports the gain-of-function of mutant forms of p53 (mutp53s). However, whether mutp53 directly perturbs the DNA replication checkpoint remains unclear. Previously, we have demonstrated that TopBP1 forms a complex with mutp53s and mediates their gain-of-function through NF-Y and p63/p73. Akt phosphorylates TopBP1 and induces its oligomerization, which inhibits its ATR-activating function. Here we show that various contact and conformational mutp53s bypass Akt to induce TopBP1 oligomerization and attenuate ATR checkpoint response during replication stress...
May 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28391527/targeted-gene-disruption-coupled-with-metabolic-screen-approach-to-uncover-the-leafy-cotyledon1-like4-l1l4-function-in-tomato-fruit-metabolism
#9
Custódia Gago, Victoria Drosou, Konstantinos Paschalidis, Adriana Guerreiro, Graça Miguel, Dulce Antunes, Zoe Hilioti
Functional analysis of tomato L1L4 master transcription factor resulted in important metabolic changes affecting tomato fruit quality. Tomato fruits from mutant lines bearing targeted disruption of the heterotrimeric nuclear transcription factor Y (NF-Y) transcription factor (TF) gene LEAFY-COTYLEDON1-LIKE4 (L1L4, NF-YB6), a master regulator of biosynthesis for seed storage proteins and fatty acids, were evaluated for metabolites content and morphology. Metabolic screens using LC-MS/MS-based analysis and physico-chemical methods in different L1L4 mutants of the fourth generation allowed a comparative assessment of the effects of the TF disruption...
July 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28342963/new-insights-into-cellular-cholesterol-acquisition-promoter-analysis-of-human-hmgcr-and-sqle-two-key-control-enzymes-in-cholesterol-synthesis
#10
Vicky Howe, Laura J Sharpe, Anika V Prabhu, Andrew J Brown
BACKGROUND: The two control points of cholesterol synthesis, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) and squalene monooxygenase (SQLE) are known targets of the transcription factor sterol-regulatory element binding protein-2 (SREBP-2). Yet the location of the sterol-regulatory elements (SREs) and cofactor binding sites, nuclear factor-Y (NF-Y) and specificity protein 1 (Sp1), have not been satisfactorily mapped in the human SQLE promoter, or at all in the human HMGCR promoter...
March 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28257042/the-prr11-ska2-bidirectional-transcription-unit-is-negatively-regulated-by-p53-through-nf-y-in-lung-cancer-cells
#11
Yitao Wang, Huali Weng, Ying Zhang, Yinjiang Long, Yi Li, Yulong Niu, Fangzhou Song, Youquan Bu
We previously identified proline-rich protein 11 (PRR11) as a novel cancer-related gene that is implicated in the regulation of cell cycle and tumorigenesis. Our recent study demonstrated that PRR11 and its adjacent gene, kinetochore associated 2 (SKA2), constitute a classic head-to-head gene pair that is coordinately regulated by nuclear factor Y (NF-Y). In the present study, we further show that the PRR11-SKA2 bidirectional transcription unit is an indirect target of the tumor suppressor p53. A luciferase reporter assay revealed that overexpression of wild type p53, but not mutant p53, significantly represses the basal activity and NF-Y mediated transactivation of the PRR11-SKA2 bidirectional promoter...
March 1, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28165867/hypermethylated-ltr-retrotransposon-exhibits-enhancer-activity
#12
Tianxiang Hu, Xingguo Zhu, Wenhu Pi, Miao Yu, Huidong Shi, Dorothy Tuan
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells...
March 4, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27994614/mtnf-ya1-a-central-transcriptional-regulator-of-symbiotic-nodule-development-is-also-a-determinant-of-medicago-truncatula-susceptibility-toward-a-root-pathogen
#13
Thomas Rey, Philippe Laporte, Maxime Bonhomme, Marie-Françoise Jardinaud, Stéphanie Huguet, Sandrine Balzergue, Bernard Dumas, Andreas Niebel, Christophe Jacquet
Plant NF-Y transcription factors control a wide array of biological functions enabling appropriate reproductive and developmental processes as well as adaptation to various abiotic and biotic environments. In Medicago truncatula, MtNF-YA1 was previously identified as a key determinant for nodule development and establishment of rhizobial symbiosis. Here, we highlight a new role for this protein in compatibility to Aphanomyces euteiches, a root pathogenic oomycete. The Mtnf-ya1-1 mutant plants showed better survival rate, reduced symptoms, and increased development of their root apparatus as compared to their wild-type (WT) background A17...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27989935/the-multifaceted-roles-of-nuclear-factor-y-in-arabidopsis-thaliana-development-and-stress-responses
#14
Swadhin Swain, Zachary A Myers, Chamindika L Siriwardana, Ben F Holt
NUCLEAR FACTOR-Y (NF-Y) is a heterotrimeric transcription factor (TF) consisting of evolutionarily distinct NF-YA, NF-YB and NF-YC subunits. The functional NF-Y heterotrimer binds to CCAAT elements in eukaryotic gene promoters and influences their expression. The genome of the model organism Arabidopsis thaliana encodes 10 distinct NF-YA, NF-YB, and NF-YC proteins, allowing for enormous combinatorial and functional diversity. Two decades of research have elucidated the importance of NF-Ys in plant growth, development and stress responses; however, the molecular mechanisms of action remain largely unexplored...
October 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27989934/nf-y-and-the-immune-response-dissecting-the-complex-regulation-of-mhc-genes
#15
REVIEW
Nikoleta Sachini, Joseph Papamatheakis
Nuclear Factor Y (NF-Y) was first described as one of the CCAAT binding factors. Although CCAAT motifs were found to be present in various genes, NF-Y attracted a lot of interest early on, due to its role in Major Histocompatibility Complex (MHC) gene regulation. MHC genes are crucial in immune response and show peculiar expression patterns. Among other conserved elements on MHC promoters, an NF-Y binding CCAAT box was found to contribute to MHC transcriptional regulation. NF-Y along with other DNA binding factors assembles in a stereospecific manner to form a multiprotein scaffold, the MHC enhanceosome, which is necessary but not sufficient to drive transcription...
October 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27977687/nuclear-factor-y-subunit-a-nf-ya-proteins-positively-regulate-flowering-and-act-through-flowering-locus-t
#16
Chamindika L Siriwardana, Nerina Gnesutta, Roderick W Kumimoto, Daniel S Jones, Zachary A Myers, Roberto Mantovani, Ben F Holt
Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal "CORE" elements, respectively, in the FT promoter...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27939756/plant-nf-y-transcription-factors-key-players-in-plant-microbe-interactions-root-development-and-adaptation-to-stress
#17
REVIEW
María Eugenia Zanetti, Carolina Rípodas, Andreas Niebel
NF-Ys are heterotrimeric transcription factors composed by the NF-YA, NF-YB and NF-YC subunits. In plants, NF-Y subunits are encoded by multigene families whose members show structural and functional diversifications. An increasing number of NF-Y genes has been shown to play key roles during different stages of root nodule and arbuscular mycorrhizal symbiosis, as well as during the interaction of plants with pathogenic microorganisms. Individual members of the NF-YA and NF-YB families have also been implicated in the development of primary and lateral roots...
December 8, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27939755/nf-y-in-cancer-impact-on-cell-transformation-of-a-gene-essential-for-proliferation
#18
REVIEW
Aymone Gurtner, Isabella Manni, Giulia Piaggio
NF-Y is a ubiquitous heterotrimeric transcription factor with a binding affinity for the CCAAT consensus motif, one of the most common cis-acting element in the promoter and enhancer regions of eukaryote genes in direct (CCAAT) or reverse (ATTGG) orientation. NF-Y consists of three subunits, NF-YA, the regulatory subunit of the trimer, NF-YB, and NF-YC, all required for CCAAT binding. Growing evidence in cells and animal models support the notion that NF-Y, driving transcription of a plethora of cell cycle regulatory genes, is a key player in the regulation of proliferation...
December 9, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27929718/lotus-japonicus-nf-ya1-plays-an-essential-role-during-nodule-differentiation-and-targets-members-of-the-shi-sty-gene-family
#19
Md Shakhawat Hossain, Arina Shrestha, Sihui Zhong, Mandana Miri, Ryan S Austin, Shusei Sato, Loretta Ross, Terry Huebert, Alexandre Tromas, Ivone Torres-Jerez, Yuhong Tang, Michael Udvardi, Jeremy D Murray, Krzysztof Szczyglowski
Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation...
December 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27837431/obesity-induced-endoplasmic-reticulum-stress-suppresses-nuclear-factor-y-expression
#20
Yulan Liu, Yuwei Zhang, Yanjie Zhang, Jinlong Zhang, Yin Liu, Peiqun Feng, Zhiguang Su
Nuclear transcription factor Y (NF-Y) is an evolutionarily conserved transcription factor composed of three subunits, NF-YA, NF-YB, and NF-YC. NF-Y plays crucial roles in pre-adipocyte maintenance and/or commitment to adipogenesis. NF-YA dysfunction in adipocyte resulted in an age-dependent progressive loss of adipose tissue associated with metabolic complications. Endoplasmic reticulum (ER) stress has emerged as an important mediator in the pathogenesis of obesity. However, it is not known if NF-YA is involved in the ER stress-mediated pathogenesis of obesity...
February 2017: Molecular and Cellular Biochemistry
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