Genomes and Genes
Summary: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
- Yao S, Buzo B, Pham D, Jiang L, Taparowsky E, Kaplan M, et al. Interferon regulatory factor 4 sustains CD8(+) T cell expansion and effector differentiation. Immunity. 2013;39:833-45 pubmed publisher..Mechanistically, IRF4 promoted the expression and function of Blimp1 and T-bet, two transcription factors required for CD8(+) T cell effector differentiation, and simultaneously repressed genes that mediate cell ..
- Riddell J, Gazit R, Garrison B, Guo G, Saadatpour A, Mandal P, et al. Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors. Cell. 2014;157:549-64 pubmed publisher..We show that transient expression of six transcription factors Run1t1, Hlf, Lmo2, Prdm5, Pbx1, and Zfp37 imparts multilineage transplantation potential onto otherwise ..
- Varelas X. The Hippo pathway effectors TAZ and YAP in development, homeostasis and disease. Development. 2014;141:1614-26 pubmed publisher..Here, I provide an overview of these and other regulatory mechanisms and outline important developmental processes controlled by TAZ and YAP. ..
- Postnikova O, Shao J, Nemchinov L. In silico identification of transcription factors in Medicago sativa using available transcriptomic resources. Mol Genet Genomics. 2014;289:457-68 pubmed publisherb>Transcription factors (TFs) are proteins that govern organismal development and response to the environment by regulating gene expression...
- Hu M, Qin Y. Dynamic fluid flow stimulation on cortical bone and alterations of the gene expressions of osteogenic growth factors and transcription factors in a rat functional disuse model. Arch Biochem Biophys. 2014;545:154-61 pubmed publisher..effects of DHS on cortical bone and its alterations on gene expressions of osteogenic growth factors and transcription factors as a function of time...
- Dunn S, Martello G, Yordanov B, Emmott S, Smith A. Defining an essential transcription factor program for naïve pluripotency. Science. 2014;344:1156-1160 pubmed publisher..We propose that propagation of ES cell identity is not determined by a vast interactome but rather can be explained by a relatively simple process of molecular computation. ..
- Koster M, Yildirim A, Weil P, Holstege F, Timmers H. Suppression of intragenic transcription requires the MOT1 and NC2 regulators of TATA-binding protein. Nucleic Acids Res. 2014;42:4220-9 pubmed publisher..These data reveal cooperation of negative regulation of TBP with specific chromatin regulators to inhibit intragenic transcription. ..
- Xiong M, Li B, Zhu Q, Wang Y, Zhang H. Identification of transcription factors for drug-associated gene modules and biomedical implications. Bioinformatics. 2014;30:305-9 pubmed publisher..However, the transcription factors (TFs) regulating the modules remain largely unknown...
- Ba X, Bacsi A, Luo J, Aguilera Aguirre L, Zeng X, Radak Z, et al. 8-oxoguanine DNA glycosylase-1 augments proinflammatory gene expression by facilitating the recruitment of site-specific transcription factors. J Immunol. 2014;192:2384-94 pubmed publisher..Taken together, these results show that nonproductive binding of OGG1 to 8-oxoG in promoter sequences could be an epigenetic mechanism to modulate gene expression for a prompt innate immune response. ..
- Boroviak T, Loos R, Bertone P, Smith A, Nichols J. The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification. Nat Cell Biol. 2014;16:516-28 pubmed publisher..These findings suggest that formation of the epiblast coincides with competence for ERK-independent self-renewal in vitro and consequent propagation as ESC lines. ..
- Parra Damas A, Valero J, Chen M, España J, Martín E, Ferrer I, et al. Crtc1 activates a transcriptional program deregulated at early Alzheimer's disease-related stages. J Neurosci. 2014;34:5776-87 pubmed publisher..Our results reveal a critical role of Crtc1-dependent transcription on spatial memory formation and provide the first evidence that targeting brain transcriptome reverses memory loss in AD. ..
- Gröschel S, Sanders M, Hoogenboezem R, de Wit E, Bouwman B, Erpelinck C, et al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell. 2014;157:369-381 pubmed publisher..Our data show that structural rearrangements involving the chromosomal repositioning of a single enhancer can cause deregulation of two unrelated distal genes, with cancer as the outcome. ..
- Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, et al. REST and stress resistance in ageing and Alzheimer's disease. Nature. 2014;507:448-54 pubmed publisher..Finally, REST levels during ageing are closely correlated with cognitive preservation and longevity. Thus, the activation state of REST may distinguish neuroprotection from neurodegeneration in the ageing brain. ..
- Hazelett D, Rhie S, Gaddis M, Yan C, Lakeland D, Coetzee S, et al. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 2014;10:e1004102 pubmed publisher..the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology...
- Shazman S, Lee H, Socol Y, Mann R, Honig B. OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res. 2014;42:D167-71 pubmed publisher..c2b2.columbia.edu/OnTheFly/index.php), a database comprising a systematic collection of transcription factors (TFs) of Drosophila melanogaster and their DNA-binding sites...
- Maguire S, Wang C, Holland L, Brunel F, Neuvéglise C, Nicaud J, et al. Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. PLoS Genet. 2014;10:e1004076 pubmed publisher..Sre1 appears to have an ancestral role in the regulation of filamentation, which became decoupled from its role in sterol gene regulation by the arrival of Upc2 in the Saccharomycotina. ..
- Verginelli F, Perin A, Dali R, Fung K, Lo R, Longatti P, et al. Transcription factors FOXG1 and Groucho/TLE promote glioblastoma growth. Nat Commun. 2013;4:2956 pubmed publisher..Here we show that the transcription factors FOXG1 and Groucho/TLE are expressed in poorly differentiated astroglial cells in human GBM specimens and ..
- Muiño J, Smaczniak C, Angenent G, Kaufmann K, van Dijk A. Structural determinants of DNA recognition by plant MADS-domain transcription factors. Nucleic Acids Res. 2014;42:2138-46 pubmed publisherPlant MADS-domain transcription factors act as key regulators of many developmental processes...
- Kaitsuka T, Noguchi H, Shiraki N, Kubo T, Wei F, Hakim F, et al. Generation of functional insulin-producing cells from mouse embryonic stem cells through 804G cell-derived extracellular matrix and protein transduction of transcription factors. Stem Cells Transl Med. 2014;3:114-27 pubmed publisher..we tried to establish an effective method of differentiation through the protein transduction of three transcription factors (Pdx1, NeuroD, and MafA) important to pancreatic ? cell development...
- Hossain D, Panda A, Manna A, Mohanty S, Bhattacharjee P, Bhattacharyya S, et al. FoxP3 acts as a cotranscription factor with STAT3 in tumor-induced regulatory T cells. Immunity. 2013;39:1057-69 pubmed publisher..These results suggest a function of FoxP3, where, failing to achieve direct promoter occupancy, FoxP3 promotes transcription in association with the locus-specific transcription factor STAT3. ..
- Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 2014;42:2976-87 pubmed publisher..The motifs discovered here have been used in parallel studies to validate the specificity of antibodies, understand cooperativity between data sets and measure the variation of motif binding across individuals and species. ..
- Hu G, Chen J. A genome-wide regulatory network identifies key transcription factors for memory CD8? T-cell development. Nat Commun. 2013;4:2830 pubmed publisher..To identify transcription factors and their interactions in memory CD8? T-cell development, we construct a genome-wide regulatory network ..
- Sebastián A, Contreras Moreira B. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics. 2014;30:258-65 pubmed publisher..Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb. ..
- Sharma N, Bhalla P, Singh M. Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha. BMC Genomics. 2013;14:915 pubmed publisherb>Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism...
- Voss T, Hager G. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat Rev Genet. 2014;15:69-81 pubmed publisher..We also explore the involvement of these dynamic and stochastic processes in the evolution of fluctuating transcriptional activity states that are now commonly reported in eukaryotic systems. ..
- Asangani I, Dommeti V, Wang X, Malik R, Cieslik M, Yang R, et al. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature. 2014;510:278-82 pubmed publisher..Taken together, these studies provide a novel epigenetic approach for the concerted blockade of oncogenic drivers in advanced prostate cancer. ..
- Persikov A, Rowland E, Oakes B, Singh M, Noyes M. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res. 2014;42:1497-508 pubmed publisher..In sum, the described approach enables comprehensive large-scale selection and characterization of ZF specificities and should be a great aid in furthering our understanding of the ZF domain. ..
- De S, Barnes B. B cell transcription factors: Potential new therapeutic targets for SLE. Clin Immunol. 2014;152:140-51 pubmed publisher..A complex network of transcription factors regulates this transition as well as subsequent effector functions...
- Beyer T, Weiss A, Khomchuk Y, Huang K, Ogunjimi A, Varelas X, et al. Switch enhancers interpret TGF-? and Hippo signaling to control cell fate in human embryonic stem cells. Cell Rep. 2013;5:1611-24 pubmed publisher..These studies define switch-enhancer elements and provide a framework to understand how cellular context dictates interpretation of the same morphogen signal in development. ..
- Crispino J, Weiss M. Erythro-megakaryocytic transcription factors associated with hereditary anemia. Blood. 2014;123:3080-8 pubmed publisher..A less common class of genetic anemia is caused by mutations that alter the functions of erythroid transcription factors (TFs)...
- Xu Z, Chen H, Ling J, Yu D, Struffi P, Small S. Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila. Genes Dev. 2014;28:608-21 pubmed publisher..These results underscore the importance of combinatorial binding in enhancer function and provide data that will help predict regulatory activities based on DNA sequence. ..
- Franco Zorrilla J, Lopez Vidriero I, Carrasco J, Godoy M, Vera P, Solano R. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A. 2014;111:2367-72 pubmed publisherb>Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes...
- Lamouille S, Xu J, Derynck R. Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol. 2014;15:178-96 pubmed publisher..This switch in cell differentiation and behaviour is mediated by key transcription factors, including SNAIL, zinc-finger E-box-binding (ZEB) and basic helix-loop-helix transcription factors, the ..
- Puisieux A, Brabletz T, Caramel J. Oncogenic roles of EMT-inducing transcription factors. Nat Cell Biol. 2014;16:488-94 pubmed publisher..Here we discuss the roles of EMT-inducing transcription factors in creating a pro-tumorigenic setting characterized by an intrinsic ability to withstand oncogenic insults ..
- Tania M, Khan M, Fu J. Epithelial to mesenchymal transition inducing transcription factors and metastatic cancer. Tumour Biol. 2014;35:7335-42 pubmed publisher..Some of the transcription factors, which are actively involved in EMT process, have a significant role in the EMT-metastasis linkage...
- Hu J, Lei Y, Wong W, Liu S, Lee K, He X, et al. Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors. Nucleic Acids Res. 2014;42:4375-90 pubmed publisher..activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression...
- Lohberger A, Coste A, Sanglard D. Distinct roles of Candida albicans drug resistance transcription factors TAC1, MRR1, and UPC2 in virulence. Eukaryot Cell. 2014;13:127-42 pubmed publisher..The expression of these genes is controlled by the transcription factors (TFs) TAC1 (involved in the control of CDR1 and CDR2), MRR1 (involved in the control of MDR1), and UPC2 (..
- Jung M, Philpott M, Muller S, Schulze J, Badock V, Eberspächer U, et al. Affinity map of bromodomain protein 4 (BRD4) interactions with the histone H4 tail and the small molecule inhibitor JQ1. J Biol Chem. 2014;289:9304-19 pubmed publisher..Our study extends the knowledge on the contribution of individual BRD4 amino acids to histone and JQ1 binding and may help in the design of new BET antagonists with improved pharmacological properties. ..
- Kim W, Reca I, Kim Y, Park S, Thomashow M, Keegstra K, et al. Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana. Plant Mol Biol. 2014;84:577-87 pubmed publisher..of MYB46-mediated transcriptional regulation of secondary wall biosynthesis, we reasoned that additional transcription factors are involved in the CSLA9 regulation...
- Sandler V, Lis R, Liu Y, Kedem A, James D, Elemento O, et al. Reprogramming human endothelial cells to haematopoietic cells requires vascular induction. Nature. 2014;511:312-8 pubmed publisher..umbilical vein endothelial cells or adult dermal microvascular endothelial cells were transduced with the transcription factors FOSB, GFI1, RUNX1 and SPI1 (hereafter referred to as FGRS), and then propagated on serum-free instructive ..
- Yang L, Zhou T, Dror I, Mathelier A, Wasserman W, Gordân R, et al. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014;42:D148-55 pubmed publisher..Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object...
- Wolfram V, Southall T, Gunay C, Prinz A, Brand A, Baines R. The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression. J Neurosci. 2014;34:2538-43 pubmed publisher..Our previous studies have identified LIM-homeodomain (HD) transcription factors (TFs), expressed by developing neurons, that are specifically able to regulate ion channel gene expression...
- Okashita N, Kumaki Y, Ebi K, Nishi M, Okamoto Y, Nakayama M, et al. PRDM14 promotes active DNA demethylation through the ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells. Development. 2014;141:269-80 pubmed publisher..Together, our analysis provides mechanistic insight into DNA demethylation in naive pluripotent stem cells and developing PGCs. ..
- Ohnishi K, Semi K, Yamamoto T, Shimizu M, Tanaka A, Mitsunaga K, et al. Premature termination of reprogramming in vivo leads to cancer development through altered epigenetic regulation. Cell. 2014;156:663-77 pubmed publisher..These findings suggest that epigenetic regulation associated with iPSC derivation may drive development of particular types of cancer. ..
- Wang V, Li Y, Kim D, Zhong X, Du Q, Ghassemian M, et al. Bcl3 Phosphorylation by Akt, Erk2, and IKK Is Required for Its Transcriptional Activity. Mol Cell. 2017;67:484-497.e5 pubmed publisher..This work links Akt and MAPK pathways to NF-?B through Bcl3 and provides mechanistic insight into how Bcl3 functions as an oncoprotein through collaboration with IKK1/2, Akt, and Erk2. ..
- Godbole G, Shetty A, Roy A, D Souza L, Chen B, Miyoshi G, et al. Hierarchical genetic interactions between FOXG1 and LHX2 regulate the formation of the cortical hem in the developing telencephalon. Development. 2018;145: pubmed publisher..Therefore, Foxg1 and Lhx2 form a genetic hierarchy in the spatiotemporal regulation of cortical hem specification and positioning, and together ensure the normal development of this hippocampal organizer. ..
- Tillo D, Ray S, Syed K, Gaylor M, He X, Wang J, et al. The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine. Biochemistry. 2017;: pubmed publisher..Our results identify new DNA sequences that are well-bound by the viral B-ZIP protein Zta only when they contain 5mC or 5hmC, uncovering the potential for discovery of new viral and host regulatory programs controlled by EBV...
- Olp M, Zhu N, Smith B. Metabolically Derived Lysine Acylations and Neighboring Modifications Tune the Binding of the BET Bromodomains to Histone H4. Biochemistry. 2017;56:5485-5495 pubmed publisher..These results suggest acyl-CoA levels tune or block recruitment of the BET bromodomains to histones, linking metabolism to bromodomain-mediated transcription. ..
- Lin P, Wu T, Wu D, Wang L, Chen C, Lee H. An increase in BAG-1 by PD-L1 confers resistance to tyrosine kinase inhibitor in non-small cell lung cancer via persistent activation of ERK signalling. Eur J Cancer. 2017;85:95-105 pubmed publisher..We therefore suggest a combination of an ERK inhibitor with a TKI as a potential strategy for conquering PD-L1-mediated tumour invasion and TKI resistance in NSCLC patients whose tumours harbour high PD-L1/high BAG-1 expression. ..
- Brunquell J, Snyder A, Cheng F, Westerheide S. HSF-1 is a regulator of miRNA expression in Caenorhabditis elegans. PLoS ONE. 2017;12:e0183445 pubmed publisher..Our work therefore uncovers an interesting potential role for HSF-1 in post-transcriptionally controlling gene expression in C. elegans, and suggests a mechanism for cross-talk between stress responses. ..
- Hübner K, Grassme K, Rao J, Wenke N, Zimmer C, Korte L, et al. Wnt signaling positively regulates endothelial cell fate specification in the Fli1a-positive progenitor population via Lef1. Dev Biol. 2017;430:142-155 pubmed publisher..Our data indicate a novel role of ?-catenin dependent Wnt signaling in regulating EC specification during vasculogenesis. ..
- Wei Y, Cai S, Ma F, Zhang Y, Zhou Z, Xu S, et al. Double sex and mab-3 related transcription factor 1 regulates differentiation and proliferation in dairy goat male germline stem cells. J Cell Physiol. 2017;: pubmed publisher..These findings identify a central role for Dmrt1 in controlling population stability and injury restoring of SSCs. ..
- Choi S, Mun G, Choi E, Kim S, Kwon Y, Na Y, et al. The Conjugated Double Bond of Coniferyl Aldehyde Is Essential for Heat Shock Factor 1 Mediated Cytotoprotection. J Nat Prod. 2017;80:2379-2383 pubmed publisher..These results suggested that the vinyl moiety of 1 and 2 is necessary for inducing HSF1, which may be useful for developing small molecules for cytoprotection of normal cells against damage by cytotoxic drugs and radiation. ..
- Dierck F, Kuhn C, Rohr C, Hille S, Braune J, Sossalla S, et al. The novel cardiac z-disc protein CEFIP regulates cardiomyocyte hypertrophy by modulating calcineurin signaling. J Biol Chem. 2017;292:15180-15191 pubmed publisher..In summary, we report on a previously uncharacterized protein CEFIP that modulates calcineurin/NFAT signaling in cardiomyocytes, a finding with possible implications for the pathogenesis of cardiomyopathy. ..
- Yates L, Knappskog S, Wedge D, Farmery J, González S, Martincorena I, et al. Genomic Evolution of Breast Cancer Metastasis and Relapse. Cancer Cell. 2017;32:169-184.e7 pubmed publisher..These include a number of clinically actionable alterations and mutations inactivating SWI-SNF and JAK2-STAT3 pathways. ..
- Zhang H, Zhao M, Yi X, Ou Z, Li Y, Shi Y, et al. Characterization of the distal-less homologue gene, PfDlx, involved in regulating the expression of Pif in the pearl oyster, Pinctada fucata. Comp Biochem Physiol B Biochem Mol Biol. 2017;212:51-58 pubmed publisherDistal-less (Dlx) homeobox transcription factors play an important role in regulating various aspects of vertebrate biology. In vertebrates and invertebrates, distal-less is a highly conserved and well-studied transcription factor...