The Transcription Factor Encyclopedia

Yusuf, Dimas; Butland, Stefanie; Swanson, Magdalena I.; Bolotin, Eugene I.; Ticoll, Amy; Cheung, Warren A.; Zhang, Xiao Yu Cindy; Dickman, Christopher Td; Fulton, Debra L.; Lim, Jonathan; Schnabl, Jake; Ramos, Oscar Henrique Pereira; Vasseur-Cognet, Mireille; Leeuw, Charles N. de; Simpson, Elizabeth M.; Ryffel, Gerhart U.; Lam, Eric; Kist, Ralf; Wilson, Miranda S. C.; Marco-Ferreres, Raquel; Brosens, Jan J.; Beccari, Léonardo; Bovolenta, Paola; Benayoun, Bérénice A.; Monteiro, Lara J.; Schwenen, Helma D.C.; Grøntved, Lars; Wederell, Elizabeth D.; Mandrup, Susanne; Veitia, Reiner A.; Chakravarthy, Harini; Hoodless, Pamela A.; Mancarelli, Michela Michela; Torbett, Bruce E.; Banham, Alison H.; Reddy, Sekhar P.; Cullum, Rebecca; Liedtke, Michaela; Tschan, Mario P.; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J.; Eijkelenboom, Astrid; Brown, Philip J.; Laperrière, David; Leprince, Dominique; Cristofaro, Tiziana de; Prince, Kelly L.; Putker, Marrit; Peso, Luis del; Camenisch, Gieri; Wenger, Roland H.; Mikula, Michał; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J.; Rechem, Capucine Van; Boulay, Gaylor; Olechnowicz, Sam W. Z.; Breslin, Mary B.; Lan, Michael S.; Nanan, Kyster K.; Wegner, Michael; Hou, Juan; Mullen, Rachel D.; Colvin, Stephanie C.; Noy, Peter J.; Webb, Carol F.; Witek, Matthew E.; Ferrell, Scott J.; Daniel, Juliet M.; Park, Jason; Waldman, Scott A.; Peet, Daniel J.; Taggart, Michael J.; Jayaraman, Padma Sheela; Karrich, Julien J.; Blom, Bianca; Vesuna, Farhad; O’Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M.; Woodcroft, Mark W.; Hough, Margaret R.; Chen, Edwin; Europe-Finner, Nicholas; Karolczak‐Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; LeBrun, David P.; Biswal, Shyam; Harvey, Christopher J.; DeBruyne, Jason P.; Hogenesch, John B.; Hevner, Robert F.; Héligon, Christophe; Luo, Xin; Blank, Marissa C.; Millen, Kathleen J.; Sharlin, David S.; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Élodie; Sladek, Frances M.; Bradley, Philip; Wasserman, Wyeth W.

doi:10.1186/gb-2012-13-3-r24

Cited by 109 publications

(114 citation statements)

References 38 publications

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“…Among those genes there were a number of growth factors (EGF-like growth factors and Von Willebrand growth factors). Those types of growth factors are known to participate in cell growth/division in response to stimuli (65). Interestingly, homologs of genes from the Tgf-β/Bmp pathway, one of the regulators of mammalian pluripotency, were also present among the early response genes.…”

Section: Resultsmentioning

confidence: 94%

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Wasik

Gurtowski

Zhou

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

100

138

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The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cellfate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50 = 222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.F latworms belong to the superphylum Lophotrochozoa, a vast assembly of protostome invertebrates (1, 2) (Fig. 1A). The evolutionary relationships within this clade are poorly resolved and the specific position of flatworms is currently debated (3, 4). Flatworms have attracted scientific attention for centuries because of their astonishing regenerative capabilities (5, 6), as well as their ability to "degrow" in a controlled way when starved (7). As far back as the early 1900s, Thomas Morgan recognized the potential of flatworms and conducted a number of fascinating regeneration experiments on planarian flatworms before his focus shifted to Drosophila genetics (8).Macrostomum lignano is (Fig. 1B), a free-living, regenerating flatworm isolated from the coast of the Mediterranean Sea. M. lignano is an obligatorily cross-fertilizing simultaneous hermaphrodite (9) that belongs to Macrostomorpha, whereas the other often-studied freeliving flatworms and human parasitic flatworms all belong to clades that are potentially more derived (less ancestral) in comparison with Macrostomorpha (2) (Fig. 1C).Many flatworms can regenerate nearly their entire body or amputated organs. This regenerative capacity is thought to be attributable to the presence of somatic stem cells, termed neoblasts (10, 11). In Schmidtea mediterranea (planarian flatworm), even a single transplanted neoblast has the ability to rescue, regenerate, and change the genotype of a fatally irradiated worm (12). M. lignano can regenerate every tissue, with the exception of the head region containing the brain (13,14).Neoblasts in M. lignano ( Fig. 1 D and E), in contrast to most vertebrate somatic stem cells, are plentiful, making up about ...

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Section: Resultsmentioning

confidence: 94%

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Wasik

Gurtowski

Zhou

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

100

138

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“…Transcription factors are classifi ed into several classes and members of each class share structural characteristics [for a detailed description please refer to the " transcription factor encylopedia " (Yusuf et al, 2012) at http://www.cisreg.ca/tfe; and to the " transcription factor catalogue " (Fulton et al, 2009) Many transcription factors are common to all infl ammatory cell types (ubiquitous), such as AP-1 and NF-κ B, and may play a general role in the regulation of infl ammatory genes, whereas others are much more cell-specifi c and may determine the phenotypic characteristics of a cell, such as FoxP3. Activation of transcription factors generally involves kinase activation pathways including protein kinase A (PKA), mitogen-activated protein (MAP) kinases (MAPK)s, Janus kinases (JAKs), and protein kinases C family members (PKCs) stimulated by cell-surface receptors (Gilmore, 2006;Saklatvala, 2004) (Figures 1 and 2).…”

Section: Transcription Factorsmentioning

confidence: 99%

Role of Transcription Factors in the Pathogenesis of Asthma and COPD

Caramori¹,

Casolari²,

Adcock

2013

Cell Communication & Adhesion

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Infl ammation is a central feature of asthma and chronic obstructive pulmonary disease (COPD). Despite recent advances in the knowledge of the pathogenesis of asthma and COPD, much more research on the molecular mechanisms of asthma and COPD are needed to aid the logical development of new therapies for these common and important diseases, particularly in COPD where no effective treatments currently exist. In the future the role of the activation/repression of different transcription factors and the genetic regulation of their expression in asthma and COPD may be an increasingly important aspect of research, as this may be one of the critical mechanisms regulating the expression of different clinical phenotypes and their responsiveness to therapy, particularly to anti-infl ammatory drugs.

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“…The promoter-driven HNF4␣ isoforms exhibit tissue-specific expression patterns: the P1-driven HNF4␣1/2 is expressed in the fetal and adult liver and kidney, whereas the P2-driven HNF4␣7/8 is expressed in the fetal liver and the adult stomach and pancreas; both isoforms are expressed in the large and small intestines (18,19,22,23). The HNF4␣ gene structure, promoter sequences, and expression patterns are highly conserved between humans and mice (19), suggesting that P1-and P2-driven HNF4␣ play important yet distinct functional roles. Indeed, exon-swap mice that express just a single HNF4␣ N-terminal isoform show subtle yet significant metabolic differences in unstressed animals (22).…”

mentioning

confidence: 99%

“…Several splice variants of HNF4␣ are generated via two alternative promoters (proximal promoter P1 and distal promoter P2) and two distinct 3= splicing events (19). P1-driven HNF4␣1/2, which includes the full-length N-terminal A/B domain, was cloned from adult rat liver (1), while the P2-driven HNF4␣7/8 with a distinct N-terminal domain was cloned from an embryonic cell line (20) (see Fig.…”

mentioning

confidence: 99%

Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells

Vuong

Chellappa

Dhahbi

et al. 2015

Molecular and Cellular Biology

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The nuclear receptor hepatocyte nuclear factor 4␣ (HNF4␣) is tumor suppressive in the liver but amplified in colon cancer, suggesting that it also might be oncogenic. To investigate whether this discrepancy is due to different HNF4␣ isoforms derived from its two promoters (P1 and P2), we generated Tet-On-inducible human colon cancer ( Thus, the HNF4␣ isoforms play distinct roles in colon cancer, which could be due to differential interactions with the Wnt/␤-catenin/TCF4 and AP-1 pathways.

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The Transcription Factor Encyclopedia

Cited by 109 publications

References 38 publications

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Role of Transcription Factors in the Pathogenesis of Asthma and COPD

Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells

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