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*  Biomedicines | Free Full-Text | Decoding the Pluripotency Network: The Emergence of New Transcription Factors | HTML
Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.
  http://www.mdpi.com/2227-9059/1/1/49/htm
*  Abstract 611: AP-1 and ETS Family Transcription Factors Co-localize at Enhancers in Human Aortic Endothelial Cells |...
Introduction: Sequence-specific transcription factors bind DNA regulatory elements and play a key role in establishing cellular identity. Studies comparing macrophages to B cells have revealed that small numbers of such collaborative or lineage-determining transcription factors (LDTF) establish distinct enhancers in each cell type. These factors also allow for the binding of signal dependent transcription factors. Here we present data which suggest members of the AP-1, ETS, and STAT transcription factor families serve as collaborative transcriptional regulators in human aortic endothelial cells (HAEC).. Hypothesis: We hypothesize that a set of AP-1 and ETS transcription factors collaborate to establish key endothelial cell enhancers.. Methods: Working in HAEC, we measured poised and active enhancers using ...
  http://atvb.ahajournals.org/content/35/Suppl_1/A611
*  PLOS ONE: Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites
BackgroundIn studies of gene regulation the efficient computational detection of over-represented transcription factor binding sites is an increasingly important aspect. Several published methods can be used for testing whether a set of hypothesised co-regulated genes share a common regulatory regime based on the occurrence of the modelled transcription factor binding sites. However there is little or no information available for guiding the end users choice of method. Furthermore it would be necessary to obtain several different software programs from various sources to make a well-founded choice.MethodologyWe introduce a software package, Asap, for fast searching with position weight matrices that include several standard methods for assessing over-representation. We have compared the ability of these methods to detect over-represented transcription factor binding sites in ...
  http://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0001623.t003
*  Silkworm Transcription Factor Database (SilkTF)
... is a protein database which contains information on transcription factors (TFs) of silkworm.
  http://seriport.in/silktf/
*  The Oxidative Stress Responsive Transcription Factor Pap1 Confers DNA Damage Resistance on Checkpoint-Deficient Fission Yeast...
The Oxidative Stress Responsive Transcription Factor Pap1 Confers DNA Damage Resistance on Checkpoint-Deficient Fission Yeast Cells. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
  http://libros.duhnnae.com/2017/jun8/149835185890-The-Oxidative-Stress-Responsive-Transcription-Factor-Pap1-Confers-DNA-Damage-Resistance-on-Checkpoint-Deficient-Fission-Yeast-Cells.php
*  Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence - Current Protocols in Bioinformatics - Schug - Wiley...
This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a ...
  http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0206s21/abstract?globalMessage=0
*  Sandwalk: Are most transcription factor binding sites functional?
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the ...
  http://sandwalk.blogspot.co.za/2017/06/are-most-transcription-factor-binding.html
*  Sandwalk: Are most transcription factor binding sites functional?
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the ...
  http://sandwalk.blogspot.com/2017/06/are-most-transcription-factor-binding.html
*  Sandwalk: Are most transcription factor binding sites functional?
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the ...
  http://sandwalk.blogspot.de/2017/06/are-most-transcription-factor-binding.html
*  Sandwalk: Are most transcription factor binding sites functional?
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the ...
  http://sandwalk.blogspot.fi/2017/06/are-most-transcription-factor-binding.html
*  Estrogen Regulates Tumor Growth Through a Nonclassical Pathway that Includes the Transcription Factors ERβ and KLF5 | Science...
Clinical evidence suggests that antiestrogens inhibit the development of androgen-insensitive prostate cancer. Here, we show that the estrogen receptor β (ERβ) mediates inhibition by the antiestrogen ICI 182,780 (ICI) and its enhancement by estrogen. ERβ associated with gene promoters through the tumor-suppressing transcription factor KLF5 (Krüppel-like zinc finger transcription factor 5). ICI treatment increased the recruitment of the transcription coactivator CBP [CREB (adenosine 3′,5′-monophosphate response element-binding protein)-binding protein] to the promoter of FOXO1 through ERβ and KLF5, which enhanced the transcription of FOXO1. The increase in FOXO1 abundance led to anoikis in prostate cancer cells, thereby suppressing tumor growth. In contrast, estrogen induced the formation of complexes containing ERβ, KLF5, and the ubiquitin ligase WWP1 (WW domain containing E3 ubiquitin ...
  http://stke.sciencemag.org/content/4/168/ra22
*  Recombinant Human SP2 transcription factor protein (ab117031)
Buy our Recombinant Human SP2 transcription factor protein. Ab117031 is a full length protein produced in Wheat germ and has been validated in WB, ELISA…
  http://www.abcam.com/recombinant-human-sp2-transcription-factor-protein-ab117031.html
*  Transcription Factors - QIAGEN
Transcription factors directly control when, where, and the extent to which genes are expressed. Signal transduction pathways are responsible for either activating or inhibiting many of them. Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). Posttranslational modifications and coregulating proteins provide additional layers of regulation. Transcription factors are involved in a wide variety of processes, such as development, stress responses, and immunity. Activation or inhibition of transcription factors is often dysregulated during oncogenesis. ...
  https://www.qiagen.com/au/shop/genes-and-pathways/complete-biology-list/transcription-factors/
*  Extracting transcription factor binding sites from unaligned gene sequences with statistical models | BMC Bioinformatics | Full...
Understanding transcription is central to understanding genetic regulatory mechanisms. The transcription of a gene is generally dependent on the presence of specific signals located at upstream regions of the core-promoter. These specific signals derive from their use as binding sites by transcription factors (TFs), and are therefore termed transcription factor binding sites (TFBSs). Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1-2 kilobases resolution [1]. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the TFBSs (motif ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S12-S7
*  A Novel Knowledge Based Method to Predicting Transcription Factor Targets - ppt download
Background TF-TFBS-TFT triplets -Transcription factors(TF) regulate transcription factor target(TFT) through binding to transcription factor DNA binding sites(TFBS).
  http://slideplayer.com/slide/4226591/
*  Plus it
Breast cancer is one of the most common malignant diseases in women. Epithelial-mesenchymal transition (EMT) has been documented to play an important role in proliferation, invasion and metastasis of tumor cells as well as drug resistance. Even though the signal transducer and activator of transcription 3 (STAT3) is not a master transcription factor of EMT, STAT3 is involved in the regulation of EMT-related gene expression. However, it remains unclear whether targeted inhibitors of STAT3 affect EMT-mediated proliferation, migration, invasion and drug resistance of tumor cells. In this paper, we investigated the effects of STAT3 and its interaction with Twist, a master transcription factor, in EMT program and subsequent changes in proliferation, migration and invasion of breast cancer cells by interfering STAT3 signaling pathway with different strategies such as STAT3 inactivation and STAT3 silencing. ...
  http://cancerres.aacrjournals.org/content/77/13_Supplement/LB-082
*  Neural Development - The roles of Brn3a, Islet1, and Hmx1 transcription factors in nervous system development | Center for...
The Turner lab has focused on the role of transcription factors in the development of peripheral sensory neurons, the spinal cord, midbrain, and habenula. Transcription factors are proteins which bind to DNA in the nucleus to switch on or off the genes which characterize specific cell types. Without the correct complement of transcription factors, cells undergo an "identity crisis" and fail to execute their correct developmental programs. Many genetic disorders in the brain and other organ systems have been linked to defective transcription factor function. Most of the Turner Lab studies have been conducted in transgenic mice in which they either "knockout" the factor of interest, or express a tracer protein in the neurons that express the factor. Studies have focused mainly ...
  http://depts.washington.edu/cibr/?page_id=752
*  Transcription Factors May Dictate Differences Between Individuals - Redorbit
Researchers are only beginning to understand how individual variation in gene regulation can have a lasting impact on one's health and susceptibility to certain diseases. Now, an ambitious survey of the human genome has identified differences in the binding of master regulators called transcription factors to DNA that affect how genes are expressed in different people.. The study, which is published in the March 18, 2010, issue of Science, looked at two common transcription factors. HHMI medical research fellow Maya Kasowski and her colleagues in the laboratory of molecular biologist Michael Snyder at Yale University conducted the work with Jan Korbel at the European Molecular Biology Laboratory. Snyder has since joined the faculty at Stanford University.. Transcription factors account for as much as 10 percent of the coding genome in humans and other organisms. When ...
  http://www.redorbit.com/news/health/1838955/transcription_factors_may_dictate_differences_between_individuals/
*  Ppargc1a - Peroxisome proliferator-activated receptor gamma coactivator 1-alpha - Mus musculus (Mouse) - Ppargc1a gene & protein
Transcriptional coactivator for steroid receptors and nuclear receptors. Greatly increases the transcriptional activity of PPARG and thyroid hormone receptor on the uncoupling protein promoter. Can regulate key mitochondrial genes that contribute to the program of adaptive thermogenesis. Plays an essential role in metabolic reprogramming in response to dietary availability through coordination of the expression of a wide array of genes involved in glucose and fatty acid metabolism. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. Also involved in the integration of the circadian rhythms and energy metabolism. Required for oscillatory expression of clock genes, such as ARNTL/BMAL1 and NR1D1, through the coactivation of RORA and RORC, and metabolic genes, such as PDK4 and PEPCK. Isoform 4 specifically activates the expression of IGF1 and suppresses myostatin ...
  http://www.uniprot.org/uniprot/O70343
*  PLOS ONE: A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide...
Background How transcription factors (TFs) interact with cis-regulatory sequences and interact with each other is a fundamental, but not well understood, aspect of gene regulation. Methodology/Principal Findings We present a computational method to address this question, relying on the established biophysical principles. This method, STAP (sequence to affinity prediction), takes into account all combinations and configurations of strong and weak binding sites to analyze large scale transcription factor (TF)-DNA binding data to discover cooperative interactions among TFs, infer sequence rules of interaction and predict TF target genes in new conditions with no TF-DNA binding data. The distinctions between STAP and other statistical approaches for analyzing cis-regulatory sequences include the utility of physical principles and the treatment of the DNA binding data as quantitative representation of binding ...
  http://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0008155&imageURI=info:doi/10.1371/journal.pone.0008155.t002
*  Genome‐Wide Location Analysis by Pull Down of In Vivo Biotinylated Transcription Factors - Current Protocols
Recent development of methods for genome‐wide identification of transcription factor binding sites by chromatin immunoprecipitation (ChIP) has led to novel insights into transcriptional regulation and greater understanding of the function of individual transcription factors
  http://www.currentprotocols.com/WileyCDA/CPUnit/refId-mb2120.html?quicktabs_cp=materials
*  Plus it
Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics (1,2,3,4). Super-enhancers are acquired in cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs) (5). In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 transcription factor. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in ...
  http://cancerres.aacrjournals.org/content/75/22_Supplement_1/PR14
*  From co-expression to co-regulation: how many microarray experiments do we need? | Genome Biology | Full Text
It is important to note that even when all experiments are included, the best results produce clusters with only a 28% true positive rate (see Figure E.1.a in Additional data file 1). That is, most of the genes in a given cluster do not share a common, known transcription factor. There are several possible reasons for this. First, with the present state of knowledge, it is possible that genes in the same cluster do in fact share a common transcription factor that is not (yet) represented in the databases used as gold standards (YPD, SCPD and ChIP data). We note for example, that when one compares ChIP data to YPD, the false-negative rate is approximately 80% using the recommended p-value of 0.001. That is, known gene transcription factor interactions from YPD are identified only about 20% of the time by ChIP (see Table F in Additional data file 1). Hence, it ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-7-r48
*  Transcription factor and DNA molecule - Stock Image A617/0259 - Science Photo Library
Transcription factor and DNA molecule. Molecular model of glucocorticoid receptor (GR) transcription factor protein (purple and blue) complexed with a molecule of DNA (deoxyribonucleic acid, pink and green). Transcription factors regulate the transcription of DNA to RNA (ribonucleic acid) by the enzyme RNA polymerase. RNA is the intermediate product between a gene and its protein. When glucocorticoid binds to GR, GR enters the cell's nucleus and binds to the DNA, causing an increase in the production of the apoptosis (programmed cell death) protein bax. - Stock Image A617/0259
  http://www.sciencephoto.com/media/7346/view
*  PLOS Genetics: Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA-Binding Domain
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with ...
  http://journals.plos.org/plosgenetics/article/comments?id=10.1371/journal.pgen.1002614&imageURI=info:doi/10.1371/journal.pgen.1002614.g007