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*  AP Bio Gene Expression/Control Review Sheet
You need to be familiar with all of the different ways and levels at which cells can control gene expression, including gene expression, Chromatin packing, DNA methylation, Histone acetylation, control elements and transcription factors, alternative RNA splicing, mRNA degredation, translational control by regulatory proteins, proteasomic protein degradation, etc. (Damn, that s a lot of control ...
http://ww2.kcd.org/staff/johnson/classes/APBio/AP_Gene_Expression_revsheet.html
*  PLOS Biology: Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region
The physical distance to the poly(A) tail is a crucial determinant to define a termination codon as premature in human cells. This indicates evolutionary conservation of the basic mechanism of nonsense-mediated mRNA decay and provides a novel mechanism for translation-dependent posttranscriptional gene regulation.
http://journals.plos.org/plosbiology/article/authors?id=10.1371/journal.pbio.0060092&imageURI=info:doi/10.1371/journal.pbio.0060092.g004
*  Post‐transcriptional gene expression control by NANOS is up‐regulated and functionally important in pRb‐deficient cells | The...
RBF1 and E2F2 are components of the Drosophila, Rb, E2F, and Myb‐associated protein (dREAM) complex, a transcriptional silencing complex that represses many E2F target genes (Korenjak et al, 2004). To determine whether components of the Pum complex are targets for dREAM‐mediated repression, we analyzed datasets of published genome‐wide dREAM ChIP experiments from Drosophila Kc cells (Georlette et al, 2007) and found a strong ChIP enrichment for all of the dREAM components (E2F2, Myb, Mip120, Mip130, and Lin‐52) on the pumilio, nanos, and brat genes (Supplementary Fig S1B). To establish the functional significance of E2F2/RBF1 binding to these promoters, we assayed gene expression levels from Drosophila S2 cells and flies containing dsRNA or RNAi sequences targeting E2F/RBF family members. Depletion of RBF1 or E2F2 (but not E2F1) strongly induced the expression of nanos and modestly elevated the levels of pum and brat (Fig ...
http://emboj.embopress.org/content/early/2014/08/06/embj.201488057
*  Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks | Science Signaling
Transcriptional regulators are sometimes believed to be the only targets through which signal transduction pathways regulate gene expression. Although it is certainly true that many well-characterized intercellular signaling pathways operate by modifying the activity of specific transcription factors, an increasing body of evidence indicates that external signals can modulate gene expression by posttranscriptional mechanisms. RNA binding motifs are combined with other conserved domains, such as protein-interaction domains and consensus phosphorylation motifs, to allow gene expression to be regulated at the level of the RNA in response to extracellular signals. In this review, I discuss evidence that reveals how a particular family of RNA binding proteins, called signal transduction and activation of RNA (STAR) proteins, function in signaling and in the development of multicellular organisms. Furthermore, ...
http://stke.sciencemag.org/content/2003/179/re6
*  A Data Integration Method for Exploring Gene Regulatory Mechanisms
Systems biology aims to understand the behavior of and interaction between various components of the living cell, such as genes, proteins, and metabolites. A large number of components are involved in these complex systems and the diversity of relationships between the components can be overwhelming, and there is therefore a need for analysis methods incorporating data integration. We here present a method for exploring gene regulatory mechanisms which integrates various types of data to assist the identification of important components in gene regulation mechanisms. By first analyzing gene expression data, a set of differentially expressed genes is selected. These genes are then further investigated by combining various types of biological information, such as clustering results, promoter sequences, binding sites, transcription factors and other previously published ...
http://his.diva-portal.org/smash/record.jsf?pid=diva2:227217
*  Regulation of Gene Expression in Plants | SpringerLink
Except for one area of gene expression control, plant research has significantly fallen behind studies in insects and vertebrates. The advances made in animal gene expression control have benefited pl
https://link.springer.com/book/10.1007%2F978-0-387-35640-2
*  Cell Cycle Programs of Gene Expression Control Morphogenetic Protein Localization | JCB
Constitutive BUD10 expression from the MET3 promoter and delayed periodic expression from the BUD3 promoter both affected Bud10p function. Cells displayed a reduction in the ability to direct the axial budding pattern, and Bud10p was not properly localized. In wild-type cells, Bud10p concentrates to the incipient bud site, in the mother-bud neck, and at the division sites of newly divided cells. Both alterations led to uniform distribution of Bud10p throughout the plasma membrane. Taken together, these results imply that a cell cycle-specific pulse of BUD10 expression in late G1 is critical for Bud10p localization and subsequent function. To examine this hypothesis further, we artificially induced pulses of BUD10 expression. An artificial pulse of BUD10 expression around late G1 restored correct localization of Bud10p, whereas pulses of expression outside this time led to mislocalization of Bud10p throughout ...
http://jcb.rupress.org/content/151/7/1501
*  "Four-dimensional gene expression control: memories on the fly" by Benjamin M. Leung and Scott Waddell
To understand the role of a gene in adult behavior, it is necessary to control its expression in four dimensions: space and time. Two recent papers describe implementation of different but related technologies that now provide this missing element in fly behavioral research.
http://escholarship.umassmed.edu/neurobiology_pp/75/
*  Imprinted silencing of Slc22a2 and Slc22a3 does not need transcriptional overlap between Igf2r and Air | The EMBO Journal
Mammalian genomic imprinting is an epigenetic gene regulatory mechanism that results in parental‐specific gene expression of a small number of genes in diploid somatic cells (Beechey et al., 2001; Reik and Walter, 2001; Li, 2002; Sleutels and Barlow, 2002). Several features of the imprinting mechanism have been identified; however, it is not yet clear whether imprinting is regulated by a unique process or whether it is part of the general epigenetic apparatus used to regulate mammalian gene expression. Clustering and coordinate regulation is one feature imprinted genes share with non‐imprinted genes (Engemann et al., 2000; Onyango et al., 2000), and it is now clear that many imprinted genes are functionally grouped such that imprinted expression of several ...
http://emboj.embopress.org/content/22/14/3696
*  Updates and new concepts in regulation of pro-inflammatory gene expression by steroid hormones | Frontiers Research Topic
Over several decades, the therapeutic use of glucocorticoids have established these molecules as potent inflammation suppressors. The description of transcriptional repression of pro-inflammatory genes as a nuclear receptor mediated mechanism represents a more recent topic of glucocorticoid signaling. However, new evidences suggest that steroidal regulation of inflammation is more complex, including epigenetic and receptor-independent pathways. It is also likely that sets of genes behaves in contradictory ways, making gene repression not a rule, but rather one of the possible modulatory modes. A similar level of complexity might apply to other steroidal hormones, such as those involved in sexually dimorphic immune responses. In fact, some autoimmune diseases are much more prevalent in one gender compared to the other. In addition to well-known steroid hormones, including aldosterone and vitamin D, this review topic intends ...
https://www.frontiersin.org/research-topics/3757/updates-and-new-concepts-in-regulation-of-pro-inflammatory-gene-expression-by-steroid-hormones
*  Plus it
99 Tumorigenesis is often attributed to aberrant gene expression control leading to altered cell cycle control, resistance to apoptosis, abnormal differentiation, decreased genomic stability and inefficient DNA repair. The activity of chromatin remodeling complexes is vital to maintaining proper control of gene expression. The SWI/SNF complex is conserved from yeast to man and is responsible for remodeling up to 6% of the human genome, with many of those genes known to be associated with cell cycle control. Therefore, impaired or defective activity of SWI/SNF chromatin remodeling complex, involved in regulation of gene transcription, could encourage tumor development. The complex is composed of 10 or more members but requires only three core members to do the basic task of remodeling nucleosomes: BRG1/BRM, SNF5, and BAF155. BRG1 and SNF5 both lead to tumor development in ...
http://cancerres.aacrjournals.org/content/66/8_Supplement/23.5
*  A Novel Transcriptional Mechanism of Cell Type-Specific Regulation of Vascular Gene Expression by Glucose | Arteriosclerosis,...
The present study describes a novel cell type-specific mechanism of transcriptional regulation of TSP-1 in vascular cells in response to glucose. We report here that unlike our recently identified short promoter region (−280/+66) responsible for the increased THBS1 transcription in ECs, a longer promoter fragment (−1270/+66) is required for THBS1 regulation in HASMCs, as was described for specialized pericytes and mesangial cells.27 Interestingly, glucose responsiveness in ECs was in fact inhibited by the distal fragment of the promoter,10 suggesting the presence of an inhibitory element in this region, which is not active in either VSMCs or mesangial cells.27 The longer promoter region, −1270/+66, responsible for the increased THBS1 transcription in HASMCs contained distinctly different binding elements, as identified by MatInspector, located in the distal end of the promoter. These binding elements had no similarity to those in the EC-specific THBS1 promoter fragment, ...
http://atvb.ahajournals.org/content/31/3/634
*  Two distinct mechanisms of interleukin-2 gene expression in human T lymphocytes
Abstract: Interleukin-2 (IL-2) gene regulation was investigated in primary cultures of highly purified human peripheral blood CD28+T cells. Two discrete mechanisms for induction of T-cell proliferation could be distinguished by examining cell cycle progression and the expression of the IL-2 gene. Stimulation of cells by CD3 MoAb induced only transiently expressed, small amounts of IL-2 mRNA that was completely suppressed by cyclosporine. Costimulation of T cells with CD3 MoAb and either CD28 MoAb or PMA, but not calcium ionophore, induced a 50-100-fold increased in IL-2 gene expression and secretion. High levels of IL-2 gene expression could also be achieved by stimulation with calcium ionophore and PMA or CD28 MoAb and PMA, but not by CD28 MoAb plus calcium ionophore. IL-2 gene expression and T-cell proliferation induced by CD3 MoAb plus ...
https://deepblue.lib.umich.edu/handle/2027.42/27894
*  Neurons Break Their Own DNA to Enable Memory Formation
How are these breaks linked with the apparent boost in early-response gene expression?. Following a computer analysis of the DNA sequences neighboring these genes, an enzyme known as topoisomerase IIβ was found to be responsible for the DNA breaks in response to stimulation.. They also studied the DNA sequences near these genes and discovered that they were enriched with a motif, or sequence pattern, for binding to a protein called CTCF. This "architectural" protein is known to create loops or bends in DNA.. In the early-response genes, the bends created by this protein act as a barrier that prevents different elements of DNA from interacting with each other - a crucial step in the genes' expression.. The double strand breaks created by the cells allow them to collapse this barrier, and enable the early response genes to be expressed, Tsai says.. The findings have ...
http://reliawire.com/neuron-dna-memory-formation/
*  Ci-MLC4
Kusakabe T., Yoshida, R., Ikeda, Y., Tsuda, M. (2004). "Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona." Dev Biol 276:563-580. (PUBMED ...
http://dbtgr.hgc.jp/v2/name/Ci-MLC4
*  m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence | Genome...
We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G0), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G0 TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G0-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-6-r55
*  Plus it
Introduction: Lung cancer is the number one cancer killer in the United States accounting for nearly 30% of all cancer deaths. Survival rates continue to be abysmal with 5-year survival only 15% despite contemporary therapies, making it clear that novel therapeutic agents need to be discovered. The translation of mRNA into protein, a central control point in the gene expression pathway, has been increasingly implicated as a critical checkpoint in tumor genesis and progression. This checkpoint serves as a traffic signal at the intersection of cell pathways controlling cell division and survival. The cell machinery controlling the first step in protein synthesis, a hetero-trimer designated eIF4F, is stuck in the "on" position in many human cancers. When this happens cells evade restraints on proliferation and survival. The activation state of eIF4F is controlled at multiple levels with the primary mechanism being negative regulation by the 4E ...
http://cancerres.aacrjournals.org/content/72/8_Supplement/2347
*  Regulation of ob gene expression in rodents and humans
The discovery of the obese gene in the mouse and its conserved homologue in humans has led to important discoveries in energy metabolism. One of the chief findings was the fact that the expression of the leptin gene was regulated and that it, in turn, could regulate metabolism and behavior. Much of the literature has focused on the physiological role of leptin in driving processes as diverse as reproduction, starvation defence, feeding behavior or body weight, all dependent on expression levels of the ob gene. Here, we will describe our work, in which we have begun to elucidate the regulatory processes controlling obese gene expression.. Keywords: Gene Expression Regulation ; Obesity. ...
https://infoscience.epfl.ch/record/135513
*  Publications - Jeremy Sanford - Page 1 - MyScienceWork
... :Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA p
https://www.mysciencework.com/publication/author/jeremy.sanford
*  "Stress Activated Protein Kinase Regulation of Gene Expression in Apopt" by Gerard S. De Zutter
Summary Basic biological processes require gene expression. Tightly regulated molecules known as transcription factors mediate the expression of genes in development and disease. Signal transduction pathways, which respond to environmental cues or stressors are major regulators of the transcription factors. Use of macromolecular synthesis inhibitors in models of normal neurodevelopment and neurodegenerative cell death has led to the discovery that gene expression is required for these processes to occur (Martin et. al.,(1988), J Cell Biol 106 p829). To date, however, the identities of very few of the genes required in these events have been revealed. Hence, the activation or requirement of specific signaling pathways leading to the expression of known apoptotic genes is not well established. Utilizing the neurothrophic factor deprivation and ...
http://escholarship.umassmed.edu/gsbs_diss/168/
*  Translational contributions to tissue specificity in rhythmic and constitutive gene expression - pdf descargar
Translational contributions to tissue specificity in rhythmic and constitutive gene expression. . 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/jun8/149841731469-Translational-contributions-to-tissue-specificity-in-rhythmic-and-constitutive-gene-expression.php
*  CECAD: Stirling Churchman (USA) 'From the nucleus to the mitochondria: gene expression regulation at high resolution'
The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases provides an extremely dynamic environment for research into the aging process and its diseases.
http://cecad.uni-koeln.de/Article.372.0.html?&tx_ttnews%5Btt_news%5D=749&cHash=6192ebed27b8a88ed75648d50742090d
*  BIOL6027 | Regulation of Gene Expression | University of Southampton
This module covers the structure and expression of genetic material in eukaryotic cells. Regulation of eukaryotic gene expression will be discussed. Selected examples where gene expression has been disrupted will also be covered; this will include the study of transcription factors as oncogenes and tumour suppressor genes. . In subsequent lectures the role of microRNAs in gene regulation and disease will be discussed, together with the factors and mechanisms that control the process of translation. ...
https://www.southampton.ac.uk/courses/modules/biol6027.page
*  Why do clones have different markings? - Chronicle Forums
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isn't always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. That's how identical cells can have different ...
https://www.chronofhorse.com/forum/forum/discussion-forums/sport-horse-breeding/224757-why-do-clones-have-different-markings?391712-Why-do-clones-have-different-markings=