E2F – at the Crossroads of Life and Death
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Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression
International Journal of Molecular Sciences Review The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression Tingting Zou and Zhenghong Lin * School of Life Sciences, Chongqing University, Chongqing 401331, China; [email protected] * Correspondence: [email protected] Abstract: The cell cycle is a collection of events by which cellular components such as genetic materials and cytoplasmic components are accurately divided into two daughter cells. The cell cycle transition is primarily driven by the activation of cyclin-dependent kinases (CDKs), which activities are regulated by the ubiquitin-mediated proteolysis of key regulators such as cyclins, CDK inhibitors (CKIs), other kinases and phosphatases. Thus, the ubiquitin-proteasome system (UPS) plays a pivotal role in the regulation of the cell cycle progression via recognition, interaction, and ubiquitination or deubiquitination of key proteins. The illegitimate degradation of tumor suppressor or abnormally high accumulation of oncoproteins often results in deregulation of cell proliferation, genomic instability, and cancer occurrence. In this review, we demonstrate the diversity and complexity of the regulation of UPS machinery of the cell cycle. A profound understanding of the ubiquitination machinery will provide new insights into the regulation of the cell cycle transition, cancer treatment, and the development of anti-cancer drugs. Keywords: cell cycle regulation; CDKs; cyclins; CKIs; UPS; E3 ubiquitin ligases; Deubiquitinases (DUBs) Citation: Zou, T.; Lin, Z. The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression. 1. Introduction Int. J. Mol. Sci. 2021, 22, 5754. https://doi.org/10.3390/ijms22115754 The cell cycle is a ubiquitous, complex, and highly regulated process that is involved in the sequential events during which a cell duplicates its genetic materials, grows, and di- Academic Editors: Kwang-Hyun Bae vides into two daughter cells. -
Nuclear Localization of DP and E2F Transcription Factors by Heterodimeric Partners and Retinoblastoma Protein Family Members
Journal of Cell Science 109, 1717-1726 (1996) 1717 Printed in Great Britain © The Company of Biologists Limited 1996 JCS7086 Nuclear localization of DP and E2F transcription factors by heterodimeric partners and retinoblastoma protein family members Junji Magae1, Chin-Lee Wu2, Sharon Illenye1, Ed Harlow2 and Nicholas H. Heintz1,* 1Department of Pathology, University of Vermont, Burlington VT 05405, USA 2Massachusetts General Hospital Cancer Center, Charlestown MA 02129, USA *Author for correspondence SUMMARY E2F is a family of transcription factors implicated in the showed that regions of E2F-1 and DP-1 that are required regulation of genes required for progression through G1 for stable association of the two proteins were also required and entry into the S phase. The transcriptionally active for nuclear localization of DP-1. Unlike E2F-1, -2, and -3, forms of E2F are heterodimers composed of one polypep- E2F-4 did not accumulate in the nucleus unless it was coex- tide encoded by the E2F gene family and one polypeptide pressed with DP-2. p107 and p130, but not pRb, stimulated encoded by the DP gene family. The transcriptional activity nuclear localization of E2F-4, either alone or in combina- of E2F/DP heterodimers is influenced by association with tion with DP-2. These results indicate that DP proteins the members of the retinoblastoma tumor suppressor preferentially associate with specific E2F partners, and protein family (pRb, p107, and p130). Here the intracellu- suggest that the ability of specific E2F/DP heterodimers to lar distribution of E2F and DP proteins was investigated in localize in the nucleus contributes to the regulation of E2F transiently transfected Chinese hamster and human cells. -
Universidade Nova De Lisboa Instituto De Higiene E Medicina Tropical
Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina Catarina Sofia Bento Monteiro DISSERTAÇÃO PARA A OBTENÇÃO DO GRAU DE MESTRE EM PARASITOLOGIA MÉDICA JANEIRO, 2018 Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina Autor: Catarina Sofia Bento Monteiro Orientador: Doutora Ana Isabel Amaro Gonçalves Domingos (IHMT, UNL) Coorientador: Doutora Sandra Isabel da Conceição Antunes (IHMT, UNL) Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de mestre em parasitologia médica The results obtained during the development of this master project were reported at two international conferences: Monteiro, C, Domingos, A, and Antunes, S 2017, ´Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina´, COST action: EuroNegVec, 11-13 September, Crete, Greece. Monteiro, C, Domingos, A, and Antunes, S 2017 ´Is the apoptosis pathway in Rhipicephalus annulatus ticks regulated by the protozoan Babesia bigemina?´ Conference: Biotecnología Habana 2017: ´La Biotecnología Agropecuaria en el siglo XXI´, 3-6 December, Varadero, Cuba. i Acknowledgments Quero, desde já, agradecer à Doutora Ana Domingos por se ter disponibilizado a orientar-me e por não ter desistido de mim. À Doutora Sandra Antunes, pelo apoio constante e compreensão durante toda esta longa jornada. Admiro a simplicidade com que encaras a vida. À Joana Couto pela boa disposição e prontidão em ajudar. És das pessoas mais genuínas que já conheci. À Joana Ferrolho com quem partilho o mesmo gosto pela medicina veterinária. -
Master Biomedizin 2018 1) UCSC & Uniprot 2) Homology 3) MSA 4) Phylogeny
Master Biomedizin 2018 1) UCSC & UniProt 2) Homology 3) MSA 4) Phylogeny Pablo Mier 1 [email protected] Genomics *Images from: Wikipedia 1 a. Get the fasta sequence of the human (Homo sapiens) protein P53 from UniProt (https://www.uniprot.org/). Which one of all the isoforms should you download? P04637 b. Find the P53 protein from mouse (Mus musculus). As you see, there is more than one entry for mouse. Which UniProt entry should you select? P02340 c. BLAT the human P53 using “hg38” as database (in UCSC, http://genome.ucsc.edu/cgi-bin/hgBlat), and answer: How many amino acids has the query sequence? 393 aa And how many nucleotides? 1179 nt Is it a perfect alignment? No Which is the genomic locus of the target? Chr17 7669612-7676594 d. Visualize and navigate through the P53 genome region, and answer: Which genes are around? ATP1B2 and WRAP53 How many exons does it have? 9 exons e. BLAT the mouse P53 against the human genome “hg38”. What do you observe? The result is worse (85%) Human Mouse (Homo sapiens) (Mus musculus) Pablo Mier 2 [email protected] Genomics *Images from: UniProt 1 a. P04637 (P53_HUMAN). The canonical. b. P02340 (P53_MOUSE). Pablo Mier 3 [email protected] Genomics *Images from: UCSC 1 c. 393 amino acids Not a perfect alignment chr17 393*3 = 1179 nucleotides (“lpennvl”) 7669612-7676594 d. ATP1B2 and WRAP53. 9 exons (9 blocks). 9 8 7 6 5 4 3 2 1 e. The result is worse (85%). Pablo Mier 4 [email protected] UniProt database 2 a. -
TP63 and TP73 in Cancer, an Unresolved В€Œfamily∕ Puzzle Of
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 588 (2014) 2590–2599 journal homepage: www.FEBSLetters.org Review TP63 and TP73 in cancer, an unresolved ‘‘family’’ puzzle of complexity, redundancy and hierarchy Antonio Costanzo a, Natalia Pediconi b,c, Alessandra Narcisi a, Francesca Guerrieri c,d, Laura Belloni c,d, ⇑ Francesca Fausti a, Elisabetta Botti a, Massimo Levrero c,d, a Dermatology Unit, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sapienza University of Rome, Italy b Laboratory of Molecular Oncology, Department of Molecular Medicine, Sapienza University of Rome, Italy c Center for Life Nanosciences (CNLS) – IIT/Sapienza, Rome, Italy d Laboratory of Gene Expression, Department of Internal Medicine (DMISM), Sapienza University of Rome, Italy article info abstract Article history: TP53 belongs to a small gene family that includes, in mammals, two additional paralogs, TP63 and Received 19 May 2014 TP73. The p63 and p73 proteins are structurally and functionally similar to p53 and their activity as Revised 16 June 2014 transcription factors is regulated by a wide repertoire of shared and unique post-translational mod- Accepted 16 June 2014 ifications and interactions with regulatory cofactors. p63 and p73 have important functions in Available online 28 June 2014 embryonic development and differentiation but are also involved in tumor suppression. The biology Edited by Shairaz Baksh, Giovanni Blandino of p63 and p73 is complex since both TP63 and TP73 genes are transcribed into a variety of different and Wilhelm Just isoforms that give rise to proteins with antagonistic properties, the TA-isoforms that act as tumor- suppressors and DN-isoforms that behave as proto-oncogenes. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Mitogen Requirement for Cell Cycle Progression in the Absence of Pocket Protein Activity
ARTICLE Mitogen requirement for cell cycle progression in the absence of pocket protein activity Floris Foijer,1 Rob M.F. Wolthuis,1 Valerie Doodeman,1 Rene´ H. Medema,2 and Hein te Riele1,* 1 Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands 2 Present address: Experimental Oncology, University Medical Center, Stratenum 2.103, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands *Correspondence: [email protected] Summary Primary mouse embryonic fibroblasts lacking expression of all three retinoblastoma protein family members (TKO MEFs) have lost the G1 restriction point. However, in the absence of mitogens these cells become highly sensitive to apoptosis. CIP1 KIP1 Here, we show that TKO MEFs that survive serum depletion pass G1 but completely arrest in G2. p21 and p27 inhibit Cyclin A-Cdk2 activity and sequester Cyclin B1-Cdk1 in inactive complexes in the nucleus. This response is alleviated by mi- togen restimulation or inactivation of p53. Thus, our results disclose a cell cycle arrest mechanism in G2 that restricts the proliferative capacity of mitogen-deprived cells that have lost the G1 restriction point. The involvement of p53 provides a ra- tionale for the synergism between loss of Rb and p53 in tumorigenesis. Introduction Despite the critical role of pRb in controlling the G1 restriction point, pRb knockout primary mouse embryonic fibroblasts Proliferation of cells in culture is dependent on the presence of (MEFs) do not proliferate in the absence of mitogens but still ar- mitogenic stimuli. In the absence of mitogens, cells fail to prog- rest (Herrera et al., 1996; Almasan et al., 1995). -
Product Sheet CA1009
API5 Antibody Applications: WB, IHC Detected MW: 51 kDa Cat. No. CA1009 Species & Reactivity: Human, Rat Isotype: Rabbit IgG BACKGROUND APPLICATIONS The apoptosis inhibitor-5 [API5; antiapoptosis Application: *Dilution: clone 11 (AAC-11); fibroblast growth factor-2 WB 1:1000 (FGF2)-interacting factor (FIF)] is a 504-aa IP n/d nuclear protein whose expression has been shown IHC 1:50-200 to prevent apoptosis after growth factor ICC n/d deprivation. It was shown that its antiapoptotic action seems to be mediated, at least in part, by FACS n/d *Optimal dilutions must be determined by end user. the suppression of the transcription factor E2F1- induced apoptosis. Moreover, it was also reported that API5 interacts with, and negatively regulates Acinus, a protein involved in apoptotic DNA QUALITY CONTROL DATA fragmentation. API5 can form homo-oligomers, through a leucine-zipper (LZ) motif, and oligomerization-deficient mutants of AAC-11 can no longer inhibit apoptosis nor interact with Acinus.1 The API5gene has been shown to be highly expressed in multiple cancer cell lines as well as in some metastatic lymph node tissues and in B-cell chronic lymphoid leukemia. API5 expression seems to confer a poor outcome in subgroups of patients with non-small cell lung carcinoma, whereas its depletion seems to be tumor cell lethal under condition of low-serum stress. Interestingly, API5 overexpression has been reported to promote both cervical cancer cells growth and invasiveness. Combined, these observations implicate API5as a putative metastatic oncogene and suggest that API5 could constitute a therapeutic target in cancer.2 References: 1. -
Runx3 Plays a Critical Role in Restriction-Point and Defense Against Cellular Transformation
OPEN Oncogene (2017) 36, 6884–6894 www.nature.com/onc ORIGINAL ARTICLE Runx3 plays a critical role in restriction-point and defense against cellular transformation X-Z Chi1, J-W Lee1, Y-S Lee1, IY Park2,YIto3 and S-C Bae1 The restriction (R)-point decision is fundamental to normal differentiation and the G1–S transition, and the decision-making machinery is perturbed in nearly all cancer cells. The mechanisms underlying the cellular context–dependent R-point decision remain poorly understood. We found that the R-point was dysregulated in Runx3−/−mouse embryonic fibroblasts (MEFs), which formed tumors in nude mice. Ectopic expression of Runx3 restored the R-point and abolished the tumorigenicity of Runx3−/−MEFs and K-Ras–activated Runx3−/−MEFs (Runx3−/−;K-RasG12D/+). During the R-point, Runx3 transiently formed a complex with pRb and Brd2 and induced Cdkn1a (p21Waf1/Cip1/Sdi1; p21), a key regulator of the R-point transition. Cyclin D–CDK4/6 promoted dissociation of the pRb–Runx3–Brd2 complex, thus turning off p21 expression. However, cells harboring oncogenic K-Ras maintained the pRb– Runx3–Brd2 complex and p21 expression even after introduction of Cyclin D1. Thus, Runx3 plays a critical role in R-point regulation and defense against cellular transformation. Oncogene (2017) 36, 6884–6894; doi:10.1038/onc.2017.290; published online 28 August 2017 INTRODUCTION general, the p53 pathway is inactivated during MEF immortaliza- The restriction (R)-point is a critical event in which a mammalian tion, but the immortalized MEFs are not tumorigenic, which cell makes the decision in response to mitogen stimulation. -
DNA Damage Triggers a Prolonged P53- Dependent G^ Arrest Ana Long-Term Induction of Cipl in Normal Human Fibroblasts
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press DNA damage triggers a prolonged p53- dependent G^ arrest ana long-term induction of Cipl in normal human fibroblasts Aldo Di Leonardo/'^'^ Steven P. Linke/'^'^ Kris Clarkin/ and Geoffrey M. Wahl** ^Gene Expression Lab, The Salk Institute, La Jolla, California 92037 USA; ^Department of Cell and Developmental Biology, University of Palermo, Italy; ^Department of Biology, University of California, San Diego, La Jolla, California 92037 USA The tumor suppressor p53 is a cell cycle checkpoint protein that contributes to the preservation of genetic stability by mediating either a G^ arrest or apoptosis in response to DNA damage. Recent reports suggest that p53 causes growth arrest through transcriptional activation of the cyclin-dependent kinase (Cdk)-inhibitor Cipl. Here, we characterize the p53-dependent Gj arrest in several normal human diploid fibroblast (NDF) strains and p53-deficient cell lines treated with 0.1-6 Gy gamma radiation. DNA damage and cell cycle progression analyses showed that NDF entered a prolonged arrest state resembling senescence, even at low doses of radiation. This contrasts with the view that p53 ensures genetic stability by inducing a transient arrest to enable repair of DNA damage, as reported for some myeloid leukemia lines. Gamma radiation administered in early to mid-, but not late, G^ induced the arrest, suggesting that the p53 checkpoint is only active in Gj until cells commit to enter S phase at the Gi restriction point. A log-linear plot of the fraction of irradiated GQ cells able to enter S phase as a function of dose is consistent with single-hit kinetics. -
AP-1 in Cell Proliferation and Survival
Oncogene (2001) 20, 2390 ± 2400 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc AP-1 in cell proliferation and survival Eitan Shaulian1 and Michael Karin*,1 1Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, California, CA 92093-0636, USA A plethora of physiological and pathological stimuli extensively discussed previously (Angel and Karin, induce and activate a group of DNA binding proteins 1991; Karin, 1995). that form AP-1 dimers. These proteins include the Jun, The mammalian AP-1 proteins are homodimers and Fos and ATF subgroups of transcription factors. Recent heterodimers composed of basic region-leucine zipper studies using cells and mice de®cient in individual AP-1 (bZIP) proteins that belong to the Jun (c-Jun, JunB proteins have begun to shed light on their physiological and JunD), Fos (c-Fos, FosB, Fra-1 and Fra-2), Jun functions in the control of cell proliferation, neoplastic dimerization partners (JDP1 and JDP2) and the closely transformation and apoptosis. Above all such studies related activating transcription factors (ATF2, LRF1/ have identi®ed some of the target genes that mediate the ATF3 and B-ATF) subfamilies (reviewed by (Angel eects of AP-1 proteins on cell proliferation and death. and Karin, 1991; Aronheim et al., 1997; Karin et al., There is evidence that AP-1 proteins, mostly those that 1997; Liebermann et al., 1998; Wisdom, 1999). In belong to the Jun group, control cell life and death addition, some of the Maf proteins (v-Maf, c-Maf and through their ability to regulate the expression and Nrl) can heterodimerize with c-Jun or c-Fos (Nishiza- function of cell cycle regulators such as Cyclin D1, p53, wa et al., 1989; Swaroop et al., 1992), whereas other p21cip1/waf1, p19ARF and p16.