Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence.

PubWeight™: 0.84‹?›

🔗 View Article (PMC 3701195)

Published in Genes Dev on June 11, 2013

Authors

Jesse M Platt1, Paul Ryvkin, Jennifer J Wanat, Greg Donahue, M Dan Ricketts, Steven P Barrett, Hannah J Waters, Shufei Song, Alejandro Chavez, Khaled Omar Abdallah, Stephen R Master, Li-San Wang, F Brad Johnson

Author Affiliations

1: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Articles cited by this

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20

Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell (2010) 23.97

Telomere shortening and tumor formation by mouse cells lacking telomerase RNA. Cell (1997) 13.34

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05

A mutant with a defect in telomere elongation leads to senescence in yeast. Cell (1989) 8.69

Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders. Nature (2011) 8.45

SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev (1997) 7.81

An alternative pathway for yeast telomere maintenance rescues est1- senescence. Cell (1993) 6.89

Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a). Mol Cell (2004) 6.48

Dynamics of replication-independent histone turnover in budding yeast. Science (2007) 6.41

Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29

Aging, cellular senescence, and cancer. Annu Rev Physiol (2012) 5.08

A protein-counting mechanism for telomere length regulation in yeast. Science (1997) 4.79

The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol (1996) 4.72

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature (1999) 4.71

Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell (1999) 4.71

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods (2008) 3.79

SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell (1993) 3.77

Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein. Mol Cell Biol (1988) 3.69

Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast. J Cell Biol (1992) 3.48

Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol (2009) 3.43

RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev (1993) 3.18

Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science (2008) 3.09

Elevated histone expression promotes life span extension. Mol Cell (2010) 3.09

Interactions of TLC1 (which encodes the RNA subunit of telomerase), TEL1, and MEC1 in regulating telomere length in the yeast Saccharomyces cerevisiae. Mol Cell Biol (1999) 2.88

Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev (1996) 2.85

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature (2012) 2.85

Telomere dysfunction increases mutation rate and genomic instability. Cell (2001) 2.62

Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature (2004) 2.51

The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell (1996) 2.42

The biology of replicative senescence. Eur J Cancer (1997) 2.42

Telomere length regulates the epigenetic status of mammalian telomeres and subtelomeres. Nat Genet (2007) 2.37

Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J Mol Biol (1993) 2.23

Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev (2009) 2.13

Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol Cell (2009) 2.06

Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat Struct Mol Biol (2010) 2.04

Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev (1996) 2.02

The Saccharomyces cerevisiae WRN homolog Sgs1p participates in telomere maintenance in cells lacking telomerase. EMBO J (2001) 1.99

Telomerase and Tel1p preferentially associate with short telomeres in S. cerevisiae. Mol Cell (2007) 1.98

Exonuclease-1 deletion impairs DNA damage signaling and prolongs lifespan of telomere-dysfunctional mice. Cell (2007) 1.96

The nature of telomere fusion and a definition of the critical telomere length in human cells. Genes Dev (2007) 1.88

Increased chromosome mobility facilitates homology search during recombination. Nat Cell Biol (2012) 1.88

Rap1 prevents telomere fusions by nonhomologous end joining. EMBO J (2005) 1.87

Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol Cell Biol (1999) 1.87

Short telomeres induce a DNA damage response in Saccharomyces cerevisiae. Mol Biol Cell (2003) 1.86

A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet (2006) 1.86

Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery. Nat Cell Biol (2012) 1.86

Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites. Nat Cell Biol (2010) 1.69

Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol (2006) 1.61

Telomeres and age-related disease: how telomere biology informs clinical paradigms. J Clin Invest (2013) 1.58

A two-step model for senescence triggered by a single critically short telomere. Nat Cell Biol (2009) 1.51

MEC3, MEC1, and DDC2 are essential components of a telomere checkpoint pathway required for cell cycle arrest during senescence in Saccharomyces cerevisiae. Mol Biol Cell (2002) 1.48

Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Mol Cell Biol (2001) 1.48

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res (2010) 1.48

Telomerase- and recombination-independent immortalization of budding yeast. Genes Dev (2004) 1.47

The dynamics of yeast telomeres and silencing proteins through the cell cycle. J Struct Biol (2000) 1.46

DNA breaks are masked by multiple Rap1 binding in yeast: implications for telomere capping and telomerase regulation. Genes Dev (2007) 1.45

GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain. EMBO J (1993) 1.41

Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination. Genes Dev (2012) 1.36

The DNA damage response at eroded telomeres and tethering to the nuclear pore complex. Nat Cell Biol (2009) 1.36

Human telomeric proteins occupy selective interstitial sites. Cell Res (2011) 1.30

The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 1.27

Metabolic analysis of senescent human fibroblasts reveals a role for AMP in cellular senescence. Biochem J (2003) 1.24

Perspectives on the DNA damage and replication checkpoint responses in Saccharomyces cerevisiae. DNA Repair (Amst) (2009) 1.22

Contacts between the factor TUF and RPG sequences. J Biol Chem (1990) 1.21

A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20

Telomere capping in non-dividing yeast cells requires Yku and Rap1. EMBO J (2010) 1.12

Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells. Mol Cell Proteomics (2010) 1.12

Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters. Genome Res (2010) 1.01

Inactivation of the Sas2 histone acetyltransferase delays senescence driven by telomere dysfunction. EMBO J (2009) 1.00

Human Rap1 interacts directly with telomeric DNA and regulates TRF2 localization at the telomere. J Biol Chem (2012) 0.98

Regulation of histone gene expression in budding yeast. Genetics (2012) 0.98

Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast. Genetics (1995) 0.93

End-joining inhibition at telomeres requires the translocase and polySUMO-dependent ubiquitin ligase Uls1. EMBO J (2013) 0.92

TRF2 controls telomeric nucleosome organization in a cell cycle phase-dependent manner. PLoS One (2012) 0.89

Yeast Rap1 contributes to genomic integrity by activating DNA damage repair genes. EMBO J (2008) 0.87

Distinct DNA elements contribute to Rap1p affinity for its binding sites. J Mol Biol (2004) 0.85

Localization of telomeres and telomere-associated proteins in telomerase-negative Saccharomyces cerevisiae. Chromosome Res (2007) 0.84

Articles by these authors

Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet (2011) 10.07

Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature (2009) 8.09

Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med (2014) 6.12

Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions. Nat Genet (2010) 5.52

Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature (2009) 3.83

Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell (2012) 3.80

The serine/threonine kinase Pim-2 is a transcriptionally regulated apoptotic inhibitor. Genes Dev (2003) 3.79

Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. Nat Genet (2011) 2.97

The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. Nature (2012) 2.94

Meta-analysis confirms CR1, CLU, and PICALM as alzheimer disease risk loci and reveals interactions with APOE genotypes. Arch Neurol (2010) 2.91

Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Proc Natl Acad Sci U S A (2004) 2.89

Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science (2010) 2.78

Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. JAMA (2013) 2.58

Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron (2013) 2.45

Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics (2006) 2.18

A critical role for TCF-1 in T-lineage specification and differentiation. Nature (2011) 2.15

Novel late-onset Alzheimer disease loci variants associate with brain gene expression. Neurology (2012) 2.08

Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev (2013) 2.08

Telomere shortening exposes functions for the mouse Werner and Bloom syndrome genes. Mol Cell Biol (2004) 1.99

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Res (2007) 1.98

Differential expression of miRNAs in papillary thyroid carcinoma compared to multinodular goiter using formalin fixed paraffin embedded tissues. Endocr Pathol (2007) 1.89

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol (2005) 1.79

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev (2013) 1.78

Fibroblast growth factor 23 is not associated with and does not induce arterial calcification. Kidney Int (2013) 1.66

A human model of inflammatory cardio-metabolic dysfunction; a double blind placebo-controlled crossover trial. J Transl Med (2012) 1.59

Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet (2010) 1.56

Persistent parity-induced changes in growth factors, TGF-beta3, and differentiation in the rodent mammary gland. Mol Endocrinol (2002) 1.56

Cdc13 OB2 dimerization required for productive Stn1 binding and efficient telomere maintenance. Structure (2012) 1.56

Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res (2013) 1.53

Bcl-X(L) affects Ca(2+) homeostasis by altering expression of inositol 1,4,5-trisphosphate receptors. Proc Natl Acad Sci U S A (2002) 1.51

Global analysis of RNA secondary structure in two metazoans. Cell Rep (2012) 1.50

Evidence for a role of the rare p.A152T variant in MAPT in increasing the risk for FTD-spectrum and Alzheimer's diseases. Hum Mol Genet (2012) 1.46

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45

Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res (2009) 1.44

Nuclear factor {kappa}B-mediated transactivation of telomerase prevents intimal smooth muscle cell from replicative senescence during vascular repair. Arterioscler Thromb Vasc Biol (2010) 1.44

Comparison of cerebrospinal fluid levels of tau and Aβ 1-42 in Alzheimer disease and frontotemporal degeneration using 2 analytical platforms. Arch Neurol (2012) 1.42

Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics (2002) 1.41

Senescent cells harbour features of the cancer epigenome. Nat Cell Biol (2013) 1.34

Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study. BMC Neurol (2010) 1.32

Role for G-quadruplex RNA binding by Epstein-Barr virus nuclear antigen 1 in DNA replication and metaphase chromosome attachment. J Virol (2009) 1.29

Defects in telomere maintenance molecules impair osteoblast differentiation and promote osteoporosis. Aging Cell (2007) 1.29

HAMR: high-throughput annotation of modified ribonucleotides. RNA (2013) 1.24

Activation drives PD-1 expression during vaccine-specific proliferation and following lentiviral infection in macaques. Eur J Immunol (2008) 1.23

SORL1 is genetically associated with late-onset Alzheimer's disease in Japanese, Koreans and Caucasians. PLoS One (2013) 1.23

An iPSC line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression. Cell Rep (2013) 1.21

Unbiased statistical analysis for multi-stage proteomic search strategies. J Proteome Res (2010) 1.19

Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae. Nat Struct Mol Biol (2011) 1.14

Design of comprehensive Alzheimer's disease centers to address unmet national needs. Alzheimers Dement (2010) 1.14

Genomic landscape of a three-generation pedigree segregating affective disorder. PLoS One (2009) 1.13

Interaction of human telomeric DNA with N-methyl mesoporphyrin IX. Nucleic Acids Res (2012) 1.11

Evidence that the S.cerevisiae Sgs1 protein facilitates recombinational repair of telomeres during senescence. Nucleic Acids Res (2006) 1.10

Significant correlation of species longevity with DNA double strand break recognition but not with telomere length. Mech Ageing Dev (2009) 1.10

Race and gender variation in response to evoked inflammation. J Transl Med (2013) 1.10

A novel telomere structure in a human alternative lengthening of telomeres cell line. Cancer Res (2005) 1.09

Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinformatics (2010) 1.08

Sumoylation and the structural maintenance of chromosomes (Smc) 5/6 complex slow senescence through recombination intermediate resolution. J Biol Chem (2010) 1.08

ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology. Acta Neuropathol (2014) 1.07

A Bayesian approach to efficient differential allocation for resampling-based significance testing. BMC Bioinformatics (2009) 1.07

Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA. J Am Chem Soc (2012) 1.07

Supervised multi-view canonical correlation analysis (sMVCCA): integrating histologic and proteomic features for predicting recurrent prostate cancer. IEEE Trans Med Imaging (2014) 1.07

Age-correlated gene expression in normal and neurodegenerative human brain tissues. PLoS One (2010) 1.06

Functional unresponsiveness and replicative senescence of myeloid leukemia antigen-specific CD8+ T cells after allogeneic stem cell transplantation. Clin Cancer Res (2009) 1.06

Senescent mouse cells fail to overtly regulate the HIRA histone chaperone and do not form robust Senescence Associated Heterochromatin Foci. Cell Div (2010) 1.05

Comparisons of telomere lengths in peripheral blood and cerebellum in Alzheimer's disease. Alzheimers Dement (2009) 1.05

Homologous recombination-dependent rescue of deficiency in the structural maintenance of chromosomes (Smc) 5/6 complex. J Biol Chem (2010) 1.05

Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer's disease. Neurobiol Aging (2012) 1.04

The Werner syndrome protein affects the expression of genes involved in adipogenesis and inflammation in addition to cell cycle and DNA damage responses. Cell Cycle (2009) 1.03

Isobaric labeling and tandem mass spectrometry: a novel approach for profiling and quantifying proteins differentially expressed in amniotic fluid in preterm labor with and without intra-amniotic infection/inflammation. J Matern Fetal Neonatal Med (2010) 1.02

Evidence that a RecQ helicase slows senescence by resolving recombining telomeres. PLoS Biol (2007) 1.02

Inactivation of the Sas2 histone acetyltransferase delays senescence driven by telomere dysfunction. EMBO J (2009) 1.00

Timeless Maintains Genomic Stability and Suppresses Sister Chromatid Exchange during Unperturbed DNA Replication. J Biol Chem (2008) 1.00

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J Comput Biol (2014) 0.99

Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia. Blood (2013) 0.99

DACTAL: divide-and-conquer trees (almost) without alignments. Bioinformatics (2012) 0.98

Quality control and protein microarrays. Clin Chem (2009) 0.98

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evol Biol (2006) 0.98

In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie (2008) 0.97

Identification of Flt3⁺CD150⁻ myeloid progenitors in adult mouse bone marrow that harbor T lymphoid developmental potential. Blood (2011) 0.96

High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res (2013) 0.96

Erythrocytosis-associated HIF-2alpha mutations demonstrate a critical role for residues C-terminal to the hydroxylacceptor proline. J Biol Chem (2009) 0.96

Validation and quality control of protein microarray-based analytical methods. Mol Biotechnol (2007) 0.96

Sgs1 RecQ helicase inhibits survival of Saccharomyces cerevisiae cells lacking telomerase and homologous recombination. J Biol Chem (2008) 0.95

Enhanced position weight matrices using mixture models. Bioinformatics (2005) 0.94

Cdc13 N-terminal dimerization, DNA binding, and telomere length regulation. Mol Cell Biol (2010) 0.94

SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res (2012) 0.94

Prolyl hydroxylase domain protein 2 (PHD2) binds a Pro-Xaa-Leu-Glu motif, linking it to the heat shock protein 90 pathway. J Biol Chem (2013) 0.93

Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery. BMC Bioinformatics (2011) 0.93

Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints. BMC Genomics (2014) 0.90