The Rap1_Martinez project in PAZAR Help

Description

Rap1 is a component of the shelterin complex at mammalian telomeres, but its in vivo role in telomere biology has remained largely unknown to date. Here we show that Rap1 deficiency is dispensable for telomere capping but leads to increased telomere recombination and fragility. We generated cells and mice deleted for Rap1; mice with Rap1 deletion in stratified epithelia were viable but had shorter telomeres and developed skin hyperpigmentation in adulthood. By performing chromatin immunoprecipitation coupled with ultrahigh-throughput sequencing, we found that Rap1 binds to both telomeres and to extratelomeric sites through the (TTAGGG)(2) consensus motif. Extratelomeric Rap1-binding sites were enriched at subtelomeric regions, in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. More than 70% of extratelomeric Rap1-binding sites were in the vicinity of genes, and 31% of the genes deregulated in Rap1-null cells contained Rap1-binding sites, suggesting a role for Rap1 in transcriptional control. These findings place a telomere protein at the interface between telomere function and transcriptional regulation.

Statistics

Regulated genes (or markers): 126
Regulatory sequences (genomic): 133
Regulatory sequences (artificial): 0
Transcription factors: 1
Transcription factor profiles: 0
Annotated publications: 1

Generate GFF

If you would like to generate a current GFF file for this project immediately, click the button below to do so. The file will be made available for download in a new window. The new window may be safely closed once you have downloaded the file. Note that GFF file generation may take a significant amount of time for larger projects.
Pre-generated GFF files are available in the downloads section. Public projects are checked weekly and updated files are generated if there are changes.

Access project data

View all data now in or (not recommended—please use a filter to reduce output size and load time)
Restrict to species »
Mus musculus
Restrict to genomic region »
chromosome
also restrict by base pair   start   end
Restrict to one or more regulated genes or markers »
5S ribosomal RNA ENSMUSG00000088075
activated leukocyte cell adhesion molecule ENSMUSG00000022636
acyl-CoA synthetase long-chain family member 4 ENSMUSG00000031278
acyl-CoA thioesterase 2 ENSMUSG00000021226
adenylate cyclase 8 ENSMUSG00000022376
aldehyde dehydrogenase 1 family, member L2 ENSMUSG00000020256
aldehyde dehydrogenase family 1, subfamily A2 ENSMUSG00000013584
alpha-2-HS-glycoprotein ENSMUSG00000022868
androgen-induced 1 ENSMUSG00000019806
angiopoietin-like 4 ENSMUSG00000002289
aquaporin 1 ENSMUSG00000004655
arrestin domain containing 3 ENSMUSG00000074794
BCL2/adenovirus E1B interacting protein 3 ENSMUSG00000078566
brain derived neurotrophic factor ENSMUSG00000048482
c-mer proto-oncogene tyrosine kinase ENSMUSG00000014361
carnitine deficiency-associated gene expressed in ventricle 3 ENSMUSG00000032803
cellular retinoic acid binding protein I ENSMUSG00000032291
ceruloplasmin ENSMUSG00000003617
ChaC, cation transport regulator-like 1 ENSMUSG00000027313
chemokine ligand 1 ENSMUSG00000029380
chloride channel calcium activated 4 ENSMUSG00000037033
claudin 15 ENSMUSG00000001739
coiled-coil domain containing 68 ENSMUSG00000038903
collagen, type I, alpha 2 ENSMUSG00000029661
connective tissue growth factor ENSMUSG00000019997
CSA-conditional, T cell activation-dependent protein ENSMUSG00000047363
dickkopf homolog 2 ENSMUSG00000028031
distal-less homeobox 2 ENSMUSG00000023391
DNA segment, Chr 14, ERATO Doi 668, expressed ENSMUSG00000068245
DNA segment, Chr 6, Miriam Meisler 5, expressed ENSMUSG00000030041
DNA-damage-inducible transcript 4 ENSMUSG00000020108
dual specificity phosphatase 6 ENSMUSG00000019960
elastin microfibril interfacer 2 ENSMUSG00000024053
epidermal growth factor-containing fibulin-like extracellular matrix protein 1 ENSMUSG00000020467
ERBB receptor feedback inhibitor 1 ENSMUSG00000028967
ets variant gene 5 ENSMUSG00000013089
eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked ENSMUSG00000069049
eukaryotic translation initiation factor 4 gamma, 3 ENSMUSG00000028760
family with sequence similarity 198, member B ENSMUSG00000027955
fibroblast growth factor 10 ENSMUSG00000021732
fibroblast growth factor 21 ENSMUSG00000030827
fibroblast growth factor 5 ENSMUSG00000029337
follistatin ENSMUSG00000021765
forkhead box G1 ENSMUSG00000020950
G protein-coupled receptor 124 ENSMUSG00000031486
G protein-coupled receptor, family C, group 5, member B ENSMUSG00000008734
glutamic pyruvate transaminase 2 ENSMUSG00000031700
granzyme K ENSMUSG00000042385
growth arrest and DNA-damage-inducible 45 alpha ENSMUSG00000036390
growth arrest specific 2 ENSMUSG00000030498
heme binding protein 1 ENSMUSG00000042770
high mobility group AT-hook 2 ENSMUSG00000056758
homeobox A2 ENSMUSG00000014704
hyaluronan synthase 2 ENSMUSG00000022367
hypermethylated in cancer 1 ENSMUSG00000043099
hypoxia inducible factor 1, alpha subunit ENSMUSG00000021109
inhibin beta-A ENSMUSG00000041324
integrin alpha 8 ENSMUSG00000026768
interleukin 1 receptor-like 1 ENSMUSG00000026069
Janus kinase 3 ENSMUSG00000031805
junctophilin 1 ENSMUSG00000042686
latent transforming growth factor beta binding protein 4 ENSMUSG00000040488
lectin, galactose binding, soluble 9 ENSMUSG00000001123
leucine rich repeat and Ig domain containing 3 ENSMUSG00000051067
lymphocyte specific 1 ENSMUSG00000018819
matrilin 2 ENSMUSG00000022324
matrix Gla protein ENSMUSG00000030218
matrix metallopeptidase 8 ENSMUSG00000005800
mechanistic target of rapamycin ENSMUSG00000028991
Mid1 interacting protein 1 ENSMUSG00000008035
myeloid-associated differentiation marker-like 2 ENSMUSG00000025141
N-acetylneuraminate pyruvate lyase ENSMUSG00000042684
notum pectinacetylesterase homolog ENSMUSG00000042988
nudix -type motif 6 ENSMUSG00000050174
periostin, osteoblast specific factor ENSMUSG00000027750
peroxisome proliferator activated receptor gamma ENSMUSG00000000440
phosphate regulating gene with homologies to endopeptidases on the X chromosome ENSMUSG00000057457
phospholipid scramblase 2 ENSMUSG00000032372
platelet derived growth factor receptor, alpha polypeptide ENSMUSG00000029231
platelet-derived growth factor, C polypeptide ENSMUSG00000028019
predicted gene 867 ENSMUSG00000050157
prostaglandin I2 synthase ENSMUSG00000017969
prostaglandin-endoperoxide synthase 1 ENSMUSG00000047250
prostaglandin-endoperoxide synthase 2 ENSMUSG00000032487
protease, serine, 22 ENSMUSG00000045027
protein tyrosine phosphatase, receptor type, E ENSMUSG00000041836
protocadherin 20 ENSMUSG00000050505
PYD and CARD domain containing ENSMUSG00000030793
regulator of G-protein signaling 16 ENSMUSG00000026475
retinol binding protein 4, plasma ENSMUSG00000024990
RIKEN cDNA 1200009I06 gene ENSMUSG00000021280
RIKEN cDNA 2310008H04 gene ENSMUSG00000041974
scavenger receptor class A, member 3 ENSMUSG00000034463
secreted phosphoprotein 1 ENSMUSG00000029304
serine peptidase inhibitor, clade B, member 6b ENSMUSG00000042842
serine , member 9 ENSMUSG00000058260
serum deprivation response ENSMUSG00000045954
serum/glucocorticoid regulated kinase 2 ENSMUSG00000017868
SLIT and NTRK-like family, member 6 ENSMUSG00000045871
Smg-6 homolog, nonsense mediated mRNA decay factor ENSMUSG00000038290
solute carrier family 30 , member 4 ENSMUSG00000005802
solute carrier organic anion transporter family, member 2a1 ENSMUSG00000032548
SPARC related modular calcium binding 2 ENSMUSG00000023886
SRY-box containing gene 2 ENSMUSG00000074637
ST3 beta-galactoside alpha-2,3-sialyltransferase 1 ENSMUSG00000013846
sulfatase 1 ENSMUSG00000016918
tetratricopeptide repeat domain 9 ENSMUSG00000042734
thrombomodulin ENSMUSG00000074743
thymosin, beta 4, X chromosome ENSMUSG00000049775
thymus cell antigen 1, theta ENSMUSG00000032011
transmembrane 4 superfamily member 1 ENSMUSG00000027800
transmembrane emp24 protein transport domain containing 5 ENSMUSG00000063406
tribbles homolog 2 ENSMUSG00000020601
tripartite motif-containing 30A ENSMUSG00000030921
tripartite motif-containing 30D ENSMUSG00000057596
tumor necrosis factor, alpha-induced protein 2 ENSMUSG00000021281
U6 spliceosomal RNA ENSMUSG00000064992
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 ENSMUSG00000026994
UFM1-specific peptidase 2 ENSMUSG00000031634
unc-5 homolog B ENSMUSG00000020099
uroplakin 3B ENSMUSG00000042985
xanthine dehydrogenase ENSMUSG00000024066
Restrict to sequence length »
Only show results with a sequence length that is bases
Restrict to one or more regulating factors »
TERF2IP_MOUSE ENSMUST00000098390
Restrict to a specific TF classification class or family »
There are no class or family annotations to filter in this project.
Restrict to protein-DNA interaction quality »
Restrict to sequences where interaction is
Restrict to expression outcome »
Restrict to sequences where expression is
Restrict to one or more evidence types »
ADMC
curated
predicted
Restrict to one or more experimental methods »
15688014
COMPILED
COMPUTATIONAL PREDICTION
DNASE I FOOTPRINTING
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::DIRECT GEL SHIFT
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::DIRECT GEL SHIFT WITH WESTERN BLOT DETECTION
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::GEL SHIFT COMPETITION
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::SUPERSHIFT
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::UNKNOWN
EMSA
EXPERT CURATED::LITERATURE DERIVED
GENE CO-EXPRESSION::CO-EXPRESSED GENES DETERMINED THROUGH REPORTER GENE EXPERIMENTS
IN-VIVO HUMAN CD4 ASSAY
MUTAGENESIS::EXONUCLEASE DIGESTION
MUTAGENESIS::EXONUCLEASE III DIGESTION
MUTAGENESIS::OLIGONUCLEOTIDE SYNTHESIS
MUTAGENESIS::PCR
MUTAGENESIS::RESTRICTION ENDONUCLEASE DIGESTION
MUTAGENESIS::SITE-DIRECTED
MUTAGENESIS::UNKNOWN
N/A
NA
PROTEIN BINDING ASSAY :: CHROMATIN IMMUNOPRECIPITATION WITH TAG SEQUENCING (CHIP-TS)
PROTEIN BINDING ASSAY::CHROMATIN IMMUNOPRECIPITATION (CHIP)
PROTEIN BINDING ASSAY::CHROMATIN IMMUNOPRECIPITATION WITH TAG SEQUENCING (CHIP-TS)
PROTEIN BINDING ASSAY::DNA-PROTEIN PRECIPITATION ASSAY
PROTEIN BINDING ASSAY::DNA-PROTEIN PRECIPITATION ASSAY WITH ELISA DETECTION
PROTEIN BINDING ASSAY::DNASE FOOTPRINTING ASSAY
PROTEIN BINDING ASSAY::DNASE FOOTPRINTING COMPETITION ASSAY
PROTEIN BINDING ASSAY::IN-VIVO FOOTPRINTING ASSAY
PROTEIN BINDING ASSAY::METHYLATION INTERFERENCE
PROTEIN BINDING ASSAY::METHYLATION INTERFERENCE ASSAY
PROTEIN BINDING ASSAY::UNKNOWN
PROTEIN BINDING ASSAY::WESTERN BLOT ASSAY
PROTEIN BINDING ASSAY::YEAST 1-HYBRID ASSAY
PROTEIN EXPRESSION ASSAY::ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA)
PROTEIN EXPRESSION ASSAY::INDIRECT IMMUNOFLUORESCENCE
PROTEIN EXPRESSION ASSAY::LUCIFERASE EXPRESSION ASSAY
PROTEIN EXPRESSION ASSAY::WESTERN BLOT ASSAY
REPORTER GENE ASSAY
REPORTER GENE ASSAY:: TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY
REPORTER GENE ASSAY:: TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY WITH ELISA DETECTION
REPORTER GENE ASSAY::BETA-GLOBIN EXPRESSION ASSAY
REPORTER GENE ASSAY::CHLORAMPHENICOL ACETYLTRANSFERASE (CAT) ASSAY
REPORTER GENE ASSAY::DUAL LUCIFERASE REPORTER GENE ASSAY
REPORTER GENE ASSAY::IN-VITRO VIRUS REPLICATION ASSAY
REPORTER GENE ASSAY::IN-VIVO CHLORAMPHENICOL ACETYLTRANSFERASE (CAT) ASSAY
REPORTER GENE ASSAY::IN-VIVO GENE EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO GFP EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO LACZ EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO LUCIFERASE EXPRESSION ASSAY
REPORTER GENE ASSAY::RABBIT BETA-GLOBIN EXPRESSION ASSAY
REPORTER GENE ASSAY::SECRETED ALKALINE PHOSPHATASE (SEAP) ASSAY
REPORTER GENE ASSAY::SITE-SPECIFIC STABLE TRANSFECTION GFP ASSAY BY CRE-LOX RECOMBINATION
REPORTER GENE ASSAY::STABLE TRANSFECTION CAT ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION DSRED ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION LACZ ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION LUCIFERASE ASSAY
REPORTER GENE ASSAY::STABLY INCORPORATED GFP TRANSGENE ASSAY
REPORTER GENE ASSAY::TARGETED IN-VIVO EXPRESSION ASSAY BY IN UTERO ELECTROPORATION
REPORTER GENE ASSAY::TARGETED IN-VIVO GENE EXPRESSION ASSAY BY NON-VIRAL INJECTION
REPORTER GENE ASSAY::TARGETED IN-VIVO GFP EXPRESSION ASSAY BY VIRAL INJECTION
REPORTER GENE ASSAY::TARGETED IN-VIVO LACZ EXPRESSION ASSAY BY VIRAL INJECTION
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION GFP ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION HUMAN GROWTH HORMONE ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION LACZ ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION LUCIFERASE ASSAY
REPORTER GENE ASSAY::UNKNOWN
REPORTER GENE ASSAY::VIRAL INFECTION LUCIFERASE ASSAY
RNA EXPRESSION ASSAY::IN-VITRO TRANSCRIPTION ASSAY WITH DETECTION BY PRIMER EXTENSION
RNA EXPRESSION ASSAY::NORTHERN BLOT
RNA EXPRESSION ASSAY::PRIMER EXTENSION ANALYSIS WITH POLY(A)+ RNA
RNA EXPRESSION ASSAY::REAL TIME PCR
RNA EXPRESSION ASSAY::REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION (RT-PCR)
RNA EXPRESSION ASSAY::RNASE PROTECTION ASSAY (RPA)
RNA EXPRESSION ASSAY::WHOLE-MOUNT IN SITU HYBRIDIZATION
RNA STABILITY ASSAY::RNA SYNTHESIS BLOCKING
SELEX
SEQUENCE CONSERVATION::CO-EXPRESSED GENE CONSERVATION
SEQUENCE CONSERVATION::CONSERVATION FOUND BY ALIGNMENT
SEQUENCE CONSERVATION::ORTHOLOGOUS GENE CONSERVATION
SITE-DIRECTED MUTAGENESIS
UNKNOWN::CHROMATIN IMMUNOPRECIPITATION (CHIP)
UNKNOWN::UNKNOWN
YEAST ONE-HYBRID
View filtered data in or