The nucleic acid data:
IRESite Id: 35 Version: 22
Originaly submitted by: Tomáš Mašek Submission date: 2005-08-02 00:00:00
Reviewed by: Martin Pospíšek Last change: 2009-09-03 13:37:27
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  3UTR_incomplete
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  c-myc
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
34815 
The mRNA/+RNA description: 
Homo sapiens cDNA of c-myc proto-oncogene. Poly(A) tail dropped.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  unknown
The organism containing this mRNA with IRES segment in its genome:
Homo sapiens HeLa (ATCC CCL-2)
A promoter reported in cDNA corresponding to IRES sequence:
  yes
The total number of notable open-reading frames (ORFs):
  2
Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:
Summary of experiments studying integrity of the in vivo transcripts in a particular host:
Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using RNase protection:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested
Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested
Integrity (uniformity) of mRNA tested using RNAi:
not_tested
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested
Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested
The organism used:
Mus musculus
Summary of experiments studying integrity of the in vivo transcripts in a particular host:
Integrity (uniformity) of mRNA tested using Northern-blot:
not_tested
Integrity (uniformity) of mRNA tested using RNase protection:
not_tested
Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested
Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested
Integrity (uniformity) of mRNA tested using RNAi:
not_tested
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
promoter_confirmed
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested
Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested
The organism used:
Homo sapiens HeLa (ATCC CCL-2)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 3 Last change: 2008-07-08 19:13:58
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Pospíšek
The abbreviated name of this ORF/gene:
c-myc1
The description of the protein encoded in this ORF:
c-myc proto-oncogene, isoform c-myc1(CUG alternative translation initiation codon), 67 kDa.
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  yes
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  351-1955
ORF
ORF position:   2
Version: 2 Last change: 2008-05-20 20:20:17
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Pospíšek
The abbreviated name of this ORF/gene:
c-myc2
The description of the protein encoded in this ORF:
c-myc proto-oncogene, isoform c-myc2(AUG translation initiation codon), 64 kDa.
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  396-1955
Remarks:
This is the sequence encoding mRNA transcribed from major P2 promotor. P2 mRNA encodes two proteins of 67 and
64 kDa in size designated c-myc1 and c-myc2 respectively:
- c-myc1 is produced when alternative initiation of translation starting at non-canonical CUG codon occurs
- c-myc2 is translated from conventional AUG codon protein represents prevalent isoform of c-myc in mammalian
  cells

Nanbru et al., 1997 have used bi- and tri-cistronic constructs to study c-myc IRES. The two internal TATA
boxes present in c-myc UTR were masked by directed mutagenesis. Integrity of the transcripts was tested by
Northern blot. Also T7 in vitro transcripts and rabbit reticulocyte lysates were used to demonstrate IRES
activity. They conclude IRES position between -363 and -94b upstream the CUG initiation codon.


Integrity of the transcripts from pGL3Rutr transfected HeLa cells was tested by RNase protection assay. The
protected fragment contained 64b from 3'-end of Rluc, 447b of the intercistronic region and 101b from the
5'-end of Fluc. No direct RNA transfection performed or in vitro translation or promoter-less plasmid used to
test cryptic promoter presence (Stoneley et al., 1998).


Johannes et al., 1998 have shown that c-myc is associated with polysomes during poliovirus infection and that
the protein is actually being synthesized.


Stoneley et al., 2000 reported that in vaccinia virus infected human TK143 cells expressing T7 polymerase the
c-myc IRES is not functional due to the lack of "nuclear experience". Further, c-myc IRES in capped GpppG
bicistronic run-off transcripts with poly(A) of length 30 was not functional either. They have also shown in
Figure 2 that the IRES is most active in HeLa cells, with decreasing activity in MRC5, HepG2, GM637, HK293,
COS7, MCF7, Balb/c 3T3, MEL cell lines. Finally, it was concluded that c-myc IRES requires a non-canonical
translation initiation cofactor like entero- and rhinovirus IRESs and unlike cardio- and aphtovirus IRESs
(as originally reported by Borman et al. (1997), Nucleic Acids Res. 25:925-932).


Subkhankulova et al., 2001 studied effect of various stresses on c-myc and Apaf-1 IRES activity.


Creancier et al., 2001 have shown the activity of pRF based plasmids containing c-myc IRES in many cell lines
and embryonic/adult mouse tissues (c-myc IRES found inactive in adult tissues).


Kim et al., 2003 have shown that hnRNP C1 stimulates the IRES activity through its binding to internal polyU
sequence. hnRNP C1 also stimulates in a dose dependent manner translation from a downstream cistron (FFluc) in
rabbit reticulocyte lysate.


Shi et al., 2005 tested c-myc in pRF promoter-less plasmids (SV40 promoter deleted) and integrity of the
transcripts by Northern blot. T7 transcripts poorly translated in rabbit reticulocyte lysates.

Bert et al. (2006) tested c-myc IRES in HeLa cells using promoter-less plasmids with or without the enhancer
left in (Figure 2). They showed there is a cryptic promoter activatable when the enhancer is left in.
Citations:
Stoneley M., Paulin F. E., Le Quesne J. P., Chappell S. A., Willis A. E. (1998) C-Myc 5' untranslated region contains an internal ribosome entry segment. Oncogene. 16(3):423-428
Nanbru C., Lafon I., Audigier S., Gensac M. C., Vagner S., Huez G., Prats A. C. (1997) Alternative translation of the proto-oncogene c-myc by an internal ribosome entry site. J. Biol. Chem. 272(51):32061-32066
Creancier L., Mercier P., Prats A. C., Morello D. (2001) c-myc Internal ribosome entry site activity is developmentally controlled and subjected to a strong translational repression in adult transgenic mice. Mol. Cell. Biol. 21(5):1833-1840
Johannes G., Sarnow P. (1998) Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry sites. RNA. 4(12):1500-1513
Kim J. H., Paek K. Y., Choi K., Kim T. D., Hahm B., Kim K. T., Jang S. K. (2003) Heterogeneous nuclear ribonucleoprotein C modulates translation of c-myc mRNA in a cell cycle phase-dependent manner. Mol. Cell. Biol. 23(2):708-720
Kobayashi N., Saeki K., Yuo A. (2003) Granulocyte-macrophage colony-stimulating factor and interleukin-3 induce cell cycle progression through the synthesis of c-Myc protein by internal ribosome entry site-mediated translation via phosphatidylinositol 3-kinase pathway in human factor-dependen. Blood. 102(9):3186-3195
Shi Y., Sharma A., Wu H., Lichtenstein A., Gera J. (2005) Cyclin D1 and c-myc internal ribosome entry site (IRES)-dependent translation is regulated by AKT activity and enhanced by rapamycin through a p38 MAPK- and ERK-dependent pathway. J. Biol. Chem. 280(12):10964-10973
Subkhankulova T., Mitchell S. A., Willis A. E. (2001) Internal ribosome entry segment-mediated initiation of c-Myc protein synthesis following genotoxic stress. Biochem. J. 359(Pt 1):183-192
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
Chappell S. A., LeQuesne J. P., Paulin F. E., deSchoolmeester M. L., Stoneley M., Soutar R. L., Ralston S. H., Helfrich M. H., Willis A. E. (2000) A mutation in the c-myc-IRES leads to enhanced internal ribosome entry in multiple myeloma: a novel mechanism of oncogene de-regulation. Oncogene. 19(38):4437-4440
IRESs:
IRES:
Version: 10 Last change: 2009-09-03 14:55:13
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Pospíšek
The IRES name:
  c-myc
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-393
Conclusion:
  probably_not_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):



Remarks:
1-393 base range has comparable IRES activity to 1-340 region. Further deletions of 1-340 region result in
lower IRES activity. Please note that the very last 2 bases of 5'-UTR were not cloned into the pGL3Rutr alias
pRMF vector to keep the putative IRES 'in frame' with the initiator ATG codon (Evans et al. (2003), Fig. 1B
legend) while they have been replaced by 'cc' of NcoI site 'ccATGg'.


Bert et al. (2006) reported c-myc IRES is only 3x more functional than a negative control while EMCV IRES was
221x in direct RNA transfection (Figure 4).

Andreev et al. (2009) objected existence of the c-myc IRES.
Citations:
Stoneley M., Paulin F. E., Le Quesne J. P., Chappell S. A., Willis A. E. (1998) C-Myc 5' untranslated region contains an internal ribosome entry segment. Oncogene. 16(3):423-428
Evans J. R., Mitchell S. A., Spriggs K. A., Ostrowski J., Bomsztyk K., Ostarek D., Willis A. E. (2003) Members of the poly (rC) binding protein family stimulate the activity of the c-myc internal ribosome entry segment in vitro and in vivo. Oncogene. 22(39):8012-8020
Bert AG, Grépin R, Vadas MA, Goodall GJ (2006) Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 12(6):1074-1083
RNA:protein interactions:
The RNA:protein interaction:
Version: 2
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Pospíšek
The description of the protein interacting with the RNA:
p105 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
p98 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
The RNA:protein interaction:
Version: 2
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
p86 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
p61 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
p57 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
p38 bound to c-myc IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens GM03201
Remarks:
In myeloma cell line (GM2132) could be seen increased levels of 86, 61, 55, 38 kDa proteins.
Citations:
Paulin F. E., Chappell S. A., Willis A. E. (1998) A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors. Nucleic Acids Res. 26(13):3097-3103
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 1
Version: 4
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Pospíšek
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
no
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-398
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
Probing agents: DMS, kethoxal and CMCT
4.1.1. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 5
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
CMCT
Chemical reagent used with its respective buffer:
Version: 0
pH
8.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
150.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
100.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0.50
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 6
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
100.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0.50
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 7
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
kethoxal
Chemical reagent used with its respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
100.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0.50
cacodylate [mM]
0
Citations:
Le Quesne J. P., Stoneley M., Fraser G. A., Willis A. E. (2001) Derivation of a structural model for the c-myc IRES. J. Mol. Biol. 310(1):111-126
Last change to the database: 2015-04-16 16:45:23 GMT+1