Limits...
Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action.

Bresson C, Keime C, Faure C, Letrillard Y, Barbado M, Sanfilippo S, Benhra N, Gandrillon O, Gonin-Giraud S - BMC Genomics (2007)

Bottom Line: We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation.This was unexpected based upon the previously known role of v-ErbA.This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université de Lyon, Lyon, F-69003, France . bresson@cgmc.univ-lyon1.fr

ABSTRACT

Background: The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAalpha proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R). v-ErbA transforms erythroid progenitors in vitro by blocking their differentiation, supposedly by interference with T3R and RAR (Retinoic Acid Receptor). However, v-ErbA target genes involved in its transforming activity still remain to be identified.

Results: By using Serial Analysis of Gene Expression (SAGE), we identified 110 genes deregulated by v-ErbA and potentially implicated in the transformation process. Bioinformatic analysis of promoter sequence and transcriptional assays point out a potential role of c-Myb in the v-ErbA effect. Furthermore, grouping of newly identified target genes by function revealed both expected (chromatin/transcription) and unexpected (protein metabolism) functions potentially deregulated by v-ErbA. We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation. This was unexpected based upon the previously known role of v-ErbA.

Conclusion: This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

Show MeSH

Related in: MedlinePlus

Position of the c-Myb binding motif in the promoter sequences of v-ErbA target genes. The position of the c-Myb binding motif (CAGTTA) is represented as grey boxes in the promoter regions of v-ErbA repressed genes containing at least one such motif (i.e. 64% of the v-ErbA repressed genes identified by SAGE). The 4 kb sequence flanking the transcription start site (TSS, shown at position 3000) are displayed. The following parameters were used for extracting this motif: minimal motif size: 5; maximum number of examples in the negative (v-ErbA activated) set: 5; minimum number of examples in the positive (v-ErbA repressed) set: 20. Arrowheads indicate the genes that have been validated as v-ErbA repressed genes by real time PCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2194726&req=5

Figure 2: Position of the c-Myb binding motif in the promoter sequences of v-ErbA target genes. The position of the c-Myb binding motif (CAGTTA) is represented as grey boxes in the promoter regions of v-ErbA repressed genes containing at least one such motif (i.e. 64% of the v-ErbA repressed genes identified by SAGE). The 4 kb sequence flanking the transcription start site (TSS, shown at position 3000) are displayed. The following parameters were used for extracting this motif: minimal motif size: 5; maximum number of examples in the negative (v-ErbA activated) set: 5; minimum number of examples in the positive (v-ErbA repressed) set: 20. Arrowheads indicate the genes that have been validated as v-ErbA repressed genes by real time PCR.

Mentions: Since very few v-ErbA target gene promoters contain a known response element for T3R, RAR and v-ErbA, we searched for motifs that could be enriched in these promoters, without any a priori on these motifs except its minimal length. For this purpose, we used an implementation of an extended FAVST (Finite Automata-based VST construction) algorithm [27]. This allowed us to identify a c-Myb binding site (CAGTTA) [28] as a signature motif of many newly identified v-ErbA repressed target genes compared with v-ErbA activated target genes. Indeed, 64% of v-ErbA repressed genes have the c-Myb binding motif in their promoter sequences (Figure 2). Among the v-ErbA target genes that contain at least one c-Myb binding site in their promoter region, several have been validated as v-ErbA repressed target genes by real-time RT-PCR (see below). This suggests a potential role for c-Myb in the v-ErbA induced transformation.


Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action.

Bresson C, Keime C, Faure C, Letrillard Y, Barbado M, Sanfilippo S, Benhra N, Gandrillon O, Gonin-Giraud S - BMC Genomics (2007)

Position of the c-Myb binding motif in the promoter sequences of v-ErbA target genes. The position of the c-Myb binding motif (CAGTTA) is represented as grey boxes in the promoter regions of v-ErbA repressed genes containing at least one such motif (i.e. 64% of the v-ErbA repressed genes identified by SAGE). The 4 kb sequence flanking the transcription start site (TSS, shown at position 3000) are displayed. The following parameters were used for extracting this motif: minimal motif size: 5; maximum number of examples in the negative (v-ErbA activated) set: 5; minimum number of examples in the positive (v-ErbA repressed) set: 20. Arrowheads indicate the genes that have been validated as v-ErbA repressed genes by real time PCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194726&req=5

Figure 2: Position of the c-Myb binding motif in the promoter sequences of v-ErbA target genes. The position of the c-Myb binding motif (CAGTTA) is represented as grey boxes in the promoter regions of v-ErbA repressed genes containing at least one such motif (i.e. 64% of the v-ErbA repressed genes identified by SAGE). The 4 kb sequence flanking the transcription start site (TSS, shown at position 3000) are displayed. The following parameters were used for extracting this motif: minimal motif size: 5; maximum number of examples in the negative (v-ErbA activated) set: 5; minimum number of examples in the positive (v-ErbA repressed) set: 20. Arrowheads indicate the genes that have been validated as v-ErbA repressed genes by real time PCR.
Mentions: Since very few v-ErbA target gene promoters contain a known response element for T3R, RAR and v-ErbA, we searched for motifs that could be enriched in these promoters, without any a priori on these motifs except its minimal length. For this purpose, we used an implementation of an extended FAVST (Finite Automata-based VST construction) algorithm [27]. This allowed us to identify a c-Myb binding site (CAGTTA) [28] as a signature motif of many newly identified v-ErbA repressed target genes compared with v-ErbA activated target genes. Indeed, 64% of v-ErbA repressed genes have the c-Myb binding motif in their promoter sequences (Figure 2). Among the v-ErbA target genes that contain at least one c-Myb binding site in their promoter region, several have been validated as v-ErbA repressed target genes by real-time RT-PCR (see below). This suggests a potential role for c-Myb in the v-ErbA induced transformation.

Bottom Line: We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation.This was unexpected based upon the previously known role of v-ErbA.This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université de Lyon, Lyon, F-69003, France . bresson@cgmc.univ-lyon1.fr

ABSTRACT

Background: The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAalpha proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R). v-ErbA transforms erythroid progenitors in vitro by blocking their differentiation, supposedly by interference with T3R and RAR (Retinoic Acid Receptor). However, v-ErbA target genes involved in its transforming activity still remain to be identified.

Results: By using Serial Analysis of Gene Expression (SAGE), we identified 110 genes deregulated by v-ErbA and potentially implicated in the transformation process. Bioinformatic analysis of promoter sequence and transcriptional assays point out a potential role of c-Myb in the v-ErbA effect. Furthermore, grouping of newly identified target genes by function revealed both expected (chromatin/transcription) and unexpected (protein metabolism) functions potentially deregulated by v-ErbA. We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation. This was unexpected based upon the previously known role of v-ErbA.

Conclusion: This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

Show MeSH
Related in: MedlinePlus