The CCAAT box is an important promoter element regulated by NF-Y, a conserved trimer with histone-like features. We describe a new Position Specific Frequency Matrix (PSFM): we derived from 328 NF-Y promoters from the literature the p-CCAAT, and refined it by analysing ChIP on chip data (g-CCAAT). Interestingly, g-CCAAT has distinct features, such as variations within the CCAAT pentanucleotide. We validated the NF-Y-dependency of several promoters with functional assays. We examined the presence of these PSFMs in all human promoters and detail a number of parameters of CCAAT boxes: position, orientation, distance from TSS, presence of TATA, CpG islands and enrichments of nearby TF elements. The CCAAT genes fall into different GO categories, with cell cycle and chromatin/transcription specifically enriched. Additional findings surfaced: (1) the CCAAT-TATA combination, often mentioned in textbooks, is an exception, rather than the rule. CCAAT promoters are less precise in terms of TSS; (2) There is a good correlation between CCAAT and CpG islands; (3) selective TFs sites are enriched in CCAAT promoters, with precise stereoalignements of some of them. In conclusion, the new features of the CCAAT box and the link with the neighbouring elements will help in the functional classification of promoters.
A perspective of promoter architecture from the CCAAT box / D. Dolfini, F. Zambelli, G. Pavesi, R. Mantovani. - In: CELL CYCLE. - ISSN 1538-4101. - 8:24(2009), pp. 4127-4137.
A perspective of promoter architecture from the CCAAT box
D. DolfiniPrimo
;F. Zambelli;G. PavesiPenultimo
;R. MantovaniUltimo
2009
Abstract
The CCAAT box is an important promoter element regulated by NF-Y, a conserved trimer with histone-like features. We describe a new Position Specific Frequency Matrix (PSFM): we derived from 328 NF-Y promoters from the literature the p-CCAAT, and refined it by analysing ChIP on chip data (g-CCAAT). Interestingly, g-CCAAT has distinct features, such as variations within the CCAAT pentanucleotide. We validated the NF-Y-dependency of several promoters with functional assays. We examined the presence of these PSFMs in all human promoters and detail a number of parameters of CCAAT boxes: position, orientation, distance from TSS, presence of TATA, CpG islands and enrichments of nearby TF elements. The CCAAT genes fall into different GO categories, with cell cycle and chromatin/transcription specifically enriched. Additional findings surfaced: (1) the CCAAT-TATA combination, often mentioned in textbooks, is an exception, rather than the rule. CCAAT promoters are less precise in terms of TSS; (2) There is a good correlation between CCAAT and CpG islands; (3) selective TFs sites are enriched in CCAAT promoters, with precise stereoalignements of some of them. In conclusion, the new features of the CCAAT box and the link with the neighbouring elements will help in the functional classification of promoters.File | Dimensione | Formato | |
---|---|---|---|
A perspective of promoter architecture from the CCAAT box.pdf
accesso riservato
Tipologia:
Publisher's version/PDF
Dimensione
1.91 MB
Formato
Adobe PDF
|
1.91 MB | Adobe PDF | Visualizza/Apri Richiedi una copia |
Pubblicazioni consigliate
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.