PMID: 19946211Dec 1, 2009Paper

A perspective of promoter architecture from the CCAAT box

Cell Cycle
Diletta DolfiniR Mantovani

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 neighbour...Continue Reading

Citations

Mar 2, 2013·Cell Death and Differentiation·D Dolfini, R Mantovani
Dec 20, 2011·Nature Genetics·Vijay K TiwariChristian Beisel
Mar 2, 2012·Molecular Biology of the Cell·Frauke GoemanGiulia Piaggio
Mar 19, 2011·Nucleic Acids Research·Paolo BenattiCarol Imbriano
Mar 30, 2011·PloS One·Andrea FossatiRoberto Mantovani
Aug 23, 2012·PloS One·Valentina CalvenzaniChiara Tonelli
Jun 23, 2012·Journal of Molecular Endocrinology·Gioia Altobelli
Nov 20, 2014·Nature Communications·Pavan Kumar PuvvulaOliver Bischof
Nov 5, 2011·Critical Reviews in Biochemistry and Molecular Biology·Diletta DolfiniRoberto Mantovani
Jan 7, 2016·Biochimica Et Biophysica Acta·Paolo BenattiCarol Imbriano
Dec 6, 2011·Biochimica Et Biophysica Acta·Carol ImbrianoRoberto Mantovani
Jun 15, 2011·Experimental Cell Research·Yasunao KamikawaYoshihiro Yoneda
Jul 22, 2015·Biochimica Et Biophysica Acta·Elena GrossiMaite Huarte
Jul 6, 2015·Progress in Neurobiology·Marta Pulido-SalgadoJosep Saura
Aug 13, 2013·Developmental Biology·Angenee C MiltonPeter G Okkema
Aug 21, 2012·Structure·Eva M HuberAxel A Brakhage
Oct 9, 2018·Biotechnology Progress·Devon ZimmermanJacob Elmer
Sep 6, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Alisha RamosYoon Pin Lim

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