Chromatin immunoprecipitation (ChIP) on chip experiments uncover a widespread distribution of NF-Y binding CCAAT sites outside of core promoters

被引:75
作者
Testa, A
Donati, G
Yan, P
Romani, F
Huang, THM
Viganò, MA
Mantovani, R
机构
[1] Univ Modena & Reggio Emilia, Dipartimento Biol Anim, I-41100 Modena, Italy
[2] Univ Milan, Dipartimento Sci Biomol & Biotecnol, I-20143 Milan, Italy
[3] Ohio State Univ, Ctr Comprehens Canc, Dept Mol Virol Immunol & Med Genet, Div Human Canc Genet, Columbus, OH 43210 USA
关键词
D O I
10.1074/jbc.M414039200
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The CCAAT box is a prototypical promoter element, almost invariably found between -60 and -100 upstream of the major transcription start site. It is bound and activated by the histone fold trimer NF-Y. We performed chromatin immunoprecipitation (ChIP) on chip experiments on two different CpG islands arrays using chromatin from hepatic HepG2 and pre-B cell leukemia NALM-6 cell lines, with different protocols of probe preparation and labeling. We analyzed and classified 239 known or predicted targets; we validated several by conventional ChIPs with anti-YB and anti-YC antibodies, in vitro EMSAs, and ChIP scanning. The importance of NF-Y binding for gene expression was verified by the use of a dominant negative NF-YA mutant. All but four genes are new NF-Y targets, falling into different functional categories. This analysis reinforces the notion that NF-Y is an important regulator of cell growth, and novel unexpected findings emerged from this unbiased approach. (i) A remarkable proportion of NF-Y targets, 40%, are complex transcriptional units composed of divergent, convergent, and tandem promoters. (ii) 40-50% of NF-Y sites are not in core promoters but are in introns or at distant 3' or 5' locations. The abundance of "unorthodox" CCAAT positions highlights an unexpected complexity of the NF-Y-mediated transcriptional network.
引用
收藏
页码:13606 / 13615
页数:10
相关论文
共 59 条
[1]   Bidirectional gene organization: A common architectural feature of the human genome [J].
Adachi, N ;
Lieber, MR .
CELL, 2002, 109 (07) :807-809
[2]   Functional characterization of ERp18, a new endoplasmic reticulum-located thioredoxin superfamily member [J].
Alanen, HI ;
Williamson, RA ;
Howard, MJ ;
Lappi, AK ;
Jäntti, HP ;
Rautio, SM ;
Kellokumpu, S ;
Ruddock, LW .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (31) :28912-28920
[3]   A CONSERVED REGION IN INTRON-1 NEGATIVELY REGULATES THE EXPRESSION OF THE PCNA GENE [J].
ALDER, H ;
YOSHINOUCHI, M ;
PRYSTOWSKY, MB ;
APPASAMY, P ;
BASERGA, R .
NUCLEIC ACIDS RESEARCH, 1992, 20 (07) :1769-1775
[4]   Structure, function and evolution of CpG island promoters [J].
Antequera, F .
CELLULAR AND MOLECULAR LIFE SCIENCES, 2003, 60 (08) :1647-1658
[5]   Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer [J].
Ballestar, E ;
Paz, MF ;
Valle, L ;
Wei, S ;
Fraga, MF ;
Espada, J ;
Cigudosa, JC ;
Huang, THM ;
Esteller, M .
EMBO JOURNAL, 2003, 22 (23) :6335-6345
[6]   Nutrient regulation of gene expression by the sterol regulatory element binding proteins:: Increased recruitment of gene-specific coregulatory factors and selective hyperacetylation of histone H3 in vivo [J].
Bennett, MK ;
Osborne, TF .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (12) :6340-6344
[7]  
Bhattacharya A, 2003, CANCER RES, V63, P8167
[8]   DNA binding specificity of the CCAAT-binding factor CBF/NF-Y [J].
Bi, WM ;
Wu, L ;
Coustry, F ;
deCrombrugghe, B ;
Maity, SN .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1997, 272 (42) :26562-26572
[9]   Reconstitution of TIMP-2 expression in SH-SY5Y neuroblastoma cells by 5-azacytidine is mediated transcriptionally by NF-Y through an inverted CCAAT site [J].
Cappabianca, L ;
Farina, AR ;
Tacconelli, A ;
Mantovani, R ;
Gulino, A ;
Mackay, AR .
EXPERIMENTAL CELL RESEARCH, 2003, 286 (02) :209-218
[10]  
Caretti G, 1999, MOL CELL BIOL, V19, P8591