1,721,345 research outputs found
A survey of 178 NF-Y binding CCAAT boxes
Full text linkThe CCAAT box is one of the most common elements in eukaryotic promoters, found in the forward or reverse orientation. Among the various DNA binding proteins that interact with this sequence, only NF-Y (CBF, HAP2/3/4/5) has been shown to absolutely require all 5 nt. Analysis of a database with 178 bona fide NF-Y binding sites in 96 unrelated promoters confirms this need and points to specific additional flanking nucleotides (C, Pu, Pu on the 5'-side and C/G, A/G, G,A/C, G on the 3'-side) required for efficient binding. The frequency of CCAAT boxes appears to be relatively higher in TATA-less promoters, particularly in the reverse ATTGG orientation. In TATA-containing promoters the CCAAT box is preferentially located in the -80/-100 region (mean position -89) and is not found nearer to the Start site than -50. In TATA-less promoters it is usually closer to the +1 signal (at -66 on average) and is sometimes present in proximity to the Cap site. The consensus and location of NF-Y binding sites parallel almost perfectly a previous general statistical study on CCAAT boxes in 502 unrelated promoters. This is an indication that NF-Y is the major, if not the sole, CCAAT box recognizing protein and that it might serve different roles in TATA-containing and TATA-less promoters
The molecular biology of the CCAAT-binding factor NF-Y
No full textProtein coding genes are transcribed by Polymerase II, under the control of short discrete DNA elements in promoters and enhancers, recognized with high efficiency and specificity by trans-acting factors and by general transcription proteins (Tjian and Maniatis, 1994). The former regulate specific genes or set of genes, usually in a tissue-, developmental-, cell-cycle or stimuli-dependent way; the latter are involved in the activation of all promoters, as a whole multi-subunit holoenzyme (Parvis and Young, 1998). A limited set of elements, such as the GC and CCAAT-boxes, are present in a very high number of promoters. The whole process is further complicated by the need to operate in the context of higher order chromatin structures (Workman and Kingston, 1998). This review focuses on the CCAAT sequence and on the NF-Y protein, also known as CBF, which binds to it
What ENCODE is teaching us on the genomic sites of transcription factors
No full textThe binding to DNA of sequence-specific Transcription Factors -TFs- controls the deposition of histone marks and transcriptional activation. To do so, TFs tend to cooperate and synergize at multiple levels, including DNA-binding. Large scale projects, such as ENCODE, are investigating TFs genomic targets systematically. One of the emerging themes is that many TFs do not bind, or marginally bind in vivo to canonical sites previously well characterized by biochemical means in vitro. In addition, even for TFs with a canonical in vivo logo, a large cohort of their sites (20/40%) are devoid of it. ENCODE data indicate that NF-Y binding ovelaps significantly, often with precise stereoalignment, with numerous TFs involved in growth control, such as E2F, AP1 and E-box binding TFs. Some TFs lacking their canonical sites in their peaks in vivo show an abundance of NF-Y sites, with a visible theme of multiple CCAAT with precise spacing. This is quite relevant since (i) we and others have reported that p53 and p63 control certain growth promoting genes in the absence of canonical sequences and via tethering by NF-Y bound to multiple CCAAT boxes. (ii) Mutations in p63 and p53 alter the expression of such CCAAT-dependent promoters. We propose that full understanding of the strategy of TFs, including p53 family members and mutants of clinical relevance, will require the comprehension of binding to both their canonical and “unorthodox” locations in which other TFs are recruiting them onto DNA
Targeting the Y/CCAAT box in cancer : YB-1 (YBX1) or NF-Y?
No full textThe Y box is an important sequence motif found in promoters and enhancers containing a CCAAT box-one of the few elements enriched in promoters of large sets of genes overexpressed in cancer. The search for the transcription factor(s) acting on it led to the biochemical purification of the nuclear factor Y (NF-Y) heterotrimer, and to the cloning-through the screening of expression libraries-of Y box-binding protein 1 (YB-1), an oncogene, overexpressed in aggressive tumors and associated with drug resistance. These two factors have been associated with Y/CCAAT-dependent activation of numerous growth-related genes, notably multidrug resistance protein 1. We review two decades of data indicating that NF-Y ultimately acts on Y/CCAAT in cancer cells, a notion recently confirmed by genome-wide data. Other features of YB-1, such as post-transcriptional control of mRNA biology, render it important in cancer biology
Single nucleosome analysis of human cell-cycle CCAAT promoters in vivo : a positive role for KDM1
No full textThe CCAAT box is a frequent promoter element, as illustrated by bioinformatic analysis of large sets of promoters, and it is bound by NF-Y which is involved in positive, as well as negative regulation. NF-Y is responsible of the transcriptional regulation of cell-cycle genes: it is an ubiquitous histone-like trimer composed of three subunits, NF-YA, NF-YB, and NF-YC, all necessary for DNA binding. NF-YB and NF-YC contain histone fold motifs (HFM), found in all core histones, whose dimerization is a prerequisite for NF-YA association, that confers to the trimer sequence-specific DNA binding capacity.
NF-Y binding is a prerequisite for promoter activation and allows further activators/co-activators buildup.
Here, we used a MNase I-based ChIP protocol on homogeneous cell populations to study histone modifications on cell-cycle promoters at a single nucleosome level in vivo.
Core regions of active promoters have H3-H4 and are depleted of H2A-H2B, substituted by NF-Y. A complex profile of H3K4 methylations is observed: H3K4me3 increases in active conditions, but significant levels are present on inactive promoters; H3K4me2 is relatively constant. Surprisingly, H3K4me1 best correlates with transcription. Analysis of histone demethylases suggests a positive role of KDM1(LSD1) and KDM5A in transcription, whereas KDM5B is present in repressed states. The use of the KDM1 inhibitor Tranylcipromine confirms that KDM1 is indeed involved in activation of G2/M promoters.
NF-Y removal by adenovirus infection has dramatic negative effects on H3K4me3, H3K79me2, H3K36me3, H4K79me3 and leads to the appearance of H4K20me3 and recruitment of KDMs. NF-Y recruits the KDM1 partner CoREST through direct interaction. These data are the first indication that KDM1 partakes in activation of cell-cycle genes and place NF-Y at the heart of regulation of key H3K4 methylations
NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations
No full textThe CCAAT box is a frequent promoter element, as
illustrated by bioinformatic analysis, and it is bound
by NF-Y, a trimer with H2A-H2B-like subunits.
We developed a MNase I-based ChIP protocol on
homogeneous cell populations to study cell-cycle
promoters at the single nucleosome level. We analyzed
histone methylations and the association of
enzymatic activities. Two novel results emerged:
(i) H3-H4 are present on core promoters under
active conditions, with the expected cohort of ‘positive’
modifications; H2A-H2B are removed and substituted
by NF-Y. Through the use of a dominant
negative mutant we show that NF-Y is important
for H3K36me3 deposition and for elongation, not
recruitment of Pol II; (ii) H3K4 methylations are
highly dynamic and H3K4me1 is a crucial positive
mark. Functional siRNA inactivation and treatment
with Tranylcypromine determined that KDM1 (LSD1)
plays a positive role in transcription, specifically of
G2/M genes. It requires CoREST, which is recruited
on active promoters through direct interactions with
NF-Y. These data are the first in vivo indication
of a crucial interplay between core histones and
‘deviant’ histone-fold such as NF-Y, leading to
fine-tuning of histone methylations
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