Review Article Nuclear transcription factor Y and its roles in cellular processes related to human disease
Abstract: Nuclear transcription factor Y (NF-Y) is an example of a transcriptional regulation factor in eukaryotes consisting of three different subunits, NF-YA, NF-YB and NF-YC, which are all necessary for formation of NF-Y complexes and binding to CCAAT boxes in promoters of its target genes. Highly conserved between human and Drosophila, NF-Y regulates transcription of various genes related to the cell cycle and various human diseases. Drosophila models have been widely used as tools for studying genetics and developmental biology and more recently for analyzing the functions of human disease genes, including those responsible for developmental and neurological disorders, cancer, cardiovascular disease and metabolic and storage diseases, as well as genes required for function of the visual, auditory and immune systems. In this review, in vivo findings from Drosophila models relevant to the roles of NF-Y in various human diseases are summarized. Recent studies have demonstrated novel contributions of dNF-Y to apoptosis and apoptosis-induced proliferation, and in photoreceptor cell differentiation during the development of the Drosophila compound eye. Keywords: Transcription factors, NF-Y, NF-YB, apoptosis, Drosophila model
Introduction
Transcription factors are well characterized as proteins that bind to specific short DNA sequences in control regions of genes and thereby regulate their transcription, either positively or negatively [1]. They contain one or more DNA-binding domains that attach to specific sequences of DNA, while other regions are responsible for stimulatory or inhibitory effects on transcription [2]. Transcription factors play vital roles in many important cellular processes and consequently changes in these factors can lead to human diseases which can be categorized into three major groups: developmental disorders, disorders of hormone responses and cancer [3]. Nuclear transcription factor Y (NF-Y) is one of the transcriptional regulation factors that bind to the CAAT box in promoters of various genes in eukaryotes [4]. Currently NF-Y is emerging as a regulatory factor for many genes overexpressed in several different kinds of cancer [5]. In this review, we summarize information on NF-Y target genes, focusing on
the Drosophila homologue to provide clues to understanding human diseases. CCAAT box The CCAAT box is one of the most common cisacting elements found in the promoter and enhancer regions of a large number of genes in eukaryotes [4]. As detailed in a very recent review, it is believed to be enriched in promoters of large sets of genes overexpressed in several different kinds of cancers such as in the breast, colon, thyroid and prostate, as well as in leukemia [5]. Many DNA binding proteins interact with this sequence but only NF-Y has been shown to absolutely require all five nucleotides [6]. It is also reported that the frequency of CCAAT boxes appears to be relatively high in TATA-less promoters, particularly in the reverse ATTGG orientation [6]. In TATA-containing promoters, the CCAAT box is preferentially located in the -80/-100 region (mean position -89) with respect to the transcription initiation site (+1) and is not found nearer to the transcription initiation site than -50. In TATA-less promoters, it
Roles of NF-Y in cellular processes
340 Am J Cancer Res 2013;3(4):339-346
is usually located closer to the transcription initiation site (at -66 on average) and is sometimes present in close proximity [6]. Analysis of CCAAT boxes in 502 unrelated promoters indicated 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 [6]. Subunit structure of NF-Y NF-Y consists of three different subunits, NF-YA, NF-YB and NF-YC, which are all necessary for formation of NF-Y complexes and binding to CCAAT boxes [7]. These subunits are encoded by independent genes. NF-YA contains a DNA binding domain, while both NF-YB and NF-YC contain histone-fold motifs (HFMs). First, NF-YB and NF-YC interact to form heterodimers through their HFMs [7] (Figure 1). The NF-YB/ NF-YC heterodimer then interacts with NF-YA to form the heterotrimeric NF-Y transcription factor (Figure 1). The absence of any of the NF-Y subunits results in loss of binding of the NF-Y complex to DNA [8] and NF-Y-directed transcription [7]. However, there is evidence that Mes4 instead of NF-YC can also form complexes with NF-YA and NF-YB to regulate NF-Y target genes in Drosophila mesoderm [9]. NF-Y and its target genes NF-Y (also called CBF, a-CP1 and CP1) was first recognized as a protein binding to the major histocompatibility complex (MHC) class II conserved Y box [10]. Subsequently, many studies identified target genes of NF-Y and roles in various biological pathways [7, 11]. Reviewing publications over nearly three decades, we can divide the target genes of NF-Y into two major groups: cell cycle-related genes and human disease-related genes, including examples important for hematopoietic disorders and cancer.
NF-Y and cell cycle related genes
In the first group, NF-Y controls the expression of several key regulators of the cell cycle such as topoisomerase II alpha (topo IIα), cdc2, cyclins and cdc25C genes [12-14]. For example, topo IIα activated during the late S and G2/M phases of the cell cycle carries several NF-Y binding sites in its promoter. The mouse topo IIα is reported to require NF-Y to bind to and activate its promoter by disrupting the surrounding nucleosomal structure during the cell cycle [12].
Cyclin-dependent kinases (CDKs) also play an important role in the eukaryotic cell cycle progression. The Cdc2 (CDK1) gene is expressed during the late G1/S phase and is required for the G2 to M phase transition in higher eukaryotes. The adenovirus E1A protein mediates optimal transactivation of the human cdc2 gene promoter by inducing the expression and assembly of a heteromeric complex consisting of the 110-kDa protein and NF-Y which then interacts with the two CCAAT motifs of the cdc2 promoter [13]. It is also reported that NF-Y mediates transcriptional inhibition of mitotic cyclins and the cdc25C genes during p53-dependent G2 arrest induced by DNA damage. These observations suggest a transcriptional regulatory role of NF-Y in the G2 checkpoint after DNA damage [14]. Moreover, NF-Y is reported to be required for widespread activation of G2/M and anti-apoptotic genes [15]. Knockdown of NF-YB impairs G2/M progression, induces apoptosis and is sufficient to functionally activate p53, in the absence of DNA damage [15]. Impairment of Bax/Bcl-2 and Bax/Bcl-X(L) ratios contributes to failure to maintain a physiologic level of CCAAT-dependent transcription of anti-apoptotic genes. Fine balancing the NF-Y-p53 duo appears to be
Figure 1. NF-Y complex formation. NF-Y consists of three different subunits, NF-YA, NF-YB and NF-YC, which are all necessary for formation of NF-Y complexes and binding to CCAAT boxes to activate transcription. The arrow with bar indicates transcription initiation site.
Roles of NF-Y in cellular processes
341 Am J Cancer Res 2013;3(4):339-346
important for cell survival by maintaining transcription of anti-apoptotic genes and preventing p53 activation that triggers the apoptotic cascade [15]. NF-Y and human disease related genes
NF-Y can regulate transcription of several genes that are related to human diseases such as gamma-globin, Hoxb4, MHC class II, transforming growth factor beta type II receptor and the SRY-related HMG-box (Sox) family [16-22]. Laminin-1 that is related to muscular dystrophy is a major component of embryonic basement membranes and consists of α1, β1, and γ1 chains. Expression of the laminin-1 gene is induced in mouse F9 embryonic carcinoma cells upon differentiation into parietal endoderm cells. A study in Japan in 2004 showed that a combination of the actions of the ubiquitous factors, Sp1/Sp3 and NF-Y, and the parietal endoderm-specific factors, SOX7 and SOX17 controls the transcription of the mouse laminin α1 gene during the differentiation of F9 cells [23]. In the following sections NF-Y target genes related to hematopoietic disorders and cancer are described. Hematopoietic disorder diseases and the role of NF-Y
NF-Y recruits both transcription activator and repressor to modulate tissue- and developmental stage-specific expression of human gamma (γ)-globin gene [16]. The γ-globin genes (HBG1 and HBG2) are normally expressed in the fetal liver, spleen and bone marrow. Two gamma chains together with two alpha chains constitute fetal hemoglobin, which is normally replaced by adult hemoglobin at birth. In some β-thalassemias and related conditions, however, γ chain production continues to adulthood. The two types of γ chains differ at residue 136 where glycine is found in the G-γ product (HBG2) but alanine in the A-γ product (HBG1). The former is predominant at birth. The human embryonic, fetal and adult β-like globin genes provide a paradigm for tissue- and developmental stage-specific gene regulation. The fetal γ-globin gene is expressed in fetal erythroid cells but is repressed in their adult counterparts. NF-Y recruits to neighboring DNA motifs the developmentally regulated, erythroid transcription activator GATA-2 and general
repressor BCL11A, which in turn recruit erythroid repressor GATA-1 and general repressor COUP-TFII to form respectively the NF-Y/GATA-2 and the BCL11A/COUP-TFII/GATA-1 transcription repressor hubs. Both the activator and the repressor hubs are present in both the active and the repressed γ-globin promoter complexes in fetal and adult erythroid cells. Through changes in their levels and respective interactions with the co-activators and co-repressors during erythroid development, the activator and the repressor hubs modulate erythroi