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(The FASEB Journal. 1998;12:515-522.)
© 1998 FASEB

REVIEW

Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes

S. K. Swamynathana, Ashok Nambiara, and Ramareddy V. Guntakaa,1

a Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, School of Medicine, Columbia, Missouri 65212, USA


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 
Single-stranded regions, known to be important for optimal rates of transcription, have been observed in the promoters of several cellular genes as well as in the promoters of many pathogenic viruses. Several host-encoded, single-stranded DNA binding proteins capable of binding these regions have been purified and their genes isolated. In this review, information available about single-stranded regions present within various promoters and the interaction of a novel class of single-stranded DNA binding transcription factors belonging to the Y-box family of proteins is reviewed. Mechanisms by which these proteins influence transcription of both cellular and viral genes are proposed.—Swamynathan, S. K., Nambiar, A., Guntaka, R. V. Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes. FASEB J. 12, 515–522 (1998)


Key Words: regulation of transcription • gene expression • S1-sensitive sites • supercoiled DNA • eukaryotic promoters


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 
IT IS WELL ESTABLISHED that cis-acting sequences within the promoter of a given gene govern the rate of transcription. These sequences are bound in a nucleotide sequence-specific manner by cellular transcription factors, which help 1) promote formation of the transcription initiation complex or 2) stabilize the preformed transcription initiation complex. Most of these transcription factors recognize specific DNA sequences in their double-stranded form. However, recent work from several laboratories, including our own, has shown that many promoters have within them single-stranded regions that are essential for optimal transcription from such promoters. Here, we review the information available about single-stranded regions present within various promoters and the novel class of single-stranded, DNA binding transcription factors that interact with them. This leads us to the interesting proposition that transcription from several promoters is regulated not only by the primary sequence present in the promoter, but also by the type of structure these nucleotides form. We have restricted our review to cover only eukaryotic promoters, but enough evidence exists to demonstrate that similar mechanisms also operate in prokaryotes.


   PRESENCE OF SINGLE-STRANDED REGIONS WITHIN ACTIVE PROMOTERS
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 
The presence of single-stranded regions in several transcriptionally active promoters has been known for a long time (see Table 1) (1–3). Most of these studies have used the ability of S1 nuclease to specifically cleave DNA in its single-stranded, but not the double-stranded, form (reviewed in ref 4). Recent studies have shown that such regions are far more common than was previously thought (5–11). Transcriptional activity of many promoters has been shown to be dependent on the presence of S1 sensitive sites: mutant promoters wherein the S1 sensitive sites were deleted showed reduced transcriptional activity (8, 12, 13). The importance of these single-stranded regions has also been well demonstrated in experiments that show increased transcription from minimal heterologous promoters as a direct result of introduction of these S1-sensitive polypyrimidine/purine stretches (9, 13–16).


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  		Table 1. Presence of single-stranded regions within the promoters of actively transcribed genesa

An analysis of the distance of these single-stranded regions from the transcription start site shows a great deal of variability: they can exert their influence from a distance as close as 80 to 100 nucleotides in genes such as c-Ki-ras (12) and PDGF A chain (8) to as far as -1000 to -1300 bp in the human decorin gene (3) and mouse metallothionein gene (17) ( Table 1). It therefore appears that, within certain limits, the distance at which such regions are present within a given promoter is not critical. This is not surprising considering that various protein factors that bind to DNA are known to bend DNA, thus bringing the distant sequences into a close physical proximity to the core promoter elements (18–24). Such a bend or loop in the intervening DNA enables an interaction between protein factors that recognize distant sites on the promoters.

These single-stranded regions have all been studied in transcriptionally active promoters. Whether the single-stranded DNA binding factors also continue to bind to the transcriptionally inactive promoters and, if so, what changes take place during their transition into a transcriptionally active state, need to be studied. In addition, mechanisms involved in generating isolated single-stranded sites at specific points within a predominantly double-stranded genome need to be examined in detail. Nor do we know what happens to such sites when the DNA goes through replication, condensation, and decondensation during different stages of the cell cycle. Such studies will provide valuable insights about the mechanism of transcriptional regulation by S1-sensitive, single-stranded regions in the promoters.


   Y-BOX PROTEINS
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 
Efforts to unravel the mechanism by which these single-stranded regions activate transcription have concentrated on identifying the protein factor (or factors) capable of interacting with such single-stranded regions. Several such proteins have been identified, and some have been shown to be capable of activating transcription under specific conditions from a given promoter (6, 12, 25–34). Several single-stranded binding proteins have been found to be members of the Y-box family of proteins. Several Y-box protein genes have been cloned from different species by using different strategies: (human YB-1, (35–38); mouse YB-1, (39, 40); rat YB-1, (41); chicken YB-1, (42, 43); Xenopus YB-1, (44). Y-box proteins are characteristic in that they are able to bind the Y-box (defined as reverse CCAAT box, or ATTGG) through a highly conserved stretch of 70 amino acids, called the cold shock domain (CSD).2 The CSD derives its name from the fact that certain bacterial proteins expressed under cold shock conditions possess this domain (45; reviewed in ref 28).

The cDNAs encoding three different members of the Y-box family of proteins that interact with the Rous sarcoma virus long-terminal repeats (RSV LTR) have been cloned in our laboratory from a chicken embryo fibroblast cDNA library: chk-YB-1b, (42); chk-YB-2, (26); chk-YB-1HP, (46). Chk-YB-1b is the chicken homologue of human YB-1. It binds the single-stranded DNA sequence 5'GTACCACC3' present on the negative strand of the RSV LTR with great affinity. Chk-YB-2 is conserved with chk-YB-1b in the CSD, but is different at both the amino and carboxyl termini. Like chk-YB-1b, chk-YB2 also binds to the same single-stranded DNA sequence on the RSV LTR with high affinity and sequence specificity (26). Chk-YB-1HP was isolated by screening the chicken embryo fibroblast cDNA library with chk-YB-1b cDNA as the probe. Although chk-YB1-HP lacks a recognizable CSD, there is excellent homology between chkYB1b and chkYB1-HP outside the CSD (46).

As with several other eukaryotic transcription factors, Y-box proteins possess a modular structure with an array of domains serving the often separable functions of DNA binding, trans-activation, and multimerization. The well-conserved CSD is the primary DNA binding domain of Y-box proteins and contains within it the RNA binding RNP-1 motif (47, 48). Apart from the conserved CSD, there is little similarity in the primary sequence of these proteins. The amino terminus in these proteins is variable and is thought to confer tissue specificity and functional specificity to different members of the family. In spite of the diversity in primary amino acid sequence in the carboxyl terminal, Y-box proteins still retain the distinct organization of alternating clusters of acidic and basic residues, termed charge zipper. This charge zipper is believed to mediate multimerization by protein–protein interaction.

Y-box proteins have emerged as key players in cellular metabolism. These proteins are capable of binding one or more types of nucleic acids: single- or double-stranded DNA or RNA (26, 37, 39, 42, 47, 49–52). Diverse biological roles proposed for the Y-box proteins include positive or negative modulation of transcription of a wide array of genes (6, 7, 25, 27, 28, 35, 53–59), modification of chromatin (60), translational masking of mRNA (47, 61–68), participation in eukaryotic redox signaling pathway (69), RNA chaperoning (70), and stress response regulation (44, 53, 60, 71) ( Fig. 1). Y-box proteins are also known to be involved in activating genes such as thymidine kinase (39, 72), PCNA/cyclin (73), DNA polymerase {alpha} (74), and the epidermal growth factor receptor (36); see Table 2. Chk-YB-1, the chicken homologue of YB-1, has been shown to be expressed only in actively dividing cells and not in resting cells (42, 43). These observations have led to the speculation that Y-box proteins are involved in regulating cell proliferation (reviewed in ref 75).



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  		Figure 1. Schematic summarizes the involvement of Y-box proteins in various cellular processes.


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  		Table 2. Involvement of YB-1 in transcription regulationa

In addition to these functions, recent work has shown that Y-box proteins are involved in conferring drug resistance (76–79). The presence of intact Y-box elements within the promoter sequences of the human mdr1 gene, which encodes the p170 glycoprotein involved in acquisition of multiple drug resistance by breast cancer cells, is vital for its basal expression (77, 80). The recent demonstration of the involvement of YB-1 in activating transcription of the mdr1 gene above basal levels in the breast cancer cells under chemotherapy (76) has stimulated much interest in studying the mechanism of action of these single-stranded specific transcription factors due to the potential application in gene therapy to control multiple drug resistance by cancer cells during chemotherapy.

Many pathogenic viruses have developed an ability to use host-derived Y-box proteins to trans-activate transcription from viral promoters in infected cells. HTLV-1 and HIV-1 are both known to be up-regulated by human YB-1 (56, 81). Similarly, human polyomavirus JC is known to be under the control of human YB-1 (57). Work in our laboratory has demonstrated that RSV is dependent on the Y-box transcription factor chk-YB-2 for its efficient transcription in avian fibroblasts (27). Curiously, the same protein has been shown to repress transcription from the same promoter in mammalian cells (26).

MHC-I and MHC-II gene products play a crucial role in antigen processing and presentation upon infection by infectious agents (reviewed in ref 82). In the course of their successful infection, many viruses are known to repress the expression of MHC genes, thus evading immune surveillance. For instance, transcription of MHC-I is repressed by tat during HIV infection (83), by E1a during adenoviral infection (84–87), by an immediate early protein ICP47 during herpes simplex virus infection (88), and by an as yet unknown mechanism during RSV infection (89, 90). Y-box proteins are known to bind MHC promoters and overexpression of YB-1 is known to repress MHC transcription (35, 58, 91). We have shown that both chk-YB-2 and chk-YB-1b can bind the avian MHC-II Y-box positive strand in a single-stranded, sequence-specific manner (A. Nambiar, S. K. Swamynathan, and R. V. Guntaka, unpublished results).

Considering that YB-1 is known to be involved in 1) repressing the transcription of MHC-II genes and 2) activating the genes required for cell proliferation, it appears to be a clever choice by pathogenic viruses during evolution to have used this and related proteins to activate their own transcription, since they can immortalize infected cells and cause cells to escape immune surveillance. Whether or not the presence of these diverse, superficially unrelated abilities in Y-box proteins is fortuitous needs to be evaluated. Such an evaluation will shed an interesting light on the interaction of complex forces at play in the coevolution of host–pathogen systems that abound in nature.


   MECHANISM OF ACTION OF Y-BOX PROTEINS
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 
The mechanism by which Y-box proteins activate transcription is poorly understood. Human YB-1 is thought to activate the transcription of human polyomavirus JC by the novel mechanism of recruiting another trans-activator (p65 or RelA) to the viral promoter (57). The p65 subunit of NF-{kappa}B can activate transcription of polyomavirus JC via two distinct sites on the viral promoter. Whereas one of these sites is bound with high affinity by p65, the other is not. Hence, it was puzzling as to how, in the absence of DNA binding, p65 could activate transcription from the second site. This was resolved with the discovery that p65 subunit can interact with YB-1 and thus get a piggyback ride to the promoter when YB-1 binds to its recognition site on the viral promoter ( Fig. 2) (57).



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  		Figure 2. Mechanism of activation of transcription from human polyomavirus JC by human YB-1. RelA is known to activate transcription of human polyomavirus JC from two distinct sites. While RelA can bind one of these two sites, direct interaction of RelA with the second site was not detected. It is now known that RelA gets a piggyback ride to this site via its interaction with the protein YB-1.

The mechanism by which Y-box proteins repress transcription is understood fairly well, at least for some genes. A common theme of inhibition of other trans-activating proteins either by direct interaction or by inhibition of DNA binding seems to underlie repression of MHC gene transcription by YB-1. YB-1 is thought to repress transcription of the HLA DR{alpha} gene by promoting or stabilizing single-stranded DNA regions in the binding sites for CBF/NF-Y, thereby inhibiting their binding to promoter DNA (55). Direct interaction of YB-1 with CBF/NF-Y, leading to a depletion of CBF/NF-Y-mediated trans-activation, has also been shown for the HLA I-Aß promoter (91). YB-1-mediated repression of the inducibility of the grp78 core element is thought to be due to an ability of YB-1 to interact with YY1, a transcription factor required for the induction of grp78 ( Fig. 3) (92).



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  		Figure 3. Mechanism of repression of transcription from different promoters by Y-box proteins. Y-box proteins are known to repress transcription by blocking the ability of other trans-activators to bind their cognate recognition sites either by 1) blocking the binding site as demonstrated in the case of CBF/NF-Y in HLA DR{alpha} gene promoter or by 2) direct interaction with the trans-activating factor, as demonstrated in the case of CBF/NF-Y in the HLA-I Aß gene promoter and with YY1 in grp78 gene promoter.

Our studies have revealed that chkYB-2 is a potent activator of RSV LTR-driven transcription in avian cells, whereas the same protein acts as a repressor of the RSV LTR-driven transcription in mammalian cells (26, 27). In addition, we have evidence to show that the proteins chk-YB-1b and chk-YB2 can interact with each other in vitro (S. K. Swamynathan and R. V. Guntaka, unpublished results). This and the fact that the two proteins recognize the same sequence on the RSV LTR indicate that the regulatory mechanism involving these two proteins is quite complex and is fine-tuned to meet the variable situations that the cell may face.


   HOW ARE SINGLE-STRANDED REGIONS GENERATED AND MAINTAINED?
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
CONCLUSIONS
 REFERENCES
 
How S1-sensitive regions are generated and maintained in a cell is not understood. However, there are some interesting clues to address this question. In most cases, S1-sensitive sites within promoters have been found to possess an atypical distribution of nucleotides on the two strands of the duplex DNA, like polypyrimidine/purine stretches or alternating purine/pyrimidine stretches (12, 13, 93). Such sequences are known to have a potential to form Z-DNA and an ability to confer single-strand forming ability on the neighboring sequences (94, 95). In addition, it has been known for some time that atypical stretches, such as six consecutive deoxyadenosines (6A tracts), are capable of generating intrinsic bends in DNA even in the absence of protein binding (reviewed in refs 24, 96, 97).

Another factor that may potentially contribute to the generation of single-stranded regions at susceptible sites within the chromatin is supercoiling. Supercoiled DNA in the nucleus is known to be under tremendous torsional stress. Such torsional stress is thought to generate single-stranded regions at stretches of nucleotide sequences predisposed to form single-stranded regions by virtue of their possessing the atypical distribution of nucleotides mentioned above (8, 16, 23, 98). Once formed, such single-stranded regions are known to be stabilized by divalent cations such as Mg2+ or by spermidine (51, 99). In addition, several single-stranded DNA binding proteins present within the nucleus can bind and stabilize such regions.

We have demonstrated that chk-YB-2, a single-stranded DNA binding factor, is involved in transcriptional regulation of the RSV LTR (27). However, we do not know whether the chk-YB-2 binding sites in RSV LTR exist in a single-stranded form in vivo, and if so, how they are generated. The chk YB-2 binding sequences within the RSV LTR are flanked by two CArG boxes (100, 101) and by sequences proposed to have a potential to form Z-DNA (94). Serum-responsive factor (SRF), which interacts with CArG boxes, is known to bend DNA at the center of the CArG box (19, 21). Also, we have shown that the affinity of interaction between these Y-box proteins and DNA is greatly enhanced by the presence of divalent cations in the binding reaction (51, 99).

Considering these facts, we propose that the torsional stress due to the two bends induced within a short stretch of the RSV LTR DNA by SRF could lead to a partial unwinding in the sequences that reside in between, generating the single-stranded sequences required for chk-YB-2 binding. The single-stranded region so formed could then be stabilized by the presence of cations in the cell ( Fig. 4) (51). Therefore, it appears that the RSV LTR in its transcriptionally active form is an extremely complex structure in which the DNA is coated with both double- and single-stranded DNA binding protein factors, which in addition to interacting with the LTR DNA, also interact among themselves and with the components of the general transcription machinery, thus stabilizing the whole complex and leading to a better initiation of transcription ( Fig. 4).



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  		Figure 4. A model for the generation and stabilization of single-stranded regions within the RSV LTR. RSV LTR is known to be densely packed with cis-acting elements (many repeated within a short stretch of the promoter) and bound by at least six well-characterized proteins. We have shown that chk-YB-2, a single-stranded DNA binding protein, is critical to RSV LTR-driven transcription. Here, we propose that the two bends induced in the LTR DNA by binding of SRF to the sequences flanking the chk-YB-2 binding site lead to a torsional stress and a resultant partial unwinding in the chk-YB-2 binding sites due to the two Z-DNA forming stretches (shown as zigzag lines). Single-stranded DNA in such partially unwound regions is known to be stabilized by divalent cations and single-stranded DNA binding proteins present in the cell.


   CONCLUSIONS
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
REFERENCES
 
Evidence summarized in this review suggests the existence of single-stranded regions in the promoters and upstream regulatory sequences of several cellular and viral genes. These unpaired regions, in addition to the well-characterized double-stranded DNA cis elements and their cognate transcription factors, appear to be essential for optimal promoter activity. Although such influences have been known at the level of chromatin for a long time, we have only now begun to understand the nuances and importance of single-strand formation within promoters. In addition, this line of study has widened the fascinating field of Y-box proteins that specifically interact with single-stranded sites. As a result, we are now witnessing intensive investigations aimed at understanding the mechanism of generation and stabilization of the single-stranded regions within the promoters and the mechanism by which the Y-box proteins activate or repress transcription by different promoters. It is challenging, however, to delineate the mechanism by which these unwound regions are generated in the DNA and to characterize the interaction of single-stranded DNA binding proteins with these sequences, as well as with general transcription machinery.


   ACKNOWLEDGMENTS
 
Research in our laboratory was supported by National Institutes of Health grant RO1 CA54192. We would like to thank Drs. David Pintel and Mark Hannink for their critical reading of the manuscript.


   FOOTNOTES
 
1 Correspondence: guntaka{at}showme.missouri.edu

2 Abbreviations: CSD, cold shock domain; RSV LTR, Rous sarcoma virus long-terminal repeats; SRF, serum-responsive factor.


   REFERENCES
TOP
 ABSTRACT
 INTRODUCTION
 PRESENCE OF SINGLE-STRANDED...
 Y-BOX PROTEINS
 MECHANISM OF ACTION OF...
 HOW ARE SINGLE-STRANDED REGIONS...
 CONCLUSIONS
 REFERENCES
 

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