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The SAF-box domain of chromatin protein DEK.

DEK is an abundant chromatin protein in metazoans reaching copy numbers of several millions/nucleus. Previous work has shown that human DEK, a protein of 375 amino acids, has two functional DNA-binding domains, of which one resides in a central part of the molecule and contains sequences corresponding to the scaffold attachment factor-box (SAF-box) domain as found in a growing number of nuclear proteins. Isolated SAF-box peptides (amino acids 137-187) bind weakly to DNA in solution, but when many SAF-box peptides are brought into close proximity on the surface of Sephadex beads, cooperative effects lead to a high affinity to DNA. Furthermore, a peptide (amino acids 87-187) that includes a sequence on the N-terminal side of the SAF-box binds efficiently to DNA. This peptide prefers four-way junction DNA over straight DNA and induces supercoils in relaxed circular DNA just like the full-length DEK. Interestingly, however, the 87-187 amino acid peptide introduces negative supercoils in contrast to the full-length DEK, which is known to introduce positive supercoils. We found that two adjacent regions (amino acids 68-87 and 187-250) are necessary for the formation of positive supercoils. Our data contribute to the ongoing characterization of the abundant and ubiquitous DEK chromatin protein.

Amino Acid Sequence↗

RGG-boxes of the EWS oncoprotein repress a range of transcriptional activation domains.

The Ewings Sarcoma Oncoprotein (EWS) interacts with several components of the mammalian transcriptional and pre-mRNA splicing machinery and is also found in the cytoplasm and even on the cell surface. The apparently diverse cellular functions of EWS are, however, not well characterized. EWS harbours a potent N-terminal transcriptional activation domain (the EAD) that is revealed in the context of oncogenic EWS-fusion proteins (EFPs) and a C-terminal RNA-binding domain (RBD) that recruits pre-mRNA splicing factors and may couple transcription and splicing. In contrast to EFPs, the presumed transcriptional role of normal EWS remains enigmatic. Here, we report that multiple RGG-boxes within the RBD are necessary and sufficient for cis-repression of the EAD and that RGG-boxes can also repress in-trans, within dimeric partners. Lys can functionally substitute for Arg, indicating that the basic nature of the Arg side chain is the critical determinant of RGG-box-mediated repression. In addition to the EAD, RGG-boxes can repress a broad range of activation domains (including those of VP16, E1a and CREB), but repression can be alleviated by the simultaneous presence of more than one activation domain. We therefore propose that a key function of RGG boxes within native EWS is to restrict promiscuous activation by the EAD while still allowing EWS to enter functional transcription complexes and participate in other transactions involving pre-mRNAs.

Amino Acid Motifs↗

A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes.

Box H/ACA snoRNAs represent an abundant group of small non-coding RNAs mainly involved in the pseudouridylation of rRNAs and/or snRNAs in eukaryotes and Archaea. In this study, we describe a novel experimental method for systematic identification of box H/ACA snoRNAs from eukaryotes. In the specialized cDNA libraries constructed by this method with total cellular RNAs from human blood cells, the high efficiency of cloning for diverse box H/ACA snoRNAs was achieved and seven novel species of this snoRNA family were identified from human for the first time. Furthermore, the novel method has been successfully applied for the identification of the box H/ACA snoRNAs from Drosophila and the fission yeast, demonstrating a powerful ability for systematic analysis of box H/ACA snoRNAs in a broad spectrum of eukaryotes.

Animals↗

A role for the distal CCAAT box of the gamma-globin gene in Hb switching.

Hereditary persistence of fetal hemoglobin (HPFH) is a condition manifested by continued expression of the gamma-globin gene in adult life. The four types of HPFH mutations (-117 G-A, -114 C-T, -114 C-G, and 13 bp del) clustered in the vicinity of the distal CCAAT box of the gamma-globin gene suggest the relevance of this region to the fetal-to-adult hemoglobin switching. Functional analysis in erythroid cell lines showed that these HPFH mutations reduced the activity of the gamma-globin promoter in K562 expressing embryonic and fetal globin chains, but not in KU812 expressing fetal and adult globin chains. These results suggest that the distal CCAAT box region has different functions in the fetus and the adult. In vitro, binding of NFE3 to the distal CCAAT box was commonly reduced by these HPFH mutations, suggesting that the binding of NFE3 to the distal CCAAT box may repress the gamma-globin gene in adults. Overlap of the binding sites of NFE3 and CP1, a potential activator, indicates the regulation of the gamma-globin gene by the competition between these factors. In addition, an unknown factor interacting with the -114 C-T HPFH mutant CCAAT box may be involved in elevation of the gamma-globin expression in an individual with the -114 C-T mutation.

Base Sequence↗

Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens.

Characterization of seven MADS-box genes, termed PPM1-PPM4 and PpMADS1-PpMADS3, from the moss model species Physcomitrella patens is reported. Phylogeny reconstructions and comparison of exon-intron structures revealed that the genes described here represent two different classes of homologous, yet distinct, MIKC-type MADS-box genes, termed MIKC(c)-type genes-"(c)" stands for "classic"-(PPM1, PPM2, PpMADS1) and MIKC(*)-type genes (PPM3, PPM4, PpMADS2, PpMADS3). The two gene classes deviate from each other in a characteristic way, especially in a sequence stretch termed intervening region. MIKC(c)-type genes are abundantly present in all land plants which have been investigated in this respect, and give rise to well-known gene types such as floral meristem and organ identity genes. In contrast, LAMB1 from the clubmoss Lycopodium annotinum was identified as the only other MIKC(*)-type gene published so far. Our findings strongly suggest that the most recent common ancestor of mosses and vascular plants contained at least one MIKC(c)-type and one MIKC(*)-type gene. Our studies thus reveal an ancient duplication of an MIKC-type gene that occurred before the separation of the lineages that led to extant mosses and vascular plants more than about 450 MYA. The identification of bona fide K-domains in both MIKC(*)-type and MIKC(c)-type proteins suggests that the K-domain is more ancient than is suggested by a recent alternative hypothesis. MIKC(*)-type genes may have escaped identification in ferns and seed plants so far. It seems more likely, however, that they represent a class of genes which has been lost in the lineage which led to extant ferns and seed plants. The high number of P. patens MADS-box genes and the presence of a K-box in the coding region and of some potential binding sites for MADS-domain proteins and other transcription factors in the putative promoter regions of these genes suggest that MADS-box genes in mosses are involved in complex gene regulatory networks similar to those in flowering plants.

Amino Acid Sequence↗

Cloning and functional expression of an E box-binding protein from rat granulosa cells.

Ovarian granulosa cells undergo cell growth and cytodifferentiation during follicular maturation. In a number of tissues, the gene expression that is responsible for the cytodifferentiation is largely dependent on E box(es) located upstream of the responsible genes. In this study, we report on the cloning of cDNA(s) encoding E box (5'-CACGTG-3')-binding protein from a rat granulosa cell cDNA library using a yeast one-hybrid system. When multiple E box sequences were used as target, we obtained a positive clone that encodes the rat homologue of upstream stimulatory factor 2 (USF2). An analysis of the nucleotide sequence and its deduced amino acid sequence reveals that rat USF2 protein consists of 346 amino acid residues and belongs to the basic helix-loop-helix/leucine zipper protein family. Northern blot analysis shows that rat USF2 mRNA exists as multiple forms between 1.6 and 2.2 kilobases. The size of the cloned insert was identical to that of the transcript of maximal length. Electrophoretic mobility shift assays showed that in vitro-translated rat USF2 specifically binds to the E box. In addition, cotransfection experiments with luciferase-reporter constructs in HepG2 cells reveal that the overexpression of rat USF2 leads to an increase of luciferase activity in the E box sequence-dependent manner. Thus, we report molecular cloning, expression, and functional characterization of full-length rat USF2 cDNA.

Amino Acid Sequence↗

Masking of mRNA by Y-box proteins.

The Y-box proteins are defined by their ability to bind to Y-box promoter elements and to help regulate transcription of a wide variety of genes. However, Y-box proteins are also identified as abundant proteins in the cytoplasm of germ cells, where they are found bound to stored mRNA molecules. Binding of Y-box proteins to mRNA sequences, both in vitro and in vivo, has been shown to effect their translational repression ("masking"). Here we discuss the ability of Y box proteins to recognize different nucleic acid structures and to become involved in regulation of both transcription and translation.

Amino Acid Sequence↗

Presence of a "CAGA box" in the APP gene unique to amyloid plaque-forming species and absent in all APLP-1/2 genes: implications in Alzheimer's disease.

Potentially toxic amyloid beta-peptide (Abeta) in Alzheimer's disease (AD) is generated from a family of Abeta-containing precursor proteins (APP), which is regulated via the 5'-untranslated region (5'-UTR) of its mRNA. We analyzed 5'-UTRs of the APP superfamily, including amyloid plaque-forming and non-amyloid plaque-forming species, and of prions (27 different DNA sequences). A "CAGA" sequence proximal to the "ATG" start codon was present in a location unique to APP genes of amyloid plaque-forming species and absent in all other genes surveyed. This CAGA box is immediately upstream of an interleukin-1-responsive element (acute box). In addition, the proximal CAGA box is predicted to appear on a stem-loop structure in both human and guinea pig APP mRNA. This stem-loop is part of a predicted bulge-loop that encompasses a known iron regulatory element (IRE). Electrophoretic mobility shift with segments of the APP 5'-UTR showed that a region with the proximal CAGA sequence binds nuclear proteins, and this UTR fragment is active in a reporter gene functional assay. Thus, the 5'-UTR in the human APP but not those of APP-like proteins contains a specific region that may participate in APP regulation and may determine a more general model for amyloid generation as seen in AD. The 5'-UTR of human APP contains several interesting control elements, such as an acute box element, a CAGA box, an IRE, and a transforming growth factor-beta-responsive element, that could control APP expression and provide suitable and specific drug targets for AD.

5' Untranslated Regions↗

Experimental evaluation of scaphoid X-series, carpal box radiographs, planar tomography, computed tomography, and magnetic resonance imaging in the diagnosis of scaphoid fracture.

AIM: In this study, we evaluated scaphoid X-series, Carpal Box radiographs (longitudinal and transverse), planar tomography, computed tomography (CT), and magnetic resonance imaging (MRI) in the diagnosis of scaphoid fracture. The aim of this study was to evaluate the planar technique in the diagnosis of scaphoid fracture. The use of planar tomography, CT, and MRI was to see whether these methods are useful in the diagnosis of scaphoid fracture when other diagnostics modalities remains negative. METHODS: Twenty-eight embalmed human cadaver specimens were used, in 23 of which fractures of the scaphoid were produced mechanically. Scaphoid X-series, Carpal Box posterior-anterior radiographs in ulnar deviation (X-CB), Carpal Box posterior-anterior views with the hand in 15-degree supination and ulnar deviation (X-CB 15-degree) were acted in all specimens, CT in eight wrists, planar tomography in seven wrists, and MRI in five wrists. The anatomic analysis of the specimens was used as the gold standard for comparison. Scaphoid X-series, Carpal Box radiographs, and planar tomography were judged independently and in a blind fashion by six observers, and CT and MRI were also judged independently and in a blind fashion by three radiologists. The observers were asked if they could recognize a scaphoid fracture. The agreement among the six observers for the scaphoid X-series and X-CB was measured. RESULTS: In the 23 fractured wrists, scaphoid X-series, X-CB, X-CB 15-degree, was true positive in 12, 14, and 15 wrists, respectively, whereas these methods were true negative in cadaver wrists 1, 3, and 5. CT was true positive in five of five fractured wrists and true negative in three of three negative wrists. Planar tomography was true positive in one of four fractured wrists and true negative in two of three nonfractured wrists. MRI was obtained in five wrists (one without a fracture), of which the fracture was recognized in only two. The highest agreement between observers was found in the X-CB 15-degree. CONCLUSION: From the planar investigated methods, the 15-degree Carpal Box posterior-anterior, longitudinal and transverse views were most accurate in recognizing scaphoid fracture with also the highest agreement between the observers.

Cadaver↗

Comparative study of radiographic disc height changes using two different interbody devices for transforaminal lumbar interbody fusion: open box vs. fenestrated tube interbody cage.

STUDY DESIGN: Retrospective comparative study of the postoperative subsidence of two interbody devices following posterior or transforaminal lumbar interbody fusion (PLIF/TLIF) for degenerative spondylolisthesis of the lumbar spine. OBJECTIVE: To assess certain radiograph characteristics of PLIF/TLIF using two interbody fusion devices at L4-L5. SUMMARY OF BACKGROUND DATA: PLIF can achieve spinal stabilization with vertebral body support and direct neural decompression. Although various interbody devices have been used in PLIF procedures, no radiographic studies have compared the load-bearing capabilities of open box and fenestrated tube interbody cages. METHODS: Seventy-five patients who underwent one-level PLIF in the L4-L5 [corrected] segment for degenerative spondylolisthesis were retrospectively reviewed with a minimum 2-year follow-up. Fenestrated tube (Group FT: n = 30 [corrected]) or open box (Group OB: n = 45 [corrected]) cages were used for the PLIF procedure. The following radiographic parameters were evaluated to compare the load-bearing capabilities: disc space height (DH); percent increase and decrease of disc height (% IDH and % DDH, respectively); and percent coverage of the cage on the endplate (% CC). RESULTS: There were no significant differences in the baseline data, including age, segmental instability and osteoporotic status, between the two groups. Anterior %IDH and % CC were significantly higher in Group OB than in Group FT (% IDH: 69.4% vs. 57.3%; % OC: 24.5% vs. 12.9%), and anterior and posterior % DDH were significantly higher in Group FT than in Group OB (anterior: -2.9% vs. -.1%; posterior: -6.6% vs. -.3%). Although the restored DH gradually reduced over time in both groups, significant reduction to the preoperative level only occurred in Group FT. CONCLUSIONS: The load-bearing capabilities of the open box cage are superior to those of the fenestrated tube cage. Since there were no significant differences between the baseline status of the two groups, the larger cross-sectional area and stable framework design of the open box cage appears to bring about a greater load-bearing capability. Therefore, the open box cage seems to be biomechanically more advantageous as an interbody device for PLIF than the fenestrated tube cage.

Aged↗

The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.

Eukaryotic cells contain a large number of small nucleolar RNAs (snoRNAs). A major family of snoRNAs features a consensus ACA motif positioned 3 nucleotides from the 3' end of the RNA. In this study we have characterized nine novel human ACA snoRNAs (U64-U72). Structural probing of U64 RNA followed by systematic computer modeling of all known box ACA snoRNAs revealed that this class of snoRNAs is defined by a phylogenetically conserved secondary structure. The ACA snoRNAs fold into two hairpin structures connected by a single-stranded hinge region and followed by a short 3' tail. The hinge region carries an evolutionarily conserved sequence motif, called box H (consensus, AnAnnA). The H box, probably in concert with the flanking helix structures and the ACA box characterized previously, plays an essential role in the accumulation of human U64 intronic snoRNA. The correct processing of a yeast ACA snoRNA, snR36, in mammalian cells demonstrated that the cis- and trans-acting elements required for processing and accumulation of ACA snoRNAs are evolutionarily conserved. The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., GAR1) suggests that these RNAs possess closely related nucleolar functions.

Base Sequence↗

The Elongin BC complex interacts with the conserved SOCS-box motif present in members of the SOCS, ras, WD-40 repeat, and ankyrin repeat families.

The Elongin BC complex was identified initially as a positive regulator of RNA polymerase II (Pol II) elongation factor Elongin A and subsequently as a component of the multiprotein von Hippel-Lindau (VHL) tumor suppressor complex, in which it participates in both tumor suppression and negative regulation of hypoxia-inducible genes. Elongin B is a ubiquitin-like protein, and Elongin C is a Skp1-like protein that binds to a BC-box motif that is present in both Elongin A and VHL and is distinct from the conserved F-box motif recognized by Skp1. In this report, we demonstrate that the Elongin BC complex also binds to a functional BC box present in the SOCS box, a sequence motif identified recently in the suppressor of cytokine signaling-1 (SOCS-1) protein, as well as in a collection of additional proteins belonging to the SOCS, ras, WD-40 repeat, SPRY domain, and ankyrin repeat families. In addition, we present evidence (1) that the Elongin BC complex is a component of a multiprotein SOCS-1 complex that attenuates Jak/STAT signaling by binding to Jak2 and inhibiting Jak2 kinase, and (2) that by interacting with the SOCS box, the Elongin BC complex can increase expression of the SOCS-1 protein by inhibiting its degradation. These results suggest that Elongin BC is a multifunctional regulatory complex capable of controlling multiple pathways in the cell through interaction with a short degenerate sequence motif found in many different proteins.

Amino Acid Sequence↗

The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase.

Many or all of the sites of pseudouridine (Psi) formation in eukaryotic rRNA are selected by site-specific base-pairing with members of the box H + ACA class of small nucleolar RNAs (snoRNAs). Database searches previously identified strong homology between the rat nucleolar protein Nap57p, its yeast homolog Cbf5p, and the Escherichia coli Psi synthase truB/P35. We therefore tested whether Cbf5p is required for synthesis of Psi in the yeast rRNA. After genetic depletion of Cbf5p, formation of Psi in the pre-rRNA is dramatically inhibited, resulting in accumulation of the unmodified rRNA. Protein A-tagged Cbf5p coprecipitates all tested members of the box H + ACA snoRNAs but not box C + D snoRNAs or other RNA species. Genetic depletion of Cbf5p leads to depletion of all box H + ACA snoRNAs. These include snR30, which is required for pre-rRNA processing. Depletion of Cbf5p also results in a pre-rRNA processing defect similar to that seen on depletion of snR30. We conclude that Cbf5p is likely to be the rRNA Psi synthase and is an integral component of the box H + ACA class of snoRNPs, which function to target the enzyme to its site of action.

Cell Nucleolus↗

Selective assembly of HIV-1 Vif-Cul5-ElonginB-ElonginC E3 ubiquitin ligase complex through a novel SOCS box and upstream cysteines.

APOBEC3G, which induces hypermutations in newly synthesized viral DNA, is suppressed by HIV-1 Vif, acting through Cul5-ElonginB-ElonginC E3 ubiquitin ligase. We have now characterized a novel SOCS box in HIV-1 Vif that mediates its interaction with ElonginC. In this SOCS box, alanine replaces the consensus cysteine in the previously identified SOCS box. This new motif was necessary but insufficient for interaction with Cul5-ElonginB-ElonginC, as two highly conserved Cys residues outside the SOCS box were required to interact with Cul5 but not ElonginC. Therefore, selective assembly with Cul5 versus Cul2 E3 may require protein interfaces besides the SOCS-box-ElonginC interaction.

Amino Acid Sequence↗

A specific 15-bp TATA box promoter element is required for expression of a herpes simplex virus type 1 late gene.

The herpes simplex virus type 1 (HSV-1) glycoprotein C (gC) gene is a true late or gamma 2 gene in that its expression shows a strict requirement for viral DNA replication. Elements required for regulated expression of this gene were previously shown to consist of the gC TATA box, transcription start site and a large portion of the leader sequence of the gC gene. In this paper we show that transcription of the gC gene requires a 15-bp sequence, GGGTATAAATTCCGG, which contains the gC TATA box. This sequence contains specific promoter elements because replacement of this sequence with either the TATA box of the HSV-1 early thymidine kinase (tk) gene or two random TATA-like elements results in a transcriptionally inactive gC gene. In addition, we show that temporal expression of HSV beta and gamma genes at early and late times during infection are controlled by separate and distinct regulatory elements; regulatory signals distal to the TATA box are needed for early expression, whereas a gC-like TATA box is needed for late expression. These signals were identified by construction of a chimeric HSV gene that contained the distal control signals of the beta tk gene fused upstream of the TATA sequence of the gamma 2 gC gene. When RNA was isolated at various times postinfection from cells infected with a virus whose genome contained this chimeric tk-gC gene, synthesis of gC mRNA showed both early and late kinetics.

Base Sequence↗

Novel murine homeo box gene on chromosome 1 expressed in specific hematopoietic lineages and during embryogenesis.

We describe here a new murine homeo box gene, denoted Hlx, which is expressed within specific hematopoietic lineages. The cDNA sequence indicates that Hlx differs markedly from known vertebrate homeo box genes, and linkage analysis of an interspecific murine backcross showed that it resides at a novel homeo box locus on the distal portion of mouse chromosome 1. The Hlx homeo domain is most similar to that of the Drosophila H2.0 gene, but outside this region the two polypeptides are related only within a few short segments, the most notable being a motif (denoted Hep) also partially conserved in the engrailed and invected homeo proteins and possibly related to an octapeptide in certain paired box proteins. The presence of an intron within the Hlx homeo box at the same position as in several divergent Drosophila genes (H2.0, labial, Distal-less, proboscipedia, Abdominal-B, NK-1) suggests an ancient evolutionary relationship between these genes. RNA analysis of 67 murine hematopoietic cell lines and normal hematopoietic cells revealed Hlx expression throughout the myeloid/macrophage lineage and at early stages of B lymphocyte development but not in T lymphocytes, erythroid cells, or mast cells. Hence, Hlx is a candidate regulator of hematopoietic lineage commitment and maturation. It probably also functions outside the hematopoietic system, however, because Hlx mRNA could be detected in diverse adult tissues and in embryos from as early as day 8 of development.

Amino Acid Sequence↗

The paired box encodes a second DNA-binding domain in the paired homeo domain protein.

The homeo box, which encodes the DNA-binding homeo domain, is a DNA sequence motif present in several Drosophila developmental genes; it has been used to identify many homologous genes involved in mammalian development. The paired box is another conserved sequence motif, first identified in the paired (prd) and gooseberry (gsb) Drosophila homeo domain genes. It encodes a 128-amino-acid domain, the paired domain, which has since been found in other fly and mouse gene products, in association with the homeo domain or in its absence. We show that the paired box of the prd gene encodes a DNA-binding activity, independent of the DNA-binding activity of the Paired (Prd) homeo domain and with a different sequence specificity. The amino-terminal region of the paired domain, including one of the three predicted alpha-helices, is necessary and sufficient for binding. We investigate the binding of the Prd protein to two sites in the even-skipped promoter, which are composed of overlapping sequences bound by the homeo domain and by the paired domain. We also show that a mutation in the paired box of Prd, corresponding to the mutation in the paired box of the mouse Pax-1 gene thought to cause the undulated skeletal phenotype, destroys the ability of the Prd protein to bind to the paired domain-specific site. This supports the view that the undulated phenotype results from the inactivation of the DNA-binding activity of the paired domain of Pax-1.

Animals↗

Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria.

Evolutionary conservation of an interspersed repetitive DNA sequence, BOX, from Streptococcus pneumoniae was investigated to explore the mosaic nature of these elements. BOX elements consist of various combinations of three subunits, boxA, boxB, and boxC. Eight oligonucleotide probes were designed based on consensus DNA sequences of boxA, boxB, and boxC subunits. DNA hybridization studies and PCR using these probes/primers demonstrate that oligonucleotide sequences within the boxA subunit appear to be conserved among diverse bacterial species. The boxB and boxC subunits show only limited, if any, sequence conservation in bacteria other than S. pneumoniae. Intact BOX elements with boxA, boxB, and boxC subunits were only present in high copy number in pneumococcal strains. This pattern of differential conservation lends support to the modular nature of BOX repetitive elements in that boxA-like subsequences are effectively independent of boxB-like or boxC-like subunits in bacteria other than S. pneumoniae. Furthermore, dendrograms derived from repetitive sequence-based PCR (rep-PCR) fingerprints of S. pneumoniae isolates using the BOXA1R primer yielded clustering patterns that were similar to those obtained previously by other methods, suggesting that these repetitive sequence-based DNA fingerprints represent intrinsic properties of an S. pneumoniae strain's genome. Our results indicate widespread conservation of boxA-like subsequences in the bacterial kingdom, lend support to the mosaic nature of BOX in S. pneumoniae, and demonstrate the utility of boxA-based primers for rep-PCR fingerprinting of many microorganisms.

Bacteria↗