Search

Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.

Transposable elements (TEs) can donate regulatory sequences that help to control the expression of human genes. The oncogene c-Myc is a promiscuous transcription factor that is thought to regulate the expression of hundreds of genes. We evaluated the contribution of TEs to the c-Myc regulatory network by searching for c-Myc binding sites derived from TEs and by analyzing the expression and function of target genes with nearby TE-derived c-Myc binding sites. There are thousands of TE sequences in the human genome that are bound by c-Myc. A conservative analysis indicated that 816-4564 of these TEs contain canonical c-Myc binding site motifs. c-Myc binding sites are over-represented among sequences derived from the ancient TE families L2 and MIR, consistent with their preservation by purifying selection. Genes associated with TE-derived c-Myc binding sites are co-expressed with each other and with c-Myc. A number of these putative TE-derived c-Myc target genes are differentially expressed between Burkitt's lymphoma cells versus normal B cells and encode proteins with cancer-related functions. Despite several lines of evidence pointing to their regulation by c-Myc and relevance to cancer, the set of genes identified as TE-derived c-Myc targets does not significantly overlap with two previously characterized c-Myc target gene sets. These data point to a substantial contribution of TEs to the regulation of human genes by c-Myc. Genes that are regulated by TE-derived c-Myc binding sites appear to form a distinct c-Myc regulatory subnetwork.

Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology-derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes.

We evaluated the epigenetic contributions of repetitive DNA elements to human gene regulation. Human proximal promoter sequences show distinct distributions of transposable elements (TEs) and simple sequence repeats (SSRs). TEs are enriched distal from transcriptional start sites (TSSs) and their frequency decreases closer to TSSs, being largely absent from the core promoter region. SSRs, on the other hand, are found at low frequency distal to the TSS and then increase in frequency starting ∼ 150 bp upstream of the TSS. The peak of SSR density is centered around the − 35 bp position where the basal transcriptional machinery assembles. These trends in repetitive sequence distribution are strongly correlated, positively for TEs and negatively for SSRs, with relative nucleosome binding affinities along the promoters. Nucleosomes bind with highest probability distal from the TSS and the nucleosome binding affinity steadily decreases reaching its nadir just upstream of the TSS at the same point where SSR frequency is at its highest. Promoters that are enriched for TEs are more highly and broadly expressed, on average, than promoters that are devoid of TEs. In addition, promoters that have similar repetitive DNA profiles regulate genes that have more similar expression patterns and encode proteins with more similar functions than promoters that differ with respect to their repetitive DNA. Furthermore, distinct repetitive DNA promoter profiles are correlated with tissue-specific patterns of expression. These observations indicate that repetitive DNA elements mediate chromatin accessibility in proximal promoter regions and the repeat content of promoters is relevant to both gene expression and function.

Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. Eukaryotic genome annotations have improved greatly due to large-scale characterization of full-length cDNAs, transcriptional start sites (TSSs), and comparative genomics. Regulatory elements are identified in promoter regions using a variety of enumerative or alignment-based methods. Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program.

Evolutionary knowledge is often used to facilitate computational attempts at gene function prediction. One rich source of evolutionary information is the relative rates of gene sequence divergence, and in this report we explore the connection between gene evolutionary rates and function. We performed a genome-scale evaluation of the relationship between evolutionary rates and functional annotations for the yeast Saccharomyces cerevisiae. Non-synonymous ( dN) and synonymous ( dS) substitution rates were calculated for 1,095 orthologous gene sets common to S. cerevisiae and six other closely related yeast species. Differences in evolutionary rates between pairs of genes (Δ dN & Δ dS) were then compared to their functional similarities ( sGO), which were measured using Gene Ontology (GO) annotations. Substantial and statistically significant correlations were found between Δ dN and sGO, whereas there is no apparent relationship between Δ dS and sGO. These results are consistent with a mode of action for natural selection that is based on similar rates of elimination of deleterious protein coding sequence variants for functionally related genes. The connection between gene evolutionary rates and function was stronger than seen for phylogenetic profiles, which have previously been employed to inform functional inference. The co-evolution of functionally related yeast genes points to the relevance of specific function for the efficacy of natural selection and underscores the utility of gene evolutionary rates for functional predictions.

Objective : Choco is a state located on the Paci c coast of Colombia that has a majority Afro-Colombian population. The objective of this study was to characterize the genetic ancestry, admixture and diversity of the population of Choco, Colombia. Methodology : Genetic variation was characterized for a sample of 101 donors (61 female and 40 male) from the state of Choco. Genotypes were determined for each individual via the characterization of 610,545 single nucleotide polymorphisms genome-wide. Haplotypes for the uniparental mitochondrial DNA (female) and Y-DNA (male) chromosomes were also determined. These data were used for comparative analyses with a number of worldwide populations, including pu - tative ancestral populations from Africa, the Americas and Europe, along with several admixed American populations. Results : The population of Choco has predominantly African genetic ancestry (75.8%) with approximately equal parts European (13.4%) and Native American (11.1%) ancestry. Choco shows relatively high levels of three-way genetic admixture, and far higher levels of Native American ancestry, compared to other New World African populations from the Caribbean and the United States. There is a striking pattern of sex-speci c ancestry in Choco, with Native American admixture along the female lineage and European admixture along the male lineage. The population of Choco is also characterized by relatively high levels of overall genetic diversity compared to both putative ancestral populations and other admixed American populations. Conclusion : These results suggest a unique genetic heritage for the population of Choco and underscore the profound human genetic diversity that can be found in the region.

Background A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species. Results At the global level, the topological properties of the human and mouse gene coexpression networks are, essentially, identical. For instance, both networks have topologies with small-world and scale-free properties as well as closely similar average node degrees, clustering coefficients, and path lengths. However, the human and mouse coexpression networks are highly divergent at the local level: only a small fraction ( Conclusion The dissonance between global versus local network divergence suggests that the interspecies similarity of the global network properties is of limited biological significance, at best, and that the biologically relevant aspects of the architectures of gene coexpression are specific and particular, rather than universal. Nevertheless, there is substantial evolutionary conservation of the local network structure which is compatible with the notion that gene coexpression networks are subject to purifying selection.

The Histone Database is a curated and searchable collection of full-length sequences and structures of histones and nonhistone proteins containing histone-like folds, compiled from major public databases. Several new histone fold-containing proteins have been identified, including the huntingtin-interacting protein HYPM. Additionally, based on the recent crystal structure of the Son of Sevenless protein, an interpretation of the sequence analysis of the histone fold domain is presented. The database contains an updated collection of multiple sequence alignments for the four core histones (H2A, H2B, H3, and H4) and the linker histones (H1/H5) from a total of 975 organisms. The database also contains information on the human histone gene complement and provides links to three-dimensional structures of histone and histone fold-containing proteins. The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold-containing proteins. The database is available at http://research.nhgri.nih.gov/histones/.

Histone proteins play essential structural and functional roles in the transition between active and inactive chromatin states. Although histones have a high degree of conservation due to constraints to maintain the overall structure of the nucleosomal octameric core, variants have evolved to assume diverse roles in gene regulation and epigenetic silencing. Histone variants, post-translational modifications and interactions with chromatin remodeling complexes influence DNA replication, transcription, repair and recombination. The authors review recent findings on the structure of chromatin that confirm previous interparticle interactions observed in crystal structures.

Chromatin structure plays an essential role in gene regulation. The structural unit of chromatin is the nucleosome, which is composed of 147 bp of DNA wrapped in a negative superhelix around a central octamer of core histones (composed of two molecules each of H2A, H2B, H3, and H4) (25). Nucleosomes are separated by linker DNA, forming a “beads on a string” structure. A fifth histone, H1, binds to both the nucleosome and the linker DNA to drive the coiling of the nucleosomal filament to form the 30-nm fiber. The nucleosome presents a problem for regulatory proteins seeking access to DNA because so much of the DNA is protected by histones: the inner surface of the DNA is completely occluded by the central core, the external surface is at least partly protected by the core histone tail domains, and the DNA coils are so close together that their apposed surfaces are also unavailable. To cope with the intrinsically repressive nature of the nucleosome structure, regulatory proteins recruit two types of chromatin remodeling complex to promoters: (i) chromatin remodeling machines, which use ATP to move nucleosomes, effect nucleosomal conformational changes, and exchange core histones with variants (33); and (ii) chromatin modifying enzymes, which catalyze posttranslational modifications of the histones, mostly in their tail domains. These modifications are proposed to represent a “histone code” which is read by regulatory proteins that recognize particular combinations of modifications, resulting in activation or silencing of chromatin (41). Histone acetylation is generally associated with gene activation and is catalyzed by histone acetyltransferases (HATs). The identification of the Gcn5p coactivator as a HAT led to a breakthrough in the field, connecting transcription factors with chromatin (3). The current paradigm is that histone modifying complexes are cofactors recruited to promoters by sequence-specific activators or repressors. Our studies have focused on the CUP1 gene of Saccharomyces cerevisiae as a model for the role of chromatin in gene regulation (35-37). CUP1 encodes a metallothionein responsible for protecting cells from the toxic effects of copper. The induction of CUP1 by copper results in targeted acetylation of nucleosomes at the CUP1 promoter. This acetylation is dependent on SPT10 (23, 37), which encodes a putative HAT related to Gcn5p (29). SPT10 was originally identified as one of a set of SPT genes, mutations in which suppress insertion mutations due to the Ty1 transposable element (8). The SPT genes encode many proteins important in transcription, including subunits of the SAGA histone modifying complex (12), TATA-binding protein, and histones (44, 47). SPT10 is not an essential gene, but the null allele is associated with very slow growth and defects in gene regulation (7, 27, 28). SPT10 has been implicated as a global regulator of core promoter activity, acting at or near the TATA box (5, 34, 48). Recently, it has been shown that SPT10 is required for cell cycle-specific acetylation of lysine-56 of H3 at the histone gene promoters (46). However, the mechanism by which Spt10p exerts its effects through basal promoters is unclear. Spt10p has also been identified as an activator of the histone genes, which it regulates in conjunction with Spt21p, the Hir corepressor (7, 15, 38), and SWI/SNF (6, 46). In S. cerevisiae, there are four loci encoding the major core histones, each containing a pair of divergent genes transcribed from a central promoter (31). Two of these loci, HHT1-HHF1 and HHT2-HHF2, carry genes for H3 (HHT1 and -2) and H4 (HHF1 and -2) (40); the others, HTA1-HTB1 and HTA2-HTB2, carry genes for H2A (HTA1 and -2) and H2B (HTB1 and -2) (14). Chromatin immunoprecipitation (ChIP) experiments have shown that Spt10p is present at all four core histone promoters in vivo (15, 46). Here we address the mechanism by which Spt10p acts as a global regulator. Using microarray analysis, we identified hundreds of genes affected by Spt10p. However, we could demonstrate the presence of Spt10p only at the histone gene promoters in vivo, suggesting that Spt10p acts indirectly on the other genes through regulation of the histone genes. In support of this hypothesis, we present evidence that chromatin is incorrectly assembled in spt10Δ cells. Remarkably, we found that Spt10p is a sequence-specific DNA-binding protein which binds with a high affinity to the upstream activating sequences (UAS elements) in all four major core histone promoters. Due to the highly cooperative nature of the binding, no other high-affinity sites are predicted in the yeast genome.

The evolutionary implications of transposable element (TE) influences on gene regulation are explored here. An historical perspective is presented to underscore the importance of TE influences on gene regulation with respect to both the discovery of TEs and the early conceptualization of their potential impact on host genome evolution. Evidence that points to a role for TEs in host gene regulation is reviewed, and comparisons between genome sequences are used to demonstrate the fact that TEs are particularly lineage-specific components of their host genomes. Consistent with these two properties of TEs, regulatory effects and evolutionary specificity, human-mouse genome wide sequence comparisons reveal that the regulatory sequences that are contributed by TEs are exceptionally lineage specific. This suggests a particular mechanism by which TEs may drive the diversification of gene regulation between evolutionary lineages.

The identification and characterization of regulatory sequence elements in the proximal promoter region of a gene can be facilitated by knowing the precise location of the transcriptional start site (TSS). Using known TSSs from over 5700 different human full-length cDNAs, this study extracted a set of 4737 distinct putative promoter regions (PPRs) from the human genome. Each PPR consisted of nucleotides from -2000 to +1000 bp, relative to the corresponding TSS. Since many regulatory regions contain short, highly conserved strings of less than 10 nucleotides, we counted eight-letter words within the PPRs, using z-scores and other related statistics to evaluate their over- and under-representation. Several over-represented eight-letter words have known biological functions described in the eukaryotic transcription factor database TRANSFAC; however, many did not. Besides calculating a P-value with the standard normal approximation associated with z-scores, we used two extra statistical controls to evaluate the significance of over-represented words. These controls have important implications for evaluating over- and under-represented words with z-scores.

The use of λ repressor fusions to study protein-protein interactions in E. coli was first described by Hu and others (1). Since then, the repressor system has been employed by several laboratories to screen genomic (2–5) and cDNA libraries (6) for homotypic or heterotypic interactions. λ repressor consists of distinct and separable domains: the N-terminal domain which has DNA binding activity and the C-terminal domain which mediates dimerization. The repressor fusion system is based on reconstituting the activity of the repressor by replacing the C-terminal domain with a heterologous oligomerization domain. The interaction is detected when the C-terminal domain forms a dimer (or higher order oligomer) with itself (homotypic interaction) or with a different domain from other fusion (heterotypic interaction) (see Fig. 1). Fig. 1 The rationale of λ repressor fusions. Repressor fusions are used to detect protein-protein interactions in vivo. Protein or peptide targets are fused to the λ repressor DNA binding domain; these fusions can be evaluated for repressor activity ... Repressor fusions are usually expressed from multicopy plasmids; for a detailed discussion of repressor fusion plasmids available from our laboratory see ref. 7. Similar plasmids have been constructed by other groups (5,8–10) with a variety of modifications. In all cases, unique restriction sites are available for cloning a desired insert in-frame with the N-terminal domain of repressor. Table 1 lists the features of several of the repressor plasmid vectors in the literature. Table 1 Repressor Fusion Vectors Used for Peptide/Protein Lobrary Screening The identification and characterization of homotypic or heterotypic interactions is done by fusing a target DNA (fragments from a specific gene of interest, or a genomic, cDNA, randomized, or rationally designed library) to the λ repressor DNA binding domain. Repressor fusion libraries are made by using appropriate vectors with standard cloning methods. Library construction is not discussed further in this chapter (see Note 1). Here, we focus on the evaluation of the resultant repressor fusions for repressor activity using either immunity to phage infection (see Subheading 3.1.) or a variety of reporters under λ repressor control (see Table 2 and Subheadings 3.2–3.4.). Further screening is useful to ensure that the repressor activity of the fusion protein is dependent on the insert, especially when evaluating clones isolated by selection. A simple a high-throughput screening strategy based on nonsense suppression is described in Subheading 3.5. Table 2 Reporters Available for Library Screening Using Repressor Fusions 2. Materials Different subsets of the materials listed below are needed for the different protocols 2.1. General Use Media, Antibiotics, and Materials Luria-Bertani (LB) broth and agar: Premixed LB broth (DIFCO, cat. no. 244620) and agar (DIFCO, cat. no. 244620) are prepared according to the vendors instructions. 2XYT broth per L: 16 g tryptone, 10 g yeast extract, 10 g NaCl. Dissolve in 1 L distilled H2O. Autoclave. Antibiotics: Ampicillin 200 mg/mL in H2O (1000X stock, use at a final concentration of 200 μg/mL); kanamycin 20 mg/mL in H2O (1000X stock, use at a final concentration of 20 μg/mL). Sterile 96-well microplates (clinical “V bottom”). Microplate replicator 96 pin (Boekel Model 140500). Multichannel pipetter (8 or 12-channel) to handle volumes from 5–200 μL. Sterile toothpicks. 2.2. Strains Strains used are listed in Table 3. Different strains are used for each of the screening approaches described below. Table 3 E. coli Strains Used for Peptide/Protein Library Selection and Screening 2.3. For Phage Immunity Selections and Screens AG1688 and JH787 (see Note 2). λKH54 and λKH54h80 phage stocks at 109–1010 plaque forming units (pfu)/mL (see Note 3). Tryptone broth per L: 10 g Tryptone, 5 g NaCl. Dissolve in 1 L H2O. Autoclave. Tryptone agar: 13 g Bacto-Agar/L of tryptone broth before autoclaving. Tris-Magnesium (TM) buffer: 10 mM Tris-HCl, pH 8.0, 10 mM MgSO4. Autoclave. Tryptone top agar: 0.7 g Bacto agar/100 mL of tryptone broth before autoclaving. Chloroform. 15-cm LB plates containing ampicillin and kanamycin (see Note 4). 100-mm LB Amp Kan plates containing 25 mM sodium citrate, added from a sterile 1M stock solution. 2.4. For Screening with lacZ-Based Reporters Materials for β-galactosidase assay of choice (11).

We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated.

Background Transposition is disruptive in nature and, thus, it is imperative for host genomes to evolve mechanisms that suppress the activity of transposable elements (TEs). At the same time, transposition also provides diverse sequences that can be exapted by host genomes as functional elements. These notions form the basis of two competing hypotheses pertaining to the role of epigenetic modifications of TEs in eukaryotic genomes: the genome defense hypothesis and the exaptation hypothesis. To date, all available evidence points to the genome defense hypothesis as the best explanation for the biological role of TE epigenetic modifications. Results We evaluated several predictions generated by the genome defense hypothesis versus the exaptation hypothesis using recently characterized epigenetic histone modification data for the human genome. To this end, we mapped chromatin immunoprecipitation sequence tags from 38 histone modifications, characterized in CD4+ T cells, to the human genome and calculated their enrichment and depletion in all families of human TEs. We found that several of these families are significantly enriched or depleted for various histone modifications, both active and repressive. The enrichment of human TE families with active histone modifications is consistent with the exaptation hypothesis and stands in contrast to previous analyses that have found mammalian TEs to be exclusively repressively modified. Comparisons between TE families revealed that older families carry more histone modifications than younger ones, another observation consistent with the exaptation hypothesis. However, data from within family analyses on the relative ages of epigenetically modified elements are consistent with both the genome defense and exaptation hypotheses. Finally, TEs located proximal to genes carry more histone modifications than the ones that are distal to genes, as may be expected if epigenetically modified TEs help to regulate the expression of nearby host genes. Conclusions With a few exceptions, most of our findings support the exaptation hypothesis for the role of TE epigenetic modifications when vetted against the genome defense hypothesis. The recruitment of epigenetic modifications may represent an additional mechanism by which TEs can contribute to the regulatory functions of their host genomes.

Background Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set. Results We describe an improvement to the A-GLAM computer program, which predicts regulatory elements within DNA sequences with Gibbs sampling. The improvement adds an optional "scanning step" after Gibbs sampling. Gibbs sampling produces a position specific scoring matrix (PSSM). The new scanning step resembles an iterative PSI-BLAST search based on the PSSM. First, it assigns an "individual score" to each subsequence of appropriate length within the input sequences using the initial PSSM. Second, it computes an E-value from each individual score, to assess the agreement between the corresponding subsequence and the PSSM. Third, it permits subsequences with E-values falling below a threshold to contribute to the underlying PSSM, which is then updated using the Bayesian calculus. A-GLAM iterates its scanning step to convergence, at which point no new subsequences contribute to the PSSM. After convergence, A-GLAM reports predicted regulatory elements within each sequence in order of increasing E-values, so users have a statistical evaluation of the predicted elements in a convenient presentation. Thus, although the Gibbs sampling step in A-GLAM finds at most one regulatory element per input sequence, the scanning step can now rapidly locate further instances of the element in each sequence. Conclusion Datasets from experiments determining the binding sites of transcription factors were used to evaluate the improvement to A-GLAM. Typically, the datasets included several sequences containing multiple instances of a regulatory motif. The improvements to A-GLAM permitted it to predict the multiple instances.

Transposable elements (TEs) are abundant genomic sequences that have been found to contribute to genome evolution in unexpected ways. Here, we characterize the evolutionary and functional characteristics of TE-derived human genome regulatory sequences uncovered by the high throughput mapping of DNaseI-hypersensitive (HS) sites. Human genome TEs were found to contribute substantially to HS regulatory sequences characterized in CD4+ T cells: 23% of HS sites contain TE-derived sequences. While HS sites are far more evolutionarily conserved than non HS sites in the human genome, consistent with their functional importance, TE-derived HS sites are highly divergent. Nevertheless, TE-derived HS sites were shown to be functionally relevant in terms of driving gene expression in CD4+ T cells. Genes involved in immune response are statistically over-represented among genes with TE-derived HS sites. A number of genes with both TE-derived HS sites and immune tissue related expression patterns were found to encode proteins involved in immune response such as T cell specific receptor antigens and secreted cytokines as well as proteins with clinical relevance to HIV and cancer. Genes with TE-derived HS sites have higher average levels of sequence and expression divergence between human and mouse orthologs compared to genes with non TE-derived HS sites. The results reported here support the notion that TEs provide a specific genome-wide mechanism for generating functionally relevant gene regulatory divergence between evolutionary lineages. This article was reviewed by Wolfgang J. Miller (nominated by Jerzy Jurka), Itai Yanai and Mikhail S.Gelfand.

Background: Core histone genes are periodically expressed along the cell cycle and peak during S phase. Core histone gene expression is deeply evolutionarily conserved from the yeast Saccharomyces cerevisiae to human. Results: We evaluated the evolutionary dynamics of the specific regulatory mechanisms that give rise to the conserved histone regulatory phenotype. In contrast to the conservation of core histone gene expression patterns, the core histone regulatory machinery is highly divergent between species. There has been substantial evolutionary turnover of cis-regulatory sequence motifs along with the transcription factors that bind them. The regulatory mechanisms employed by members of the four core histone families are more similar within species than within gene families. The presence of species-specific histone regulatory mechanisms is opposite to what is seen at the protein sequence level. Core histone proteins are more similar within families, irrespective of their species of origin, than between families, which is consistent with the shared common ancestry of the members of individual histone families. Structure and sequence comparisons between histone families reveal that H2A and H2B form one related group whereas H3 and H4 form a distinct group, which is consistent with the nucleosome assembly dynamics. Conclusion: The dissonance between the evolutionary conservation of the core histone gene regulatory phenotypes and the divergence of their regulatory mechanisms indicates a highly dynamic mode of regulatory evolution. This distinct mode of regulatory evolution is probably facilitated by a solution space for promoter sequences, in terms of functionally viable cis-regulatory sites, that is substantially greater than that of protein sequences.

Nota de Investigación. El Virus del Mosaico del Pepíno (Cucumber Mosaic Virus, CMV) forma parte del grupo Cucumuvirus de la familia romoyiridae:este virus tiene su genoma dividido en tres cadenas positivas de ARN y un ARN-4 subgenómico el cual se genera de la transcripción delARN-3 y sirve como ARN mensajerop aral a síntesisd e proteínad e la cápside (Davies, 1988). EI.CMV puede infectarm ásd e 8oo especieds e plantasy se encuentra distribuido en todo el mundo.

The diverged TLX1 / HOX11 homeobox gene is frequently transcriptionally activated in T-cell acute lymphoblastic leukemia as a result of two recurrent chromosomal translocations or by as yet unknown mechanisms. Sporadic expression of TLX1 has also been detected in some other human tumors, raising the possibility that TLX1 played a role in the etiology of these malignancies. In this context, it is noteworthy that TLX1 is aberrantly expressed in the human erythroleukemia cell line K562. We previously reported that enforced TLX1 expression immortalizes myeloid progenitors in murine bone marrow and erythroid progenitors originating from murine embryonic stem cell-derived embryoid bodies. Based on these findings, we speculated that dysregulated TLX1 expression contributes to neoplastic transformation by interfering with hematopoietic differentiation programs. Here we carried out genome-wide expression profiling on these model systems to elucidate the mechanism of TLX1 -mediated differentiation arrest. Surprisingly, these investigations uncovered a latent erythroid phenotype of the TLX1 + bone marrow progenitor cell lines. Transcriptome comparison with murine GATA-1-null G1E-ER4 erythroblast cells (GEO Accession No. [GDS568][1]) showed nonrandom overlap ( P = 2.3 × 10−5) with a set of genes that immediately respond to GATA-1 activation. Included among the genes for which a positive correlation was observed were the erythropoietin (Epo) receptor and several functionally-associated downstream signaling components such as Lyn and Dok-1, as well as the SCL and FOG-1 transcription factor genes. We confirmed the biological relevance of these findings by demonstrating that TLX1 -immortalized bone marrow progenitors proliferated in response to erythropoietin, synthesizing beta-globin mRNA. We next extended this approach to iEBHX1S-4 cells, an embryoid body-derived cell line generated by conditional (doxycycline-controlled) TLX1 expression (manuscript in preparation). iEBHX1S-4 cells require IL-3 plus stem cell factor for survival and proliferation. However, when doxycycline is removed from the culture medium, the cells undergo Epo-dependent erythroid differentiation characterized by up-regulation of the TER119 surface antigen and hemoglobin synthesis. Interestingly, whereas there was statistically significant overlap of gene expression profiles between constitutive and conditional TLX1 + cells ( P = 2.5 × 10−5), there were no significant similarities between the iEBHX1S-4 transcriptome and the G1E-ER4 dataset until 6–24 hours after release of the TLX1 differentiation block. Bioinformatics analysis of the upstream regulatory regions of the genes identified implicated transcriptional networks involving GATA-1 as well as the p53, NF-kappaB and Egr-1 transcription factors. All of these transcription factors are substrates of the acetyltransferase CREB-binding protein (CBP), suggesting that inappropriate TLX1 expression might interfere with CBP activity. In agreement with this notion, acetylation of GATA-1, a key substrate of CBP-modulated erythroid differentiation, was increased upon down-regulation of TLX1 expression in iEBHX1S-4 cells. Experiments to directly confirm TLX1 inhibition of CBP as a central facet of TLX1 transforming function are ongoing, the results of which will be presented. [1]: /lookup/external-ref?link_type=NCBIGEO&access_num=GDS568&atom=%2Fbloodjournal%2F106%2F11%2F2997.atom

Understanding gene regulation is a major objective in molecular biology research. Frequently, transcription is driven by transcription factors (TFs) that bind to specific DNA sequences. These motifs are usually short and degenerate, rendering the likelihood of multiple copies occurring throughout the genome due to random chance as high. Despite this, TFs only bind to a small subset of sites, thus prompting our investigation into the differences between motifs that are bound by TFs and those that remain unbound. Here we constructed vectors representing various chromatin- and sequence-based features for a published set of bound and unbound motifs representing nine TFs in the budding yeast Saccharomyces cerevisiae. Using a machine learning approach, we identified a set of features that can be used to discriminate between bound and unbound motifs. We also discovered that some TFs bind most or all of their strong motifs in intergenic regions. Our data demonstrate that local sequence context can be strikingly different around motifs that are bound compared to motifs that are unbound. We concluded that there are multiple combinations of genomic features that characterize bound or unbound motifs.

Background The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements encode gene regulatory functions. This fact has important evolutionary implications, since repetitive DNA is the most dynamic part of the genome. We set out to assess the evolutionary rate and pattern of experimentally characterized human transcription factor binding sites (TFBS) that are derived from repetitive versus non-repetitive DNA to test whether repeat-derived TFBS are in fact rapidly evolving. We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA. Results We found numerous experimentally characterized TFBS in the human genome, 7–10% of all mapped sites, which are derived from repetitive DNA sequences including simple sequence repeats (SSRs) and TEs. TE-derived TFBS sequences are far less conserved between species than TFBS derived from SSRs and non-repetitive DNA. Despite their rapid evolution, several lines of evidence indicate that TE-derived TFBS are functionally constrained. First of all, ancient TE families, such as MIR and L2, are enriched for TFBS relative to younger families like Alu and L1. Secondly, functionally important positions in TE-derived TFBS, specifically those residues thought to physically interact with their cognate protein binding factors (TF), are more evolutionarily conserved than adjacent TFBS positions. Finally, TE-derived TFBS show position-specific patterns of sequence variation that are highly distinct from random patterns and similar to the variation seen for non-repeat derived sequences of the same TFBS. Conclusion The abundance of experimentally characterized human TFBS that are derived from repetitive DNA speaks to the substantial regulatory effects that this class of sequence has on the human genome. The unique evolutionary properties of repeat-derived TFBS are perhaps even more intriguing. TE-derived TFBS in particular, while clearly functionally constrained, evolve extremely rapidly relative to non-repeat derived sites. Such rapidly evolving TFBS are likely to confer species-specific regulatory phenotypes, i.e. divergent expression patterns, on the human evolutionary lineage. This result has practical implications with respect to the widespread use of evolutionary conservation as a surrogate for functionally relevant non-coding DNA. Most TE-derived TFBS would be missed using the kinds of sequence conservation-based screens, such as phylogenetic footprinting, that are used to help characterize non-coding DNA. Thus, the very TFBS that are most likely to yield human-specific characteristics will be neglected by the comparative genomic techniques that are currently de rigeur for the identification of novel regulatory sites.