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A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
Expression of the genetic information encoded in our genomes is usually regulated by proteins interacting with the DNA. In some cases, however, noncoding RNAs transcribed from DNA control elements cooperate with histone-modifying enzymes to regulate gene expression, as has recently been shown for noncoding RNA originating from Polycomb- and Trithorax-group response elements.
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The comprehensive identification of cis-regulatory elements on a genome scale is a challenging problem. We develop a novel, steganalysis-based approach for genome-wide motif finding, called WordSpy, by viewing regulatory regions as a stegoscript with cis-elements embedded in 'background' sequences. We apply WordSpy to the promoters of cell-cycle-related genes of Saccharomyces cerevisiae and Arabidopsis thaliana, identifying all known cell-cycle motifs with high ranking. WordSpy can discover a complete set of cis-elements and facilitate the systematic study of regulatory networks.
Polymorphonuclear leukocytes (PMNs or neutrophils) are the most prominent cellular component of the innate immune system in humans and produce an array of potent cytotoxic molecules. It is important that neutrophils undergo constitutive (spontaneous) apoptosis as a mechanism to facilitate normal cell turnover and immune system homeostasis. Conversely, several proinflammatory cytokines, including granulocyte macrophage-colony stimulating factor (GM-CSF), prolong neutrophil survival. The molecular mechanisms that regulate PMN apoptosis or survival remain incompletely defined. To that end, we compared global gene expression in human neutrophils during spontaneous apoptosis with that in cells cultured with human GM-CSF. Genes encoding proteins that inhibit apoptosis, such as myeloid cell leukemia sequence 1, caspase 8 and Fas-associated via death domain-like apoptosis regulator (CFLAR), B cell chronic lymphocytic leukemia/lymphoma 2 (BCL2)/adenovirus E1B 19 kDa-interacting protein 2 (BNIP2), and serum/glucocorticoid-regulated kinase (SGK), were down-regulated coincident with neutrophil apoptosis. In contrast, those encoding apoptosis inhibitor 5, BCL2-like 1, BNIP2, CFLAR, SGK, and tumor necrosis factor alpha-induced protein 8 were up-regulated in PMNs cultured with GM-CSF. Correspondingly, GM-CSF delayed PMN apoptosis (P<0.03), increased cell viability (P<0.03), and prolonged neutrophil phagocytic capacity (P<0.05). Prolonged functional capacity was paralleled by striking up-regulation of proinflammatory genes and proteins, including CD14, CD24, CD66, and human leukocyte antigen-DR. In addition, expression of SGK protein diminished during PMN apoptosis but was restored by culture with GM-CSF, suggesting SGK is involved in leukocyte survival. These studies provide a global view of the molecular events that regulate neutrophil survival and apoptosis.
Spontaneous labor in women and in other mammals is likely mediated by a concerted series of biochemical events that negatively impact the ability of the progesterone receptor (PR) to regulate target genes that maintain myometrial quiescence. In the present study, we tested the hypothesis that progesterone/PR inhibits uterine contractility by blocking nuclear factor kappaB (NF-kappaB) activation and induction of cyclooxygenase-2 (COX-2), a contractile gene that is up-regulated in labor. To uncover mechanisms for regulation of uterine COX-2, immortalized human fundal myometrial cells were treated with IL-1beta +/- progesterone. IL-1beta alone caused a marked up-regulation of COX-2 mRNA, whereas treatment with progesterone suppressed this induction. This was also observed in human breast cancer (T47D) cells. In both cell lines, this inhibitory effect of progesterone was blocked by RU486. Using chromatin immunoprecipitation, we observed that IL-1beta stimulated recruitment of NF-kappaB p65 to both proximal and distal NF-kappaB elements of the COX-2 promoter; these effects were diminished by coincubation with progesterone. The ability of progesterone to inhibit COX-2 expression in myometrial cells was associated with rapid induction of mRNA and protein levels of inhibitor of kappaBalpha, a protein that blocks NF-kappaB transactivation. Furthermore, small interfering RNA-mediated ablation of both PR-A and PR-B isoforms in T47D cells greatly enhanced NF-kappaB activation and COX-2 expression. These effects were observed in the absence of exogenous progesterone, suggesting a ligand-independent action of PR. Based on these findings, we propose that PR may inhibit NF-kappaB activation of COX-2 gene expression and uterine contractility via ligand-dependent and ligand-independent mechanisms.
Homeodomain factor Nkx2-5 is a central component of the transcription factor network that guides cardiac development; in humans, mutations in NKX2.5 lead to congenital heart disease (CHD). We have genetically defined a novel conserved tyrosine-rich domain (YRD) within Nkx2-5 that has co-evolved with its homeodomain. Mutation of the YRD did not affect DNA binding and only slightly diminished transcriptional activity of Nkx2-5 in a context-specific manner in vitro. However, the YRD was absolutely essential for the function of Nkx2-5 in cardiogenesis during ES cell differentiation and in the developing embryo. Furthermore, heterozygous mutation of all nine tyrosines to alanine created an allele with a strong dominant-negative-like activity in vivo: ES cell<-->embryo chimaeras bearing the heterozygous mutation died before term with cardiac malformations similar to the more severe anomalies seen in NKX2.5 mutant families. These studies suggest a functional interdependence between the NK2 class homeodomain and YRD in cardiac development and evolution, and establish a new model for analysis of Nkx2-5 function in CHD.
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Functional knowledge of individual genes encoding components of the cell signaling, metabolic and regulatory pathways is crucial to our understanding of physiology and pathophysiology. A central challenge in functional genomics is the creation of a working map delineating how eukaryotic cells coordinate and govern patterns of gene expression. This coordination is often depicted as an intertwined network or circuit of genes that alternately activate and repress each other. Multiple bioinformatic and high-throughput experimental approaches exist to aid in the reconstruction of gene networks. Albeit far from being complete, the ability to recreate gene networks from experimental data facilitates the systematic dissection of cell function at the molecular and genetic level. In this review, several different genomic technologies are discussed, and example studies that are promoting new discoveries and hypotheses are detailed.
Revealing the control mechanisms responsible for the cell's surprisingly well-organized functions should lead directly to a better understanding of how the cell adapts to extraordinarily changing environments. A general framework for describing models that can represent diverse biochemical regulatory functions systematically would help not only systematic interpretation of the various models proposed for certain systems but also further understanding of the general control mechanism and design principles underlying different biological systems. This article presents a unified mathematical framework for describing gene regulatory units. The proposed framework is fairly compatible with the classical control theoretical framework, so it should serve as a connecting bridge between engineering control theory and biological control mechanisms. It should also provide a unified view of different regulatory units and facilitate systematic comparison of different mathematical models proposed in a variety of literature.
Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.
All human genes contain a diverse array of cis-acting elements within introns and exons that are required for correct and efficient precursor messenger RNA (pre-mRNA) splicing. Recent computational analyses predict that most human exons contain elements required for splicing coinciding with an appreciation for the high frequency with which mutations that disruption pre-mRNA splicing cause disease. Minigenes provide a means to directly determine whether disease-causing mutations or single nucleotide polymorphisms (SNPs) affect splicing efficiency. Minigenes have also been instrumental in investigations of alternative splicing to identify cis elements required for cell-specific splicing events, demonstrating regulation of individual splicing events by specific RNA binding proteins, and correlating binding of these splicing regulators with splicing regulation. Here we present a versatile minigene plasmid vector designed for rapid cloning and analysis of cis elements and trans-acting factors that influence splicing efficiency or regulate cell-specific splicing. Ubiquitous expression and unique restriction sites allow for straightforward replacement of a variety of gene segments to analyze the effects of nucleotide substitutions on splicing, to identify tissue-specific regulatory elements, or to determine responsiveness to coexpressed proteins or small molecules.
OBJECTIVE: To map the regulatory domain of Escherichia coli T-protein. METHODS: Fragmentation cloning was employed in cloning of 11 fragments from T-protein. The regulatory activity of each fragment was determined respectively. RESULTS: The regulatory domain of T-protein was located in the C-terminal 270 amino acids, which was the same location as PDH domain. CONCLUSION: T-protein has no independent regulatory domain.
Metallothioneins are a group of low molecular mass and cysteine-rich metal-binding proteins, ubiquitously found in most living organisms. They play an important role in maintaining intracellular metal homeostasis, eliminating metal toxification and protecting against intracellular oxidative damages. Analysis of complete rice genome sequences revealed eleven genes encoding putative metallothionein (OsMT), indicating that OsMTs constitute a small gene family in rice. Expression profiling revealed that each member of the OsMT gene family differs not only in sequence but also in their tissue expression patterns, suggesting that these isoforms may have different functions they perform in specific tissues. On the basis of OsMT structural and phylogenetic analysis, the OsMT family was classified as two classes and class I was subdivided into four types. Additionally, in this paper we also present a complete overview of this family, describing the gene structure, genome localization, upstream regulatory element, and exon/intron organization of each member in order to provide valuable insight into this OsMT gene family.
Various actions of steroids, thyroid, vitamin D and retinoic acid are mediated by cognate nuclear hormone receptors. Hormone-liganded receptors bind to hormone response element in transcription regulatory region and homodimerize or heterodimerize with retinoid X receptor and regulate transcription of target genes. Conformational change of nuclear receptor after ligand-binding gives association with coactivators which possess histone acetyltransferase activity and are necessary for hormone-dependent transactivation. In the absence of hormone, corepressors, which associate with histone deacetyltransferase, interact to nuclear hormone receptors and repress the transcription. All these factors have important roles in the signaling of nuclear receptor and may be involved in endocrine dysfunction and disease.
To detect DNA variation of bovine lactoferrin gene, the sequence of 5'-regulatory region has been studied by PCR-SSCP. Among the five sub-sequences of this region, Blf 5'-1(227bp),Blf 5'-3(175bp) and Blf 5'-5(293bp)were found to be polymorphic. After sequencing the Blf 5'-1, G-->A and T-->G transitions were identified at the sites of -926 and -915 respectively. In the Blf 5'-3 fragment, a G insertion at -478 was found. Transversions of C-->A, G-->C at -28 and +33 respectively were also detected in the Blf 5'-5 region. The frequencies of mutated alleles were 0.101,0.112 and 0.237, respectively, in the three regions. By applying an analysis tool of TFSEARCH ver1.3, we studied the potential elements and protein factors which bind to the 5' -region, and discovered the different regulatory elements of pre-mutation and post-mutation.
The primers, RF/RR and QF1/QR,were designed based on the homologous region of swine MHC-DQB and DRB exon1 sequences and HLA-DQB and HLA-DRB sequences. The 5' proximal promoter region (URR) nucleotide sequences of swine MHC-DQB and DRB were firstly obtained by PCR, cloning and sequencing techniques. There exist highly conserved sequence motifs including W, X, Y, CCAAT, and TATA-like boxes in the obtained sequences,showing the same organization of the conserved regulatory elements as in other species. 12 DRB-URR and 14 DQB-URR alleles were found by PCR-SSCP in 313 pigs. The aligned results of these alleles showed that there exist abundant polymorphism sites in both Porcine MHC-DQB and DRB proximal promoter region.
To investigate whether the genes encoding cytokines and their regulatory elements participated in the immune response to Mycobacterium tuberculosis infection. Expression microarray was employed to compare the avirulent strain and clinically isolated strains infection induced macrophage cytokine differential expression. Results were cytokines IFN, TNF, TGF, IL and their regulatory elements are involved in the immune reaction. IL-19 was first reported to be involved in the anti-Mtb immunity. Relative expression level of theses factors before and after infection were assayed too. The data provides clues for further scrutinize the role of cytokines and related elements in the interaction between Mycobacterium tuberculosis and host macrophage.