Search

The transcription start sites used during the maternal to zygotic transition in zebrafish are mapped, revealing that the transition is characterized by a switch between two different sequence signs to guide transcription initiation, which often co-exist in core promoters. A fresh start for zygotic transcription The maternal-to-zygotic transition (MZT) during vertebrate embryogenesis represents a dramatic change of the transcriptome, when the zygotic genome is activated and maternal transcripts are degraded. This study maps the transcription start sites used during MZT in zebrafish at nucleotide resolution, and shows that the transition from maternal to zygotic transcriptome is characterized by a switch between two different promoter sequence signals. The position at which RNA transcription starts is determined by an A/T-rich motif at the maternal stage and by fundamentally different codes in the zygote. The two transcription start sites often coexist -- and may even overlap -- in core promoters and are differentially utilized at promoters active in both oocyte and embryo. A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs.sup.1 and recruits general transcription factors to initiate transcription.sup.2. The nature and causative relationship of the DNA sequence and chromatin signals that govern the selection of most TSSs by RNA polymerase II remain unresolved. Maternal to zygotic transition represents the most marked change of the transcriptome repertoire in the vertebrate life cycle.sup.3,4,5,6. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the tenth cell cycle, marking the mid-blastula transition.sup.7. This transition provides a unique opportunity to study the rules of TSS selection and the hierarchy of events linking transcription initiation with key chromatin modifications. We analysed TSS usage during zebrafish early embryonic development at high resolution using cap analysis of gene expression.sup.8, and determined the positions of H3K4me3-marked promoter-associated nucleosomes.sup.9. Here we show that the transition from the maternal to zygotic transcriptome is characterized by a switch between two fundamentally different modes of defining transcription initiation, which drive the dynamic change of TSS usage and promoter shape. A maternal-specific TSS selection, which requires an A/T-rich (W-box) motif, is replaced with a zygotic TSS selection grammar characterized by broader patterns of dinucleotide enrichments, precisely aligned with the first downstream (+1) nucleosome. The developmental dynamics of the H3K4me3-marked nucleosomes reveal their DNA-sequence-associated positioning at promoters before zygotic transcription and subsequent transcription-independent adjustment to the final position downstream of the zygotic TSS. The two TSS-defining grammars coexist, often physically overlapping, in core promoters of constitutively expressed genes to enable their expression in the two regulatory environments. The dissection of overlapping core promoter determinants represents a framework for future studies of promoter structure and function across different regulatory contexts., Author(s): Vanja Haberle [sup.1] [sup.2] , Nan Li [sup.3] , Yavor Hadzhiev [sup.3] , Charles Plessy [sup.4] [sup.5] , Christopher Previti [sup.6] [sup.11] , Chirag Nepal [sup.6] [sup.11] , Jochen [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2010.10.019 Byline: Ed Luk (1), Anand Ranjan (1), Peter C. FitzGerald (2), Gaku Mizuguchi (1), Yingzi Huang (1), Debbie Wei (1), Carl Wu (1) Abstract: Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or zero H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B, and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction. Author Affiliation: (1) Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA (2) Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA Article History: Received 27 May 2010; Revised 25 August 2010; Accepted 12 October 2010 Article Note: (miscellaneous) Published: November 24, 2010

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.07.020 Byline: Daniel F. Boyer (a)(e)(f), Yoshio Fujitani (a)(e)(f), Maureen Gannon (b)(c)(e)(f), Alvin C. Powers (b)(c)(d)(e)(f), Roland W. Stein (a)(c)(e)(f), Christopher V.E. Wright (a)(e)(f) Keywords: Pancreas; [beta] Cell; Foregut development; Enteroendocrine; Pdx1; Ipf1; Transcription factor; cis-Regulation Abstract: The unique, well-demarcated expression domain of Pdx1 within the posterior foregut suggests that investigating its transcriptional regulation will provide insight into mechanisms that regionally pattern the endoderm. Previous phylogenetic comparison identified conserved noncoding regions that stimulate transcriptional activity selectively in cultured pancreatic [beta] cells. Characterization of these regulatory elements is helping to dissect the transcription factor networks that operate within [beta] cells, which is important for understanding the etiology of [beta] cell dysfunction and diabetes, as well as for developing methods to produce [beta] cells in vitro for cell-based therapies. We recently reported that deletion of three proximally located conserved areas (Area I-II-III) from the endogenous Pdx1 locus resulted in severely reduced expression of Pdx1 in the pancreas, and a milder decrease in other foregut tissues. Here, we report transgene-based complementation experiments on Pdx1 null mice, which reveal that the proximal promoter/enhancer region, including Area I-II-III, rescues the pancreatic defects caused by Pdx1 deficiency, but only weakly promotes expression of Pdx1 in the postnatal stomach and duodenum. These results reveal a role for distal cis-regulatory elements in achieving the correct level of extra-pancreatic Pdx1 expression, which is necessary for the production of duodenal GIP cells and stomach gastrin cells. Author Affiliation: (a) Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2175, USA (b) Department of Medicine (Division of Diabetes, Endocrinology, and Metabolism), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2175, USA (c) Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2175, USA (d) VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA (e) Vanderbilt University Program in Developmental Biology.sup.1 , Nashville, Tennessee, USA (f) Beta Cell Biology Consortium.sup.2 , Nashville, Tennessee, USA Article History: Received 16 March 2006; Revised 11 July 2006; Accepted 19 July 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.04.443 Byline: Kshitish K. Acharya, Chhabi K. Govind, Amy N. Shore, Mark H. Stoler, Prabhakara P. Reddi Keywords: cis-Requirement; Round spermatid; SP-10; Spermatogenesis; Developmental regulation; Transcription; Repressor; TDP-43; Pur[alpha]; Testis Abstract: Maintenance of strict developmental stage- and cell type-specific gene expression is critical for the progression of spermatogenesis. However, the mechanisms which sustain the spatiotemporal order of gene transcription within the seminiferous epithelium are poorly understood. Previous work has established that the proximal promoter of the mouse SP-10 gene was sufficient to maintain round spermatid-specific expression (Reddi, P.P., Shore, A.N., Shapiro, J.A., Anderson, A., Stoler, M.H., Acharya, K.K., 2003b. Spermatid-specific promoter of the SP-10 gene functions as an insulator in somatic cells. Dev. Biol. 262, 173-182). The present study addressed the cis-requirement for this regulation and sought to identify the cognate transcription factor(s). We found that mutation of two 5'-ACACAC motifs (at -172 and -160) within the -186/+28 SP-10 promoter led to premature and indiscriminate expression of a reporter gene in the seminiferous epithelium of transgenic mice, whereas the wild-type -186/+28 promoter retained spermatid specificity. Neither promoter showed ectopic expression in the somatic tissues. Expression cloning using the -186/-148 portion of the promoter yielded transcriptional repressors TDP-43 and Pur[alpha] of which TDP-43 required the complementary 5'-GTGTGT elements located on the opposite strand for binding in vitro. Further, Northern analysis and immunohistochemistry of mouse testis showed the presence of TDP-43 in cell-types where the SP-10 gene remains repressed. Taken together, our results demonstrate that 5'-GTGTGT motifs on the complementary strand are required to prevent premature expression of SP-10 during spermatogenesis and implicate TDP-43 as the putative regulatory factor. The study also implied that additional level(s) of regulation keep the SP-10 gene silent in the somatic tissues. Author Affiliation: Department of Pathology, University of Virginia Health System, P.O. Box 800904, Charlottesville, VA 22908-0904, USA Article History: Received 13 July 2005; Revised 16 March 2006; Accepted 12 April 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.06.006 Byline: Clara Lago (a), Elena Clerici (a), Ludovico Dreni (a), Christine Horlow (c), Elisabetta Caporali (b), Lucia Colombo (b), Martin M. Kater (a) Keywords: TAF6; TFIID; Arabidopsis; Pollen tube; Gametophyte; Transcription Abstract: Initiation of transcription mediated by RNA polymerase II requires a number of transcription factors among which TFIID is the major core promoter recognition factor. TFIID is composed of highly conserved factors which include the TATA-binding protein (TBP) and about 14 TBP-associated factors (TAFs). Recently, the complete Arabidopsis TAF family has been identified. To obtain functional information about Arabidopsis TAFs, we analyzed a T-DNA insertion mutant for AtTAF6. Segregation analysis showed that plants homozygous for the mutant allele were never found, indicating that inhibition of the AtTAF6 function is lethal. Genetic experiments also revealed that the male gametophyte was affected by the attaf6 mutation since significant reduced transmission of the mutant allele through the male gametophyte was observed. Detailed histological and morphological analysis showed that the T-DNA insertion in AtTAF6 specifically affects pollen tube growth, indicating that the transcriptional regulation of only a specific subset of genes is controlled by this basal transcription factor. Author Affiliation: (a) Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli studi di Milano, via Celoria 26, 20133 Milan, Italy (b) Dipartimento di Biologia, Universita degli studi di Milano, via Celoria 26, 20133 Milan, Italy (c) INRA Versailles, Station de Genetique et d'Amelioration des Plantes, Route de St Cyr, F-78026 Versailles Cedex, France Article History: Received 15 March 2005; Revised 30 May 2005; Accepted 8 June 2005

The levels of transcripts of the cpc operon were highly reduced in a PD-1 mutant of cyanobacterium Synechocystis sp. strain PCC 6714. This was due to a substitution of C for T that occurred at 5 bp upstream of the transcription initiation site of the cpc operon. Any substitution for T at the -5 position drastically reduced both in vivo and in vitro promoter activity in cyanobacterium Synechococcus sp. strain PCC 7942 but not the in vivo activity in Escherichia coli. This suggests that the requirement of -5T appears to be specific for a cyanobacterial RNA polymerase-promoter combination.

Isolation and characterization of a poly-beta-hydroxybutyrate mutant of Azotobacter vinelandii are presented. Four promoters within the phbR-phbB intergenic region comprise two promoters each transcribing phbB and phbR. Results indicate that PhbR is involved in the transcription activaion, which occurs from one of the phbB promoters.

Results reveal that ToxT-dependent activation at tcpA promoter is mediated by the C-terminal domain of the RNA polymerase alpha subunit. ToxT interacts with Two adenine-rich regions of tcpA promoter assisted by the C-terminal domain of RNA polymerase alpha subunit.

This article describes the mechanism of cold shock induction of acidic cold shock proteins (CSPs) in Lactobacillus plantarum (L). Results indicate that the cspL promoter is induced in response to cold shock in a transcriptional regulation process.

Results reveal that the transcriptional regulation of protein kinase Calpha in Glioblastoma multiforme cell lines is dependent on the transcription activator factor, AP-2, which is involved in the phorbol ester-sensitive signaling pathway. Data indicate that an autoregulatory mode of trancription is operating suggesting that the enzyme may be upregulated in Glioblastoma multiforme cell lines.

To compare variation in regulatory and coding DNA, promoter sequences have been obtained from wild-derived mice and laboratory rats. The sequences are from the proximal promoter of the H2Aa, H2Ab, H2Eb, and H2K genes of 24 wild-derived inbred strains and a sample of the corresponding exon 2 sequences and of the RT1.Ba gene of six strains of laboratory rat. They reveal a high level of variation in the mouse MHC class II promoters (H2A and H2E), a low level in MHC class I (H2K), and none in the rat. The variation is pronounced in and around the cAMP response element, a major binding site for modulating promoter activity in response to external stimulation. This finding, together with the different levels of variation in MHC classes I and II, is suggestive of natural selection. However, selection operating via the MHC coding sequences must also contribute, as indicated by the minimal variation in both the MHC class II promoter and coding sequences of the rat. Furthermore CIITA (trans-activator of class II) of the mouse has been reported to have minimal variation in its promoter and none in its coding sequence. Taken together these data suggest that the regulatory and coding sequences undergo coselection. Each of the mouse class II promoters has a pattern of variation that appears to be basically dimorphic, with further variation added by recombination/mutation. The dimorphic allelic lineages are in marginally detectable linkage disequilibrium with the exon 2 sequences, particularly in H2Aa, thus lending further support to the coevolution hypothesis.

Results show that both HilC and HilD virulence regulatory proteins bind to the same target DNA sequences of promoters. However, they differ in terms of the number of binding sites and sequence specificity for binding to promoters. The promoter activity does not require any other cellular proteins besides HilC and HilD.

The regulatory CcaR protein from Streptomyces clavuligerus is an autoregulatory activator interacting with a bidirectional promoter as well as its own promoter. The purified protein binds to DNA fragments containing ccaR gene promoter regions but not to DNA fragments containing promoter regions of other genes.

The genetic organization of the lysis gene region of the temperate mycobacteriophage, Ms6, reveals that the expression of the lysis genes are mediated by its own two sigma(sup)70 -like promoters. Further, there appears to be an antitermination mechanism involvement in the phage's lysis gene transcription.

Results demonstrate that the regulatory protein HbpR binds simultaneously to both palindromic sequences of the upstream activating sequences of its promoters and further, both palindromes are involved in HbpR binding.

The best-characterized insulator in Drosophila melanogaster is the Su (Hw)-binding region contained within the gypsy retrotransposon. In the [y.sup.2] mutant, Su (Hw) protein partially inhibits yellow transcription by blocking the function of transcriptional enhancers located distally from the yellow promoter with respect to gypsy. Previously we have shown that yellow enhancers can overcome inhibition by a downstream insulator in the [y.sup.rh1] allele, when a second gypsy element is located upstream of the enhancers. To understand how two insulators neutralize each other, we isolated various deletions that terminate in the regulatory region of the [y.sup.rh1] allele. To generate these alleles we used DNA elongation by gene conversion of the truncated chromosomes at the end of the yellow regulatory region. We found that gypsy insulator can function at the end of the truncated chromosome. Addition of the gypsy insulator upstream of the yellow enhancers overcomes the enhancer-blocking activity of the gypsy insulator inserted between the yellow enhancers and promoter. These results suggest that the gypsy insulators do not form separate transcriptional domains that delimit the interactions between enhancers and promoters.

Amino acid substitution across the alpha subunit C-terminal domain of Escherichia coli RNA polymerase affects the cyclic AMP receptor protein-dependent transcription at the class I cAMP receptor protein-dependent promoter CC. Amino acid scanning, using alanine, reveals that relative contributions of individual residues within the 265 determinant depends on the promoter sequence.

Research shows that the non-histone chromatin-associated protein encoding Hmga2 promoter region mediates transcription activity. Data further indicate that the polypyrimidine tract binding protein binds to both polypyrimidinic strand of Hmga2 promoter and to ppyr-containing sequences of mouse and human promoters.

Results reveal that the tetracycline resistance determinant consists of two overlapping genes, tetA(P) and tetB(P) in an operon and are trascribed froma single promoter. Furthermore, T1 terminator is an intrinsic control element of the tet(P) operon, which prevents overexpression of the TetA(P) transmembrane protein in the presence of tetracycline.

The purified GA-1 encoded protein p6 exhibits a growth dependent repression or promotion of the GA-1 promoters in Bacillus bacteriophage GA-1. Results show that p6 production increases rapidly during initial phase of the infection cycle.

Research shows that the bacterriophage P1-derived C1-regulated promoter system in a LacZ-expression system exhibits an induction/repression ratios of 240-fold and 50-fold in Shigella flexineri and Klebsiella pneumoniae, respectively.

Research has been conducted on the activity of the P (sub)cer promoter required for the stable plasmid maintanance. The factors affecting this activity have been investigated and the results are reported.

Research describes an assay methodology, the multiple promoter comparison assay, which can be used as a general in vitro transcription system for the analysis of the RNA polymerase II genes including multiple start site TATA-less promoters.

Results demonstrate that arabinose regulon is negatively controlled by AraR protein, which represses ara promoters in vivo upon L-arabinose depletion. Data further indicate that metabolic operon and transport gene promoters are prone for catabolite repression suggesting that promoters enforce a tight and flexible control of ara regulon in Bacillus subtilis.

S1 nuclease analysis indicates that Mycobacterium tuberculosis katG gene is transcribed by two promoters, which are induced by peroxides and expressed differentially during bacterial growth in macrophages.

Results indicate that a weak sigma(sup)F specific -10 consensus, GG/tNNANNNT and a stronger -35 consensus, GTATA/T are involved in the transcription of promoter-lacZ by sigma(sup)F containing RNA polymerase in Bacillus subtilis.

Research demonstrates that the expression of the gene cfiA, which encodes carbapenemase enzyme, is promoted by two novel insertion elements. The insertion elements are situated upstream of the cfiA gene in Bacteroides fragalis.

Research examines the role of the -10 base sequence of Escherichia coli RNA polymerase-sigma(sup)70 in the formation of stable complexes with a promoter. Results indicate that each step in the multistep pathway requires different sequences even in the presence of a strong promoter, suggesting that a compromise sequence is best suited.

Research demonstrates that integration host factor facilitates correctly phased physical contact between the aromatic-responsive activator, DmpR, and the sigma (sup)54 in Pseudomonas. Furthermore, it stimulates transcription and nucleoprotein complexation of the promoter Po both in vivo and in vitro.

Research indicates that environmental and regulatory factors may affect hilA promoter of Salmonella serovar Typhimurium, which is mediated by inhibition of the upstream repressing sequences. Results show that EnvZ/OmpR regulates hilA indirectly by altering hilC expression and post-transcriptional modification of hilD.

Research demonstrates that the catabolite responsive element cre2 of Bacillus subtilis promoter region binds to carbon catabolite protein A for transcription activation. Mutagenesis data reveal that the upstream promoter sequences, beyond the protein binding region, are involved in the transcriptional activation.

Three genetic promoters, p(sub)L, p(sub)R, and p(sub)E, are involved in instituting lysogeny in coliphage 186. Data indicate that for efficient lysogeny establishment p(sub)E is essential and it inhibits lytic transcription by 50%.

Results indicate that the promoters for both the signal transducer/repressor blaRI/blaI as well as their mRNA are inducible. Data point out that the promoters also synthesize chloramphenicol acetyltransferase.

Results indicate that the iron starvation box elements in pyoverdine promoters mediate the sequence specific recognition by the alternative sigma factor PvdS for transcription initiation in pseudomonas aeruginosa.

Results indicate that the regulatory circuits of Stx-encoding phages mediate pathogenesis of Stx-producing Escherichia coli strains. Data further show that the prophage induction by late phage promoter p(sub)R via transcription plays a role in the production of toxin.

Results reveal that promoters mediating fepD and YbdA expression exhibit substantial overlap at their --10 regions. Data suggest that the promoter activity, which is regulated by iron through Fur repressor, is dependent on the relative strength of the promoters.

Results discuss identification of promoter sequences of Actinobacillus pleuropneumoniae by their ability to express promoterless lux genes and of the transcriptional start sites by primer extension analysis. A consensus promoter sequence for A. pleuropneumoniae is presented.

Results show that nucleotide changes in the --10 element region of sigma factors switch the promoter activity from the sigma(sup)X and sigma (sup)W or vice versa in Bacillus subtilis. The promoter selectivity is due to the amino acid differences in the conserved region 2 of sigma, which controls --10 element.

Research demonstrates that three DNA regions in the transcription initiation site of the 5-phosphoribosyl-1(alpha)-pyrophosphate synthetase1 (PRS1) gene control the gene expression as measured by fusion protein activity assay and gel shift analysis.