Showing papers by "Phillip A. Sharp published in 2004"
TL;DR: The ability of an miRNA to translationally repress a target mRNA is largely dictated by the free energy of binding of the first eight nucleotides in the 5' region of the miRNA, however, G:U wobble base-pairing in this region interferes with activity beyond that predicted on the basis of thermodynamic stability.
Abstract: MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of an miRNA to translationally repress a target mRNA is largely dictated by the free energy of binding of the first eight nucleotides in the 5' region of the miRNA. However, G:U wobble base-pairing in this region interferes with activity beyond that predicted on the basis of thermodynamic stability. Furthermore, an mRNA can be simultaneously repressed by more than one miRNA species. The level of repression achieved is dependent on both the amount of mRNA and the amount of available miRNA complexes. Thus, predicted miRNA:mRNA interactions must be viewed in the context of other potential interactions and cellular conditions.
1,744 citations
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TL;DR: The term RNAi — short for RNA interference — crops up again and again in biology research these days because of its power as a laboratory tool, and in part because it is a widespread natural phenomenon.
Abstract: The term RNAi — short for RNA interference — crops up again and again in biology research these days. This is in part because of its power as a laboratory tool, and in part because it is a widespread natural phenomenon.
765 citations
TL;DR: The ability to efficiently control shRNA expression by using two lentiviral vectors for conditional, Cre-lox-regulated, RNA interference was shown in cell-based experiments and should facilitate functional genetic analysis in mammals.
Abstract: We have generated two lentiviral vectors for conditional, Cre-lox-regulated, RNA interference. One vector allows for conditional activation, whereas the other permits conditional inactivation of short hairpin RNA (shRNA) expression. The former is based on a strategy in which the mouse U6 promoter has been modified by including a hybrid between a LoxP site and a TATA box. The ability to efficiently control shRNA expression by using these vectors was shown in cell-based experiments by knocking down p53, nucleophosmin and DNA methyltransferase 1. We also demonstrate the usefulness of this approach to achieve conditional, tissue-specific RNA interference in Cre-expressing transgenic mice. Combined with the growing array of Cre expression strategies, these vectors allow spatial and temporal control of shRNA expression in vivo and should facilitate functional genetic analysis in mammals.
643 citations
TL;DR: A technique for visualizing detailed miRNA expression patterns in mouse embryos is reported, elucidate the tissue-specific expression of several miRNAs during embryogenesis, and negatively regulates Hoxb8 and miR-196a, indicating that its restricted expression pattern probably reflects a role in the patterning function of the Hox complex.
Abstract: MicroRNAs (miRNAs) are a class of short (∼22-nt) noncoding RNA molecules that downregulate expression of their mRNA targets. Since their discovery as regulators of developmental timing in Caenorhabditis elegans, hundreds of miRNAs have been identified in both animals and plants1. Here, we report a technique for visualizing detailed miRNA expression patterns in mouse embryos. We elucidate the tissue-specific expression of several miRNAs during embryogenesis, including two encoded by genes embedded in homeobox (Hox) clusters, miR-10a and miR-196a. These two miRNAs are expressed in patterns that are markedly reminiscent of those of Hox genes. Furthermore, miR-196a negatively regulates Hoxb8, indicating that its restricted expression pattern probably reflects a role in the patterning function of the Hox complex.
457 citations
TL;DR: An online ESE analysis tool is described that annotates RESCUE-ESE hexamers in vertebrate exons and can be used to predict splicing phenotypes by identifying sequence changes that disrupt or alter predicted ESEs.
Abstract: A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much attention has been focused on the effects of sequence variation on the amino acid sequence, variations that disrupt gene processing signals can dramatically impact gene function. A variation that disrupts an exonic splicing enhancer (ESE), for example, could cause exon skipping which would result in the exclusion of an entire exon from the mRNA transcript. RESCUE-ESE, a computational approach used in conjunction with experimental validation, previously identified 238 candidate ESE hexamers in human genes. The RESCUE-ESE method has recently been implemented in three additional species: mouse, zebrafish and pufferfish. Here we describe an online ESE analysis tool (http://genes.mit.edu/burgelab/rescue-ese/) that annotates RESCUE-ESE hexamers in vertebrate exons and can be used to predict splicing phenotypes by identifying sequence changes that disrupt or alter predicted ESEs.
280 citations
TL;DR: The results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.
Abstract: Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE) activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE)-ESE method. Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 ± 0.05). This selection is strongest for the predicted ESEs that are located near splice sites. Our results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and also suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.
194 citations
TL;DR: The primary effect of this regulatory peptide is to modulate the apical membrane uptake machinery, thereby controlling the amount of iron absorbed from the diet.
140 citations
01 Nov 2004
TL;DR: There is emerging evidence that a number of other components of the intestinal Fe transport pathway are also Cu sensitive, suggesting that the Fe–Cu relationship may be more complex than first thought.
Abstract: The intimate relationship between Fe and Cu in human nutrition has been recognised for many years. The best-characterised link is provided by caeruloplasmin, a multiCu-binding protein that acts as a serum ferrioxidase and is essential for the mobilisation of Fe from storage tissues. Decreased Cu status has been shown to reduce holo-caeruloplasmin production and impair ferrioxidase activity, leading, in a number of cases, to decreased tissue Fe release and the generation of anaemia that is responsive to dietary supplementation with Cu but not Fe. Dietary Fe absorption also requires the presence of a multiCu ferrioxidase. Hephaestin, a caeruloplasmin homologue, works in concert with the IREG1 transporter to permit Fe efflux from enterocytes for loading onto transferrin. The essential role of hephaestin in this process has been recognised from studies in the sex-linked anaemic (sla) mouse, in which Fe efflux is markedly impaired as a result of a mutation in the hephaestin gene that results in a truncated and non-functional version of the protein. There is emerging evidence that a number of other components of the intestinal Fe transport pathway are also Cu sensitive. Divalent metal transporter 1 (DMT1), the Fe transporter located at the apical membrane of enterocytes, is also a physiologically-relevant Cu transporter, suggesting that these two metals may compete with each other for uptake into the duodenal enterocytes. Furthermore, expression of both DMT1 and the basolateral Fe-efflux transporter IREG1 can be regulated by Cu, suggesting that the Fe-Cu relationship may be more complex than first thought.
110 citations
TL;DR: A critical role for Oct-1 during development and a stringent gene dosage effect with Oct-2 in mediating postnatal survival are suggested.
Abstract: Oct-1 is a sequence-specific DNA binding transcription factor that is believed to regulate a large group of tissue-specific and ubiquitous genes. Both Oct-1 and the related but tissue-restricted Oct-2 protein bind to a DNA sequence termed the octamer motif (5'-ATGCAAAT-3') with equal affinity in vitro. To address the role of Oct-1 in vivo, an Oct-1-deficient mouse strain was generated by gene targeting. Oct-1-deficient embryos died during gestation, frequently appeared anemic, and suffered from a lack of Ter-119-positive erythroid precursor cells. This defect was cell intrinsic. Fibroblasts derived from these embryos displayed a dramatic decrease in Oct-1 DNA binding activity and a lack of octamer-dependent promoter activity in transient transfection assays. Interestingly, several endogenous genes thought to be regulated by Oct-1 showed no change in expression. When crossed to Oct-2(+/-) animals, transheterozygotes were recovered at a very low frequency. These findings suggest a critical role for Oct-1 during development and a stringent gene dosage effect with Oct-2 in mediating postnatal survival.
85 citations
TL;DR: The data suggest that TNFα could regulate dietary iron absorption and that the apical transport machinery is the target for these actions.
62 citations
TL;DR: Surprisingly, whereas the viral IE genes are expressed after high moi infection ofOct-1-deficient cells, the assembly of viral replication factories is severely impaired, revealing a second critical role for Oct-1 in HSV replication.
Abstract: Expression of the herpes simplex virus (HSV) immediate early (IE) genes is regulated by a multiprotein complex that is assembled on the TAATGARAT enhancer core element. The complex contains the cellular POU domain protein Oct-1, the viral transactivator VP16, and the cellular cofactor host cell factor 1. The current model suggests that the assembly depends on recognition of the core element by Oct-1. Here, HSV infection of Oct-1-deficient mouse embryonic fibroblast cells demonstrates that Oct-1 is critical for IE gene expression at low multiplicities of infection (moi). However, the protein is not essential for IE gene expression at high moi, indicating that VP16-mediated transcriptional induction through other IE regulatory elements is also important. This induction depends, at least in part, on the GA-binding protein binding elements that are present in each IE enhancer domain. Surprisingly, whereas the viral IE genes are expressed after high moi infection of Oct-1-deficient cells, the assembly of viral replication factories is severely impaired, revealing a second critical role for Oct-1 in HSV replication. The results have implications for both the HSV lytic and latency-reactivation cycles.
TL;DR: It is shown that mutation of this element, termed DICE (Downstream Immunoglobulin Control Element), reduces in vivo activity in B cells and identifies a DICE-interacting factor: a TFII-I-related protein known as BEN (also termed Mus-TRD1 and WBSCR11).
TL;DR: The lymphoid compartment of RAG-1–/– animals was reconstituted with Oct-1-deficient fetal liver hematopoietic cells and found that recipient mice develop B cells with levels of surface Ig expression comparable with wild type, although at slightly reduced numbers.
Abstract: The POU domain transcription factors Oct-1 and Oct-2 interact with the octamer element, a motif conserved within Ig promoters and enhancers, and mediate transcription from the Ig loci. Inactivation of Oct-2 by gene targeting results in normal B cell development and Ig transcription. To study the role of Oct-1 in these processes, the lymphoid compartment of RAG-1–/– animals was reconstituted with Oct-1-deficient fetal liver hematopoietic cells. Recipient mice develop B cells with levels of surface Ig expression comparable with wild type, although at slightly reduced numbers. These B cells transcribe Ig normally, respond to antigenic stimulation, undergo class switching, and use a normal repertoire of light chain variable segments. However, recipient mice show slight reductions in serum IgM and IgA. Thus, the Oct-1 protein is dispensable for B cell development and Ig transcription.
Patent•
05 Dec 2004TL;DR: In this article, the authors provide reagents such as cells, cell lines, and vectors that can be used to identify mammalian genes whose expression products (RNA or protein) play a role in RNA interference (RNAi) and/or to identify chemical modulators of RNAi, or for other purposes.
Abstract: The present invention provides reagents such as cells, cell lines, and vectors, that can be used to identify mammalian genes whose expression products (RNA or protein) play a role in RNA interference (RNAi) and/or to identify chemical modulators of RNAi, or for other purposes. The invention further provides a variety of methods for identifying such genes or modulators. In particular, the invention provides a mammalian cell comprising a nucleic acid that encodes a selectable marker and one or more nucleic acid templates for transcription of an RNAi-inducing agent integrated into the genome of the cell, wherein the RNAi-inducing agent reduces expression of the marker and is not naturally found in the cell. Additional cells and cell lines comprising nucleic acids that encode one or more additional markers are also provided. According to certain of the inventive methods cells such as these are mutagenized, transfected or infected with a library of genetic suppressor elements, or contacted with a test compound. Cells in which RNAi is inhibited or activated are identified using an appropriate selective condition or screening method. The identity of the mutated or inhibited gene or the identity of the compound is then determined.
TL;DR: It is reported, using a reaction in vitro, that transcription-dependent polyubiquitination of RNA Pol II consists of lysine-63-linked chains, which is specific forRNA Pol II engaged in active transcription and arrested by alpha-amanitin.
Abstract: Lysine-63-linked polyubiquitin chains are not thought to signal protein degradation but instead signal for a variety of cellular processes including some types of DNA repair. RNA polymerase (Pol) II is polyubiquitinated following DNA damage or upon treatment of nuclear extracts with the transcription inhibitor α-amanitin. Here, we report, using a reaction in vitro, that transcription-dependent polyubiquitination of RNA Pol II consists of lysine-63-linked chains. This modification is specific for RNA Pol II engaged in active transcription and arrested by α-amanitin.