7,057 research outputs found
The Centrality of RNA
No full textNew roles for RNAs in biology continue to emerge, and a glance at the history of RNAs may prepare molecular biologists for future discoveries about these powerful molecules. A striking new role for RNAs is their widespread involvement in the regulation of numerous genes, suggesting that there is much yet to discover about these amazing cellular components
Detained introns are a novel, widespread class of post-transcriptionally spliced introns
No full textDeep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as “detained” introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs—including those in Mdm4, a negative regulator of p53—was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.National Institutes of Health (U.S.) (Grant R01 GM34277-23)American Cancer Society (Novartis Institutes of Biomedical Research Postdoctoral Research Fellowship)National Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051
The Role of miRNAs in Regulating Gene Expression Networks
No full textMicroRNAs (miRNAs) are key regulators of gene expression. They are conserved across species, expressed across cell types, and active against a large proportion of the transcriptome. The sequence-complementary mechanism of miRNA activity exploits combinatorial diversity, a property conducive to network-wide regulation of gene expression, and functional evidence supporting this hypothesized systems-level role has steadily begun to accumulate. The emerging models are exciting and will yield deep insight into the regulatory architecture of biology. However, because of the technical challenges facing the network-based study of miRNAs, many gaps remain. Here, we review mammalian miRNAs by describing recent advances in understanding their molecular activity and network-wide function.United States. Public Health Service (grant RO1-CA133404)National Cancer Institute (U.S.) (grant PO1-CA42063)National Cancer Institute (U.S.) (Cancer Center Support (core) grant P30-CA14051
A Circuitous Route to Noncoding RNA
No full textMost genetic information is expressed as, and transacted by, proteins. Yet, less than 2% of the human genome actually codes for proteins, prompting a search for functions for the other 98% of the genome, once considered to be mostly “junk DNA.” Transcription is pervasive, however, and high-throughput sequencing has identified tens of thousands of distinct RNAs generated from the non—protein—coding portion of the genome (1). These so-called noncoding RNAs vary in length, but like protein-coding RNAs, appear to be linear molecules with 5′ and 3′ termini, reflecting the defined start and end points of RNA polymerase on the DNA template. But do all RNAs have to be linear
tRNAs Marked with CCACCA Are Targeted for Degradation
No full textAuthor Manuscript 2012 May 11The CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase] adds CCA to the 3′ ends of transfer RNAs (tRNAs), a critical step in tRNA biogenesis that generates the amino acid attachment site. We found that the CCA-adding enzyme plays a key role in tRNA quality control by selectively marking structurally unstable tRNAs and tRNA-like small RNAs for degradation. Instead of adding CCA to the 3′ ends of these transcripts, CCA-adding enzymes from all three kingdoms of life add CCACCA. In addition, hypomodified mature tRNAs are subjected to CCACCA addition as part of a rapid tRNA decay pathway in vivo. We conjecture that CCACCA addition is a universal mechanism for controlling tRNA levels and preventing errors in translation.National Institutes of Health (U.S.) (Training Grant in Cellular, Biochemical and Molecular Sciences 5T32-GM068411)National Institutes of Health (U.S.) (Grant R01-GM34277)National Institutes of Health (U.S.) (Grant R01-CA133404)National Cancer Institute (U.S.) (Cancer Center Support (core) Grant P30-CA14051
Quantifying argonaute proteins in and out of GW/P-bodies: Implications in microRNA activities
No full textMicroRNAs (miRNAs) are a class of ∼22nt non-coding RNAs that regulate the translational potential and stability of mRNAs. Though constituting only 1-4% of human genes, miRNAs are predicted to regulate more than 60% of all mRNAs. The action of miRNAs is mediated through their associations with Argonaute proteins and mRNA targets. Previous studies indicated that though the majority of Argonaute proteins is diffusely distributed in the cytoplasm, a small fraction is consistently observed to be concentrated in a cytoplasmic compartment called GW/P-bodies. In this chapter, we will provide a quantitative and dynamic view of the subcellular localization of miRNA function, followed by a discussion on the possible roles of PBs in miRNA silencing.National Institutes of Health (U.S.) (Grant R01-CA133404)National Cancer Institute (U.S.) (Grant P01-CA42063)National Cancer Institute (U.S.) (Grant P30-CA14051
MicroRNA Functions in Stress Responses
No full textMicroRNAs (miRNAs) are a class of ~22 nucleotide short noncoding RNAs that play key roles in fundamental cellular processes, including how cells respond to changes in environment or, broadly defined, stresses. Responding to stresses, cells either choose to restore or reprogram their gene expression patterns. This decision is partly mediated by miRNA functions, in particular by modulating the amount of miRNAs, the amount of mRNA targets, or the activity/mode of action of miRNA-protein complexes. In turn, these changes determine the specificity, timing, and concentration of gene products expressed upon stresses. Dysregulation of these processes contributes to chronic diseases, including cancers.National Institutes of Health (U.S.) (RO1-CA133404)National Cancer Institute (U.S.) (PO1-CA42063)National Cancer Institute (U.S.) (Cancer Center Support (core) grant P30-CA14051)Leukemia & Lymphoma Society of America (special fellow
The Life and Letters of William Sharp and "Fiona Macleod"
No full text"William Sharp (1855-1905) conducted one of the most audacious literary deceptions of his or any time. Sharp was a Scottish poet, novelist, biographer and editor who in 1893 began to write critically and commercially successful books under the name Fiona Macleod. This was far more than just a pseudonym: he corresponded as Macleod, enlisting his sister to provide the handwriting and address, and for more than a decade ""Fiona Macleod"" duped not only the general public but such literary luminaries as William Butler Yeats and, in America, E. C. Stedman.
Sharp wrote ""I feel another self within me now more than ever; it is as if I were possessed by a spirit who must speak out"". This three-volume collection brings together Sharp’s own correspondence – a fascinating trove in its own right, by a Victorian man of letters who was on intimate terms with writers including Dante Gabriel Rossetti, Walter Pater, and George Meredith – and the Fiona Macleod letters, which bring to life Sharp’s intriguing ""second self"".
With an introduction and detailed notes by William F. Halloran, this richly rewarding collection offers a wonderful insight into the literary landscape of the time, while also investigating a strange and underappreciated phenomenon of late-nineteenth-century English literature. It is essential for scholars of the period, and it is an illuminating read for anyone interested in authorship and identity.
Emerging Roles for Natural MicroRNA Sponges
No full textRecently, a non-coding RNA expressed from a human pseudogene was reported to regulate the corresponding protein-coding mRNA by acting as a decoy for microRNAs (miRNAs) that bind to common sites in the 3′ untranslated regions (UTRs). It was proposed that competing for miRNAs might be a general activity of pseudogenes. This study raises questions about the potential ability of thousands of non-coding transcripts to interact with miRNAs and influence the expression of miRNA target genes. Three years ago, artificial miRNA decoys termed ‘miRNA sponges’ were introduced as a means to create loss-of-function phenotypes for miRNA families in cell culture and in virally infected tissue and transgenic animals. Given the efficacy of miRNA sponges expressed from stable chromosomal insertions, it seemed plausible that natural non-coding RNAs might have evolved to sequence-specifically sequester miRNAs. The first such endogenous sponge RNA was discovered in plants and found to attenuate a miRNA-mediated response to an environmental stress. More recently, a viral non-coding RNA was observed to sequester and promote the degradation of a cellular miRNA in infected primate cells. In this review we discuss the potential and proven roles for endogenous miRNA sponges and consider some criteria for screening candidate sponge RNAs.National Cancer Institute (U.S.) (grant P30-CA14051)National Institutes of Health (U.S.)United States. Public Health Service (grant R01-CA133404
Pyruvate kinase M2-specific siRNA induces apoptosis and tumor regression
No full textOnline supplemental material is available at http://www.jem.org/cgi/content/full/jem.20111487/DC1.The development of cancer-specific therapeutics has been limited because most healthy cells and cancer cells depend on common pathways. Pyruvate kinase (PK) exists in M1 (PKM1) and M2 (PKM2) isoforms. PKM2, whose expression in cancer cells results in aerobic glycolysis and is suggested to bestow a selective growth advantage, is a promising target. Because many oncogenes impart a common alteration in cell metabolism, inhibition of the M2 isoform might be of broad applicability. We show that several small interfering (si) RNAs designed to target mismatches between the M2 and M1 isoforms confer specific knockdown of the former, resulting in decreased viability and increased apoptosis in multiple cancer cell lines but less so in normal fibroblasts or endothelial cells. In vivo delivery of siPKM2 additionally causes substantial tumor regression of established xenografts. Our results suggest that the inherent nucleotide-level specificity of siRNA can be harnessed to develop therapeutics that target isoform-specific exons in genes exhibiting differential splicing patterns in various cell types.MIT-Harvard Center for Cancer Nanotechnology ExcellenceNational Cancer Institute (U.S.) (Grant U54 CA151884)Marie D. and Pierre Casimir-Lambert FundNational Cancer Institute (U.S.) (Cancer Center Support (core) grant P30-CA14051
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