
	Where results make sense

Topic: Noncoding RNA

	Section on Environmental Gene Regulation
		Small, noncoding RNA genes are of interest because, although these RNAs have largely been overlooked until recently, there is accumulating evidence that many act as important regulators in the cell.
		Noncoding RNA genes generally are not annotated and are poor targets in genetic screens.
		OxyS RNA action is dependent on the Sm-like Hfq protein, which functions as a chaperone to facilitate OxyS RNA basepairing with its target mRNAs.
	dir2.nichd.nih.gov /nichd/cbmb/segr/segr.html (498 words)

	Mysterious molecules begin to yield their secrets
		There are tens of thousands of noncoding RNA molecules inside human cells, and even if only one percent is functional, that's still hundreds of molecules that may be participating in the control of cellular functions.
		Noncoding RNA has long been regarded as something of a stranger in the protein encoding land of RNA.
		One of the stunning conclusions of these reports is that the amount of noncoding RNA that is being expressed in cells is vast.
	www.eurekalert.org /pub_releases/2005-09/sri-mmb082905.php (1075 words)

	MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung ...
		MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer.
		The novel MALAT-1 transcript is a noncoding RNA of more than 8000 nt expressed from chromosome 11q13.
		Gottesfeld JM, and Barbas CF III, "RNA as a Transcriptional Activator".
	www.euchromatin.net /JiP01.htm (442 words)

	[Genome] reply: rnaGene table in process for Aug 6,2001 freeze?
		Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.
		Based on these observations, we developed a scanning algorithm for detecting noncoding RNA genes in genome sequences, using a fully probabilistic version of the Zuker minimum-energy folding algorithm.
		We conclude that although a distinct, stable secondary structure is undoubtedly important in most noncoding RNAs, the stability of most noncoding RNA secondary structures is not sufficiently different from the predicted stability of a random sequence to be useful as a general genefinding approach.
	www.cse.ucsc.edu /pipermail/genome/2002-January/000854.html (763 words)

	Requirement for a Noncoding RNA in Drosophila Polar Granules for Germ Cell Establishment.
		For example, nanos (nos) RNA localized in pole plasm is required for abdomen formation and for correct pole cell migration into the embryonic gonads, but not for pole cell formation per se (8).
		Pgc RNA is first detectable in germarium region 2B of ovaries when it is localized in the oocyte, and it continues to be concentrated at the posterior of the oocyte until stage 7 (Fig.
		A group of untranslatable RNAs, called Xlsirts, are localized in Xenopusgerm plasm and are required for anchoring of Vg1 RNA to the vegetal cortex of the oocyte (22).
	www.euchromatin.org /Nakamura1.htm (4108 words)

	Eddy lab :: Software (Site not responding. Last check: 2007-10-10)
		The algorithm is discussed in the paper "A dynamic programming algorithm for RNA structure prediction using pseudoknots".
		This is the code from Elena Rivas that accompanies the paper "Noncoding RNA gene detection using comparative sequence analysis".
		This is the code from Elena Rivas that goes with the paper "Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs" by Elena Rivas and Sean Eddy.
	selab.wustl.edu /cgi-bin/selab.pl?mode=software (836 words)

	Noncoding regulatory RNAs database -- Szymanski et al. 31 (1): 429 -- Nucleic Acids Research (Site not responding. Last check: 2007-10-10)
		In mammals, SRA RNA was identified as a coactivator of
		Thenie,A.C., Gicquel,I.M., Hardy,S., Ferran,H., Fergelot,P., Le Gall,J.-Y. and Mosser,J. (2001) Identification of an endogenous RNA transcribed from the antisense strand of the HFE gene.
		Klein,R.J., Misulovin,Z. and Eddy,S.R. (2002) Noncoding RNA genes identified in AT-rich hyperthermophiles.
	nar.oxfordjournals.org /cgi/content/full/31/1/429 (1874 words)

	MicroRNAs in Cancer (Site not responding. Last check: 2007-10-10)
		A fundamental effort of both cancer biology and developmental biology is to determine the genes and cellular mechanisms that establish and maintain the identity of a cell.
		The His-1 gene is expressed as a 3-kb spliced and polyadenylated RNA that is believed to function as a ncRNA.43 Although the precise function of the His-1 gene is unknown, its transcriptional activation in a series of mouse leukemias has implicated the His-1 RNA in leukemogenesis when it is abnormally expressed.
		In the other case, expression of the noncoding RNA or miRNA (bic and His-1 RNAs) is inappropriately up-regulated, commensurate with oncogenesis, leading to the idea that these miRNAs be acknowledged as oncogenes.
	web.mit.edu /mmcmanus/www/home1.2files/miRNAs_in_Cancer.html (3561 words)

	Functional Redundancy Within roX1, a Noncoding RNA Involved in Dosage Compensation in Drosophila melanogaster -- ... (Site not responding. Last check: 2007-10-10)
		NONCODING RNAs are postulated to regulate gene expression in
		Also shown are the endpoints of each deletion (see Fig 2), number of independent insertions analyzed, and the actual number of males and females counted to calculate the rescue frequency for the insertion with the highest rescue.
		RNA in situ hybridization to transgenic polytene chromosomes.
	www.genetics.org /cgi/content/full/164/3/1003 (4886 words)

	Biology International
		A noncoding gene of Drosophila melanogaster being actively studied in the Cytogenetics Laboratory of Banaras Hindu University is the 93D or the hsrw gene.
		Like several other noncoding genes, the base sequence of the unique as well as the tandem repeat region of the hsrw gene is not conserved in different species.
		The purpose of the act of translation of the short ORF in hsrw-c RNA seems to be to monitor the efficiency of cellular translational machinery.
	www.iubs.org /test/bioint/45/5.htm (1503 words)

	C. elegans noncoding RNA genes
		SRP RNA is a component of the signal recognition particle, involved in translocation of nascent proteins across the endoplasmic reticulum.
		However, this enigmatic transcript seems unlikely to be the true telomerase RNA, as cDNA sequencing has shown that the putative telomeric template region is not part of the major tts-1 transcript (SL Stricklin and SR Eddy, unpublished).
		It must be noted that it is not currently possible to systematically identify novel noncoding RNA genes that have no homology to known genes.
	www.wormbook.org /chapters/www_noncodingRNA/noncodingRNA.html (3098 words)

	[No title] (Site not responding. Last check: 2007-10-10)
		RNA 2005 will comprise oral and poster presentations covering the entire field of RNA including its structure, chemistry and biology.
		The overall mission of the RNA Society is to facilitate sharing and dissemination of experimental results and emerging concepts in RNA research.
		The RNA Society/Scaringe Award is made to the student author(s) of the best paper, as selected by the editors, published during the previous year in RNA.
	www.rnasociety.org /rnameeting (1491 words)

	Sean Eddy (Site not responding. Last check: 2007-10-10)
		A few of these noncoding RNA (ncRNA) genes may be molecular fossils of a primordial "RNA world" that preceded protein/DNA-based organisms.
		Most RNA genes appear to be more recent evolutionary innovations.
		Noncoding RNA genes and the modern RNA world.
	dbbs.wustl.edu /DBBS/website.nsf/rib/eddys (293 words)

	Newswise
		A team of investigators at The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation have discovered a way to screen hundreds and potentially thousands of "noncoding" RNA molecules to discover their functions within cells.
		Newswise — A team of investigators at The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation (GNF) have discovered a way to screen hundreds and potentially thousands of "noncoding" RNA molecules to discover their functions within cells.
		Then, the scientists established screens using a technique called RNA interference to "knock down"--or silence--the noncoding RNA within cells.
	www.newswise.com /articles/view/514101 (1110 words)

	Development (Site not responding. Last check: 2007-10-10)
		Mouse G90 gene transcript was identified as a 1.5 kb polyadenylated RNA species that is expressed at very high levels in the small intestine and at lower levels in large intestine, testis and kidney.
		An endogenous antisense Msx1-AS RNA was shown to be produceed in differentiated dental and bone cells in mice, rats, and humans.
		It is polyadenylated and transcribed by RNA transcribed by polymerase II.
	biobases.ibch.poznan.pl /ncRNA/development.html (1035 words)

	CiteULike: Noncoding RNA gene detection using comparative sequence analysis. (Site not responding. Last check: 2007-10-10)
		Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes.
		We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution.
		Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability.
	www.citeulike.org /user/marcius/article/118802 (276 words)

	The four Rs of RNA-directed evolution.
		These numbers support an RNA-centric view of evolution in which phenotypic diversity arises through extensive RNA processing and widespread RNA-directed rewriting of DNA enables dissemination of 'selfish' RNAs associated with successful outcomes [9].
		Brosius J., The contribution of RNAs and retroposition to evolutionary novelties.
		Brosius J, "Gene duplication and other evolutionary strategies: from the RNA world to the future", Journal of Structural and Functional Genomics, vol.
	www.euchromatin.org /Herbert01.htm (378 words)

	AAAS \| Science's STKE \| Focus Issue (Site not responding. Last check: 2007-10-10)
		These short, double-stranded RNA (dsRNA) fragments complement the sequence of the silenced gene and the precise mechanisms of RNA silencing are being rapidly revealed in protozoa, plants, fungi, and animals, as described by Zamore.
		A rationale for differential trafficking of mRNA in neurons is explained by Kosik and Krichevsky, in which a dynamic structure called an RNA granule delivers its cargo of specific mRNAs to regions critical for maintaining plasticity.
		Moreover, Plasterk mentions that host cells may protect their genomes from viral invasion and from transposon movement by RNA silencing mechanisms that are triggered by such dsRNA.
	stke.sciencemag.org /misc/focus.dtl (1142 words)

	A uniform system for microRNA annotation -- AMBROS et al. 9 (3): 277 -- RNA (Site not responding. Last check: 2007-10-10)
		RNA, August 1, 2005; 11(8): 1245 - 1257.
		RNA, November 18, 2004; 10(11): 1813 - 1819.
		RNA, February 1, 2004; 10(2): 185 - 191.
	www.rnajournal.org /cgi/content/full/9/3/277 (2967 words)

	RNAdb--a comprehensive mammalian noncoding RNA database -- Pang et al. 33 (Supplement 1): D125 -- Nucleic Acids Research (Site not responding. Last check: 2007-10-10)
		RNA (ncRNAs) sequences are abundant in the genomes of the eukaryotes,
		Tam,W. ((2001)) Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA.
		Nemes,J.P., Benzow,K.A., Moseley,M.L., Ranum,L.P. and Koob,M.D. ((2000)) The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1).
	nar.oxfordjournals.org /cgi/content/full/33/suppl_1/D125 (3249 words)

	Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear ... (Site not responding. Last check: 2007-10-10)
		The pairs consisting of coding and noncoding genes are shown in A and C (x-axis, noncoding gene; y-axis, coding gene), whereas the pairs consisting of both coding genes are shown in B and D.
		Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis.
		When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red.
	www.genome.org /cgi/content/full/15/4/463 (5239 words)

	The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli -- Lease et al. 186 (18): 6179 -- The ... (Site not responding. Last check: 2007-10-10)
		The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli -- Lease et al.
		RNA was extracted from cells with a vector plasmid (lanes v), a DsrA-overproducing plasmid (lanes D), or a plasmid overproducing inactive mutant DsrA (lanes M).
		The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli.
	jb.asm.org /cgi/content/full/186/18/6179 (3941 words)

	Welcome to RNAdb
		These sequences are often referred to as "junk DNA" but many of them are in fact expressed as noncoding RNAs (ncRNAs), and may account for around 98% of all genomic output in humans.
		The database also includes over 1200 putative antisense ncRNAs and almost 20,000 putative noncoding RNAs identified in high quality murine and human cDNA libraries, with more to be added in the near future.
		The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina
	research.imb.uq.edu.au /rnadb (437 words)

	Inhibition of Cell Growth and Shoot Development by a Specific Nucleotide Sequence in a Noncoding Viroid RNA -- Qi and ... (Site not responding. Last check: 2007-10-10)
		RNA gel blot analysis, using total RNA from mock-inoculated and PSTVd-infected tomato plants and protoplasts, was performed with
		Each RNA sample was prepared from a pool of equivalent systemic leaves collected from six infected plants at 1-week intervals for up to 6 weeks.
		Rodríguez-Cerezo, E., Klein, P.G., and Shaw, J.G. A determinant of disease symptom severity is located in the 3'-terminal noncoding region of the RNA of a plant virus.
	www.plantcell.org /cgi/content/full/15/6/1360 (6565 words)

	Identification and analysis of the minimal promoter activity of a novel noncoding nuclear RNA gene, AncR-1, from the ...
		Total RNAs extracted from the head (H), thorax (T), and abdomen (A) of each type of adult bee were subjected to Northern blot analysis using AncR-1-specific probes.
		organisms, as prediction of noncoding RNA genes from the genomic
		Kelley, R.L. and Kuroda, M.I. Noncoding RNA genes in dosage compensation and imprinting.
	www.rnajournal.org /cgi/content/full/10/7/1047 (7051 words)

	Noncoding RNA danger motifs bridge innate and adaptive immunity and are potent adjuvants for vaccination -- Wang et al. ... (Site not responding. Last check: 2007-10-10)
		Noncoding RNA danger motifs bridge innate and adaptive immunity and are potent adjuvants for vaccination -- Wang et al.
		Noncoding RNA danger motifs bridge innate and adaptive immunity and are potent adjuvants for vaccination
		Alexopoulou, L., Holt, A.C., Medzhitov, R., and Flavell, R.A. Recognition of double-stranded RNA and activation of NF-kappaB by Toll-like receptor 3.
	www.jci.org /cgi/content/full/110/8/1175 (6247 words)

	PNA interference mapping demonstrates functional domains in the noncoding RNA Xist -- Beletskii et al. 98 (16): 9215 -- ... (Site not responding. Last check: 2007-10-10)
		The noncoding RNA Xist has been shown to be essential for X-chromosome inactivation and to coat the inactive X-chromosome
		To perform the TaqMan assay, total RNA was isolated by using Tri-Reagent (Sigma) according to the manufacturer's instructions.
		Two lines of evidence support the conclusion that PNA activity is caused by the interference with a particular RNA structure.
	www.pnas.org /cgi/content/full/98/16/9215 (3541 words)

	Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection -- Numata et al. 13 (6): ... (Site not responding. Last check: 2007-10-10)
		Noncoding RNA (ncRNA) is a global term for transcripts that
		Pelczar, P. and Filipowicz, W. The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5'-terminal oligopyrimidine gene family.
		Tam, W. Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA.
	www.genome.org /cgi/content/full/13/6b/1301 (3719 words)

	The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina (Site not responding. Last check: 2007-10-10)
		Background: With the advent of genome-wide analyses, it is becoming evident that a large number of noncoding RNAs (ncRNAs) are expressed in vertebrates.
		Taurine Upregulated Gene 1 (TUG1) is a spliced, polyadenylated RNA that does not encode any open reading frame greater than 82 amino acids in its full-length, 6.7 kilobase (kb) RNA sequence.
		In the newborn retina, knockdown of TUG1 with RNA interference (RNAi) resulted in malformed or nonexistent outer segments of transfected photoreceptors.
	research.imb.uq.edu.au /rnadb/Articles/339.aspx (370 words)

	RNA - Induced Epigenetics
		This can achieved by the RNA product of one gene influencing the expression of another gene, or by the protein product of one gene influencing the expression of another gene.
		The ability of small noncoding RNA molecules to induce epigenetic changes such as methylation of specific DNA, activation or hydrolysis of specific RNA, and/or accumulation or destruction of specific proteins, provides the current model of riboregulation.
		Sleutels F, Zwart R, and Barlow DP, "The Noncoding Air RNA is Required for Silencing Autosomal Imprinted Genes", Nature 415: 820 (2002).
	www.euchromatin.com /RNAepi.htm (540 words)

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