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Topic: Noncoding

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	Noncoding DNA -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-26)
		an organism with `good' or membrane-bound nuclei in its cells) eukaryotes, a large percentage of many organism's (The ordering of genes in a haploid set of chromosomes of a particular organism; the full DNA sequence of an organism) genomes are noncoding.
		Some noncoding DNA is involved in (The act of controlling or directing according to rule) regulating the activity of coding regions.
		An (The act of conducting a controlled test or investigation) experiment concerning the relationship between (Sequence of a eukaryotic gene's DNA that is not translated into a protein) introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA.
	www.absoluteastronomy.com /encyclopedia/n/no/noncoding_dna2.htm (280 words)

	Benchmarking Tools for the Alignment of Functional Noncoding DNA - Methods
		Noncoding sequence evolution was simulated using a modified version of the sequence simulation program ROSE [14].
		To model the evolution of constrained blocks in noncoding sequences a modification of the ROSE sequence simulation program was developed to map constraints on ancestral sequences onto derived sequences (available for download as ROSE version 1.3 from [21]).
		Constraints on noncoding sequences were modelled as short blocks of highly conserved sequences typical of cis-regulatory sequences, and follow a lognormal distribution with parameters estimated in [4].
	rana.lbl.gov /AlignmentBenchmarking/methods.html (2783 words)

	BioMed Central \| Full text \| Benchmarking tools for the alignment of functional noncoding DNA
		Noncoding sequence evolution was simulated using a modified version of the sequence simulation program ROSE [9].
		To model the evolution of constrained blocks in noncoding sequences a modification of the ROSE sequence simulation program was developed to map constraints on ancestral sequences onto derived sequences (available for download as ROSE version 1.3 from [58]).
		Constraints on noncoding sequences were modelled as short blocks of highly conserved sequences typical of cis-regulatory sequences, and follow a lognormal distribution with parameters estimated in [25].
	www.biomedcentral.com /1471-2105/5/6 (7536 words)

	Comparative analysis of noncoding sequences of orthologous bovine and human gene pairs
		Noncoding sequences that showed conservation between human and bovine were analyzed in multispecies comparisons, using the mouse as the third organism.
		The 49 human and bovine noncoding sequences in which conservation was detected were submitted to multiple alignment analysis with the corresponding orthologous mouse sequences, using the Avid algorithm.
		Assuming that noncoding sequences that have remained similar during evolution might play roles in gene regulation, the high levels of conservation identified in the assessed sequences may infer functional elements.
	funpecrp.com.br /GMR/year2004/vol4-3/icob0002_full_text.htm (2575 words)

	Literature Review: Functional noncoding conserved sequences
		Evidence for functional noncoding conserved sequences among different mammals suggests these are not "junk DNA".
		Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.
		Multispecies DNA comparison has been proposed as a method to prioritize these conserved noncoding sequences for functional analysis based on the hypothesis that elements present in many species are more likely to be functional than elements present in limited numbers of species.
	www.iscid.org /boards/ubb-get_topic-f-18-t-000042.html (335 words)

	Lack of biological significance in the 'linguistic features' of noncoding DNA--a quantitative analysis -- ...
		As a result of these investigations, it was claimed (2) that, in clear contrast with protein coding DNA segments, the noncoding DNA parts are related with a considerable amount of redundancy.
		The overall behaviour of this graph is identical to that of a typical (mostly) noncoding sequence, which is also reflected in the values of the chi square test: 0.042 with the mean of highly coding sequences.
		This proves that the claimed difference (2) between coding and noncoding DNA sequences is not universal.
	nar.oxfordjournals.org /cgi/content/full/24/9/1676 (4399 words)

	TSRI - News & Views
		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.
		Scientists have speculated as to what these noncoding RNAs are doing based on computational approaches and analyses of the sequences, but nobody has come up with a way of experimentally determining whether the noncoding RNAs have a cellular function.
	www.scripps.edu /newsandviews/e_20050912/rna.html (876 words)

	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.
		Noncoding RNAs also are often missed by biochemical approaches.
	eclipse.nichd.nih.gov /nichd/cbmb/segr/segr.html (498 words)

	Molecular evolution of the atpB-rbcL noncoding spacer of chloroplast DNA in the moss family Hylocomiaceae
		Molecular evolution of the chloroplast noncoding region between the atpB and rbcL genes was investigated in the moss family Hylocomiaceae.
		Of 671 positions of the aligned sequences of the noncoding spacer, 289 are variable (43.1%); 226 substitutions occur in only a single taxon (autapomorphies); and 67 bases (10.0% of total) are informative for phylogenetic reconstruction.
		Evolution of a noncoding region of the chloroplast genome.
	ejournal.sinica.edu.tw /bbas/content/2000/2/bot12-01.html (4312 words)

	Frequent Mutation of the 5' Noncoding Region of the BCL-6 Gene in Acquired Immunodeficiency Syndrome-Related ...
		Mutations in the 5' noncoding sequences of BCL-6 in all AIDS-NHL subtypes.
		Nucleotide sequencing analyses of mutations of the 5' noncoding regions of BCL-6 in AIDS-NHL.
		Comparative analysis of the distribution of mutations of the 5' noncoding regions of BCL-6 with that of EBV infection and p53 mutations defined that BCL-6 mutations may occur both in the presence and in the absence of such genetic lesions (Table 4).
	www.bloodjournal.org /cgi/content/full/89/10/3755 (6083 words)

	News & Features: Functional constraints and frequency of deleterious mutations in noncoding DNA of ...
		Here, we infer the frequency of deleterious mutations in noncoding DNA of rodents by comparing rates of substitution at noncoding nucleotides with rates of substitution at the fastest evolving intronic sites of adjacent genes sampled from the whole genome sequences of mouse and rat.
		We show that the major elements of selectively constrained noncoding DNA are within 2,500 bp upstream and downstream of coding sequences and in first introns.
		Deleterious mutations in noncoding DNA have predominantly quantitative effects and could be an important source of the burden of complex genetic disease variation in human populations.
	www.iscid.org /boards/ubb-get_topic-f-1-t-000131.html (333 words)

	1
		The primary thrust of this study was to examine catarrhine phylogeny using the newly acquired noncoding DNA sequence data, that from introns 3 and 4 of the serum albumin gene.
		They indicate that noncoding DNA accumulated change at a slower rate in the cheek-pouched than in the leaf-eating cercopithecids and at a slower rate yet in hominids.
		As shown in Table 5, the rate of accumulation of noncoding nucleotide substitutions was significantly greater in the early primates in the lineage to the LCA of platyrrhines and catarrhines (63-40 Ma) than from this LCA to the living anthropoids.
	www.uchicago.edu /aff/mwc-amacad/biocomplexity/MPE2001.html (5525 words)

	JGI - Deletion of Noncoding DNA
		Various stretches of noncoding DNA have been shown to function as enhancers of gene expression, causing more of this protein or that to be produced.
		Mice with the noncoding sequences removed were essentially indistinguishable from wild-type mice, even though the deleted sequences contained many sections that are conserved between mice and humans.
		This result suggests that some noncoding sequences, even those that persist through the pressures of evolution, may indeed be disposable.
	www.jgi.doe.gov /science/highlights/nobrega1004.html (685 words)

	John Hawks Anthropology Weblog : The "dark matter" of the cell
		This short introductory article gives a good introduction to why this is important stuff, and extends the story beyond miRNA to other kinds of noncoding RNA (ncRNA) sequences and their possible functionality.
		It is also clear that the majority of the genomes of animals is indeed transcribed (12), which suggests that these genomes are either replete with largely useless transcription or that these noncoding RNA sequences are fulfilling a wide range of unexpected functions in eukaryotic biology.
		It is thus likely that sequences of noncoding transcripts have been accumulating in EST databases and have for the most part (including singleton and antisense ESTs) been erroneously interpreted as coming from the 3'-untranslated regions of protein-coding transcripts.
	johnhawks.net /weblog/reviews/genomics/evo-devo/science_special_rna_issue_2005.html (1371 words)

	MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung ... (Site not responding. Last check: 2007-10-26)
		MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer.
		MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer.The genes' association with metastasis was stage- and histology specific.
		The novel MALAT-1 transcript is a noncoding RNA of more than 8000 nt expressed from chromosome 11q13.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/9995230.html (235 words)

	Chromosomal Organization of Genes and Noncoding DNA
		The abundance of noncoding sequences in the genomes of higher organisms is illustrated in Figure 9-3, which depicts the protein-coding regions in an 80-kb stretch of DNA from the yeast S.
		Because no function has yet been found for most of the noncoding DNA in higher eukaryotes, it is commonly referred to as nonfunctional.
		However, the vast majority of single-copy DNA in the mammalian genome is noncoding DNA between genes and in introns.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?tool=bookshelf&call=bv.View..ShowSection&searchterm=satellite&rid=mcb.section.2160 (3052 words)

	Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences -- ... (Site not responding. Last check: 2007-10-26)
		As the distributions of intergenic and intronic noncoding block lengths do not differ significantly, they are plotted together.
		Jareborg, N., Birney, E., and Durbin, R. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
		Saitou, N. and Ueda, S. Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates.
	www.genome.org /cgi/content/full/11/8/1335 (6754 words)

	Nat' Academies Press, Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson (1995)
		Most of this noncoding DNA is found in very short segments separating functional genes.
		The most widely studied noncoding region of the chloroplast genome is the region downstream of the rbcL gene in the grass family (Poaceae).
		This noncoding sequence is flanked by the genes rbcL and psaI (the gene encoding photosystem I polypeptide I) and is 1694 bases long in the rice genome, making it one of the longest noncoding regions of the genome and the longest when introns are excluded (Figure 1).
	www.nap.edu /openbook.php?record_id=4910&page=217 (812 words)

	[No title]
		Some research has been done in the past with taking out noncoding portions of the genome in mice, which led to mice that were the same as their unaltered bretheren.
		The noncoding regions, it seems, are strongly affected by evolutionary pressures, but not in the way that geneticists might expect.
		Peter Andolfatto, assistant professor of biology, showed that the large portions of noncoding DNA are evolving more slowly than expected due to evolutionary pressures on the noncoding portions to remain the same.
	arstechnica.com /journals/science.ars/2005/10/31/1682 (2067 words)

	noncodingDNA.com - home
		This part of the genome is generally referred to as noncoding DNA, but has also been labeled junk DNA.
		A recent paper - the reason for the design of this site - suggests that the amount of noncoding DNA (or junk DNA) per genome is a more accurate indicator of biological complexity than either gene number or genome size.
		To help decipher the role of noncoding DNA this website will facilitate the dissemination of data related to the ideas of functional or functionless noncoding DNA, and serve as a hub for information about the latest in noncoding news and research.
	www.noncodingdna.com (374 words)

	CiteULike: Noncoding RNA gene detection using comparative sequence analysis. (Site not responding. Last check: 2007-10-26)
		Noncoding RNA gene detection using comparative sequence analysis.
		Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes.
		Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability.
	www.citeulike.org /user/marcius/article/118802 (276 words)

	Spatial Organization of Active and Inactive Genes and Noncoding DNA within Chromosome Territories.
		In one report, three coding regions of the human genome were all located in the periphery of their respective chromosome territories independent of transcriptional status, whereas a noncoding sequence was not (Kurz et al., 1996).
		However, although we have found that a ubiquitously expressed gene is indeed located at the surface of, or outside of, such subdomains and although adjacent noncoding DNA is located within the compact subdomain, we find no clear correlation between chromosome territory subdomains and the expression of tissue-restricted genes.
		Within the context of the ICD compartment model of nuclear organization (Cremer and Cremer, 2001), an extreme interpretation of these data is that most or all genes lie on the periphery of chromosome territories and that the territory interior is filled with intergenic sequence (Zirbel et al., 1993; Kurz et al., 1996).
	www.euchromatin.net /Mahy01.htm (3707 words)

	BioMed Central \| Full text \| A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic ...
		Taken together with the low proportion of intergenic sequences that we detected, our results suggest that much of the recently-discovered expanded transcriptome [4-7,9,10] may correspond to cryptic transcripts [13], suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements.
		QRNA v.1.1 [14] was used to score the alignments for noncoding RNA potential using settings determined to work optimally on a test set of ncRNAs embedded in random alignments of equivalent sequence identity (default settings with -w 100 -x 50).
		The same analysis was repeated using 390 (151 mapped to human surveyed regions) mouse annotated miRNAs, snoRNAs, snRNAs, and tRNAs downloaded from NONCODE [47] and Rfam [48] databases, and 716 human ribosomal protein exons (260 mapped to human surveyed regions) annotated in the Refseq database [18].
	www.biomedcentral.com /1471-2164/6/104 (5475 words)

	MicroRNAs in Cancer (Site not responding. Last check: 2007-10-26)
		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.
		Even further complicating the task is the fact that mutations may occur in coding genes, noncoding genes, and regulatory sequences.
		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)

	Somatic Mutation of the 5' Noncoding Region of the BCL-6 Gene Is Associated with Intraclonal Diversity and Clonal ...
		Somatic Mutation of the 5' Noncoding Region of the BCL-6 Gene Is Associated with Intraclonal Diversity and Clonal Selection in Histological Transformation of Follicular Lymphoma -- Szereday et al.
		Schematic representation of the BCL-6 5' noncoding region diversification and sequence intraclonal heterogeneity in FL (A) and transformed DLCL (B) samples.
		that genetic diversity of the 5' noncoding sequences of the
	ajp.amjpathol.org /cgi/content/full/156/3/1017 (4189 words)

	Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional ...
		Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance -- Johnson et al.
		Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance
		in the remainder of the noncoding sequences, and appear to be
	www.genome.org /cgi/content/full/14/12/2448 (4968 words)

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