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Topic: Noncoding DNA

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DNA replication

DNA sequences

mitochondrial DNA

DNA DNA hybridisation

DNA polymerases

DNA testing

junk DNA

DNA analysis

DNA motif

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Noncoding DNA

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	Benchmarking Tools for the Alignment of Functional Noncoding DNA - Methods (Site not responding. Last check: 2007-10-16)
		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)

	Noncoding DNA - Wikipedia, the free encyclopedia
		In eukaryotes, a large percentage of many organisms' total genome sizes are comprised of noncoding DNA (a puzzle known as the "C-value enigma").
		Some noncoding DNA is involved in regulating the activity of coding regions.
		This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns.
	en.wikipedia.org /wiki/Noncoding_DNA (229 words)

	What are genes?
		DNA is a vast chemical information database that carries the complete set of instructions for making all the proteins a cell will ever need.
		DNA resides in the core, or nucleus, of each of the body's trillions of cells.
		The DNA in each chromosome constitutes many genes (as well as vast stretches of noncoding DNA, the function of which is unknown).
	www.accessexcellence.org /AE/AEPC/NIH/gene03.html (419 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.
		DNA sequencing and identification of exons has revealed that in higher organisms there is a considerable amount of DNA that does not encode protein.
		Simple-sequence DNA located at centromeres is suspected to contribute to the structure and therefore the function of the kinetochore of metaphase chromosomes.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?tool=bookshelf&call=bv.View..ShowSection&searchterm=satellite&rid=mcb.section.2160 (3052 words)

	Noncoding DNA found to be important - Featured Research - Research - Children's Hospital Boston
		Noncoding DNA found to be important - Featured Research - Research - Children's Hospital Boston
		The rest, known as conserved noncoding sequences (CNCs), is of growing interest to scientists: there's growing suspicion that these areas aren't just filler, but contain functional bits of genetic sequence whose variation may contribute to human disease.
		Seeking to prove this suspicion, researchers led by Joel Hirschhorn, MD, PhD, of Children's Divisions of Genetics and Endocrinology and Program in Genomics, and also an associate member of the Broad Institute, combined a list of CNCs with two large databases: the recently released HapMap database and the chimpanzee genome sequence.
	www.childrenshospital.org /research/Site2029/mainpageS2029P27sublevel28.html (308 words)

	The Functions of Introns: From Junk DNA to Designed DNA
		Consensus sequences are DNA segments that use similar base sequences in different genes within a single gene family or across many different species for one specific function.
		Other noncoding portions also have an impact on the organism's function, and it is possible that the introns have a role in reducing or correcting these mutations.
		If functions for most or all of the noncoding DNA is found, Darwinism would be without the raw material needed to produce new genes by mutations that can be selected for evolution to occur.
	www.rae.org /introns.html (6033 words)

	BioMed Central \| Full text \| Benchmarking tools for the alignment of functional noncoding DNA (Site not responding. Last check: 2007-10-16)
		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 (7599 words)

	Comparative Genomics: Linking Noncoding DNA to Biology and Disease
		Thus, sequence variations in these noncoding DNA elements are likely to impact a broad range of biological processes and be responsible for phenotypical differences among humans, including the predisposition to diseases.
		The in silico identification of these discrete noncoding DNA sequences buried in the human genome, the experimental characterization of their functional properties, and their roles in disease processes were greatly facilitated by our ability to compare genomes from various species, and will be the main focus of this symposium.
		Topics include the presentation of bioinformatics tools designed to identify functional noncoding DNA elements in the human genome, both from the premise that several of these elements are shared with other species and have been conserved throughout evolution and also that other elements are likely to be unique to primates and/or humans.
	www.the-aps.org /meetings/eb07/abs/pg-nobrega.htm (324 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)

	Lack of biological significance in the 'linguistic features' of noncoding DNA--a quantitative analysis -- ...
		With the aid of computer simulations of natural DNA sequences, and by applying the same `linguistic' tests to both natural and artificial sequences, we investigate in detail the reasons of the appearance of the claimed `linguistic' features and the associated differences between coding and noncoding DNAs.
		It was claimed (2) that: (i) in a double-logarithmic plot, the graphs of the aforementioned relation for different DNA sequences are linear, which implies that Zipf's law applies to the present case, and (ii) the slopes of these graphs for coding and noncoding DNAs differ significantly.
		This finding indicates that the natural patchiness of DNA (11, 12) may also contribute to the appearance of different mean Zipf slopes for coding and noncoding DNAs.
	nar.oxfordjournals.org /cgi/content/full/24/9/1676 (4383 words)

	The Scientist : Regulatory DNAs may be missed
		Vast numbers of noncoding regulatory sequences may lurk in nonconserved DNA that are not detected by techniques typically used to identify these sequences, suggests research appearing online this week in Science.
		Current methods that identify functional noncoding DNA focus on comparing genomes to find conserved sequences, on the assumption that conservation over great evolutionary distances indicates selective pressure to preserve critical mechanisms.
		The researchers discovered that even though noncoding regions apparently are not conserved between the human developmental gene RET and its zebrafish counterpart ret, nearly all of the human noncoding regulatory sequences discovered at RET could also function when introduced into zebrafish.
	www.the-scientist.com /news/display/23246 (650 words)

	VISTA gives a wide view of genomic comparisons
		One way to discover them in noncoding DNA (few call it "junk" anymore) is by searching conserved areas, sequences that have persisted for millions or hundreds of millions of years of evolution.
		If a given DNA sequence is substantially similar in both mouse and human, for example, that sequence has persisted since the common ancestor of mice and humans, some 80 to 100 million years.
		Although noncoding regions in two species could be similar by accident, similarity in three or more species means they have been conserved in evolution.
	enews.lbl.gov /Science-Articles/Archive/NERSC-VISTA-Dubchak.html (1040 words)

	Junk DNA - EvoWiki
		Virtually all of this variation is in noncoding sequences, such as the noncoding repetitive elements that make up a large percentage of mammalian genomes.
		According to the skeletal DNA hypothesis, then, more noncoding DNA is necessary for larger cells -- perhaps by more widely spacing the protein and RNA-coding genes, transcription can occur more rapidly, allowing the production of more proteins necessary for the larger cell.
		Regulatory elements are stretches of DNA associated with genes that assist the molecular machinery of gene expression in determining which genes, and which exons within those genes, should be expressed.
	wiki.cotch.net /index.php/Junk_DNA (1907 words)

	Untitled Document
		Introns (noncoding regions) may have always been an integral part of the most primitive of genes from ancestral single-cell organisms that first formed on earth.
		Having a single gene code for several variants of a protein is an efficient use of DNA and may have hastened the evolution of new and potentially useful proteins.
		Noncoding regions of DNA are not thought to be the result of mutation and have no direct effect on transcription or protein synthesis.
	avconline.avc.edu /faculty/slangjahr/Phys2.html (698 words)

	Sandwalk: Junk DNA: Scientific American Gets It Wrong (again)
		First, nobody today would argue that all noncoding DNA is junk and I very much doubt that Ohno made that argument in 1972 (the orignal paper is hard to get).
		Makalowski has a particular bee in his bonnet over repetitive DNA but that shouldn't be allowed to warp his judgement when responding to a question in Scientific American.
		The occasional piece of junk DNA may be co-opted to become part of a newly evolved function.
	sandwalk.blogspot.com /2007/02/junk-dna-scientific-american-gets-it.html (1818 words)

	The Functions of Introns
		The redundancy theory suggests that most genes were once noncoding DNA and/or nonsense genes that produced nonfunctional protein which was either useless and rapidly recycled or caused harm to the cell.
		The most specific of the functional theories is the skeletal DNA hypothesis, which states that the mass of DNA (in conjunction with its folding pattern) directly determines the nuclear volume.
		In the past, evolutionary geneticists, once uncertain as to what this apparently superfluous DNA does, referred to introns and other noncoding DNA as "junk." Evidence is now being accumulated which indicates that much or most of this DNA may not be junk, but critical for life itself.
	www.asa3.org /ASA/PSCF/2001/PSCF9-01Bergman.html (5699 words)

	1
		In contrast, the DNA evidence and recent morphological evidence (Fleagle and McGrew, 1999) groups the arboreal mangabeys with the baboons and groups the drills and mandrills with the terrestrial mangabeys.
		DNA sequence data were generated for introns 3 and 4 of the serum albumin gene via the Polymerase Chain Reaction (PCR).
		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)

	Human Genome Project Science
		The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C. In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes.
		Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between.
		Additionally, finding the DNA sequences underlying such common diseases as cardiovascular disease, diabetes, arthritis, and cancers is being aided by the human variation maps (SNPs) generated in the HGP in cooperation with the private sector.
	www.ornl.gov /sci/techresources/Human_Genome/project/info.shtml (1855 words)

	Spatial Organization of Active and Inactive Genes and Noncoding DNA within Chromosome Territories.
		To clarify the relationship between the organization of chromosome territories and gene expression, we have used fluorescence in situ hybridization to analyze the spatial organization of a contiguous 1 Mb stretch of the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation syndrome region of the human genome and the syntenic region in the mouse.
		However, with the exception of the Xi, both early and late replicating DNA that are usually equated with gene-rich and gene-poor domains, respectively, appear to be distributed throughout chromosome territories (Visser et al., 1998).
		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)

	Johns Hopkins Gazette \| March 27, 2006
		Unlike DNA sequences that code for protein, noncoding DNA, sometimes referred to as "junk" DNA, follows few rules for organization and sequence patterns and therefore is more difficult to study.
		Traditionally, DNA sequences are thought to have to look similar to function similarly; this is how scientists identify genes in other species, a strategy best used for studying similar species.
		Because DNA sequences in each species have changed over time, traditional methods of comparing DNA sequences between humans and zebra fish have failed to identify any potential enhancers around the RET gene because the DNA sequences differ too much.
	www.jhu.edu /~gazette/2006/27mar06/27junk.html (686 words)

	Mutations
		In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle).
		Single-base substitutions are most apt to occur when DNA is being copied; for eukaryotes that means during S phase of the cell cycle.
		noncoding DNA in introns and flanking structural genes.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/M/Mutations.html (2842 words)

	DNA sequence - Wikipedia, the free encyclopedia
		A DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information.
		The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand - adenine, cytosine, guanine, thymine bases covalently linked to phospho-backbone.
		With regard to its biological function, which may depend on context, a sequence may be sense or anti-sense, and either coding or noncoding.
	en.wikipedia.org /wiki/DNA_sequence (226 words)

	Junk DNA - Crystalinks
		In molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified.
		Some portions of junk DNA could serve presently unknown regulatory functions, controlling the expression of certain genes and/or the development of an organism from embryo to adult.Junk DNA may serve other, unknown purposes.
		Gene deserts are long stretches of DNA between genes that were once thought to have no biological function, and were dismissed as "junk DNA." As scientists probe deeper into the DNA's double helix, however, they are discovering that many of these "non-coding" segments actually play an important role in regulating gene activity.
	www.crystalinks.com /junkdna.html (1268 words)

	Rediscovering Biology - Online Textbook: Unit 1 Genomics
		While eukaryotes generally have more genes than bacteria, the difference in gene content is not as great as the difference in DNA content: there is much more noncoding DNA in eukaryotes.
		Some of this repetitive DNA is dispersed more or less randomly throughout the genome.
		Perhaps this apparent junk DNA is actually helping provide structure to the chromosome and regulate the production of proteins in different cell types.
	www.learner.org /channel/courses/biology/textbook/genom/genom_4.html (460 words)

	Junk DNA definition - Medical Dictionary definitions of popular medical terms
		The term "junk DNA" is a disparaging one, expressing some of the disappointment felt by geneticists when they first gazed upon sizable segments of the genetic code and, instead of seeing one wonderful gene after another, they saw a few exons surrounded by vast stretches of "junk DNA."
		Exons are the regions of DNA that contain the code for producing the polypeptide molecules that make up protein.
		However, junk DNA has been found to be even more conserved than protein-coding regions of the DNA in humans and other mammalian species.
	www.medterms.com /script/main/art.asp?articlekey=13535 (204 words)

	An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example -- ...
		To identify noncoding sequences of the renin gene, we compare the upstream (5') noncoding DNA.
		This plot was used to identify the region of a 3.9-kb DNA block hRENc containing conserved sequences approximately 11-15 kb upstream of hREN.
		are strongly enriched in conserved noncoding DNA (29).
	ajpregu.physiology.org /cgi/content/full/284/4/R1147 (2717 words)

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