Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive.. Here researchers from the Washington University School of Medicine characterized the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium they identified over three thousand unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls they discovered 111 differentially expressed lncRNAs, which they termed lung cancer associated lncRNAs (LCALs). A pan-cancer analysis of 324 ...

A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we present a new motif sampling algorithm, PhyloGibbs, that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of

Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed in at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a higher fraction of differentially

Polymorphisms in the oxyR-ahpC intergenic region One low level INH-resistant isolate displayed a G → A https://www.selleckchem.com/products/MK-1775.html substitution at position 32 upstream of the transcriptional start site of ahpC in the oxyR-ahpC intergenic region, which has previously. been shown to be involved in INH -resistance [15]. Combined sensitivity and specificity of katG and inhA promoter region for INH resistance Mutations in katG315 and -15C → T in inhA ACP-196 promoter region accounted together for 73% (33/44) INH -resistance. Since none of these mutations was observed in susceptible isolates, the combined specificity is 100%. Analysis of the rpoB gene responsible for RIF-resistance In this study, 7 RIFR isolates, and 100 RIF-sensitive (RIFs) clinical isolates were examined for mutations in a 158-bp fragment of rpoB gene. Of 7 RIFR isolates, resistance-associated. mutations in the core region of rpoB were found in all 7 (100.0%) isolates (Table 3). The nucleotide and amino ...

The genetic distances among primate lineages estimated from orthologous noncoding nucleotide sequences of β-type globin loci and their flanking and intergenic DNA agree closely with the distances (del

Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...

Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...

Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...

DNA (20 pmoles) was incubated in the presence (+) or in the absence (-) of 20 pmoles of OhrR. C-Binding of OhrR. to Motif 1 buy BMS202 and Motif 2 sequences. Gel shift assay of the intergenic region and the 60 bp double strand sequences containing at their centre the genuine 17 nt corresponding to Motif 1 and Motif 2, or mutated Motif 1 with AA in place of GC (Mut1 fragment) and CCC in place of AAA (Mut2 fragment). DNA (20 pmoles) was incubated with the indicated amount of OhrR in the presence of 1 mM DTT. We took advantage of restriction sites located within the ohr-ohrR intergenic region to define further OhrR binding site. ApoI cleaved once this fragment giving a 17 bp and a 96 bp fragment. In the presence of OhrR protein the longer fragment produced two shifted bands (Figure. 3). Two HpaII sites are located within ohr-ohrR intergenic region; HpaII cleavage produced three fragments of 26, 29 and 58 bp. In the presence of OhrR, the intensity of the 58 bp fragment decreased and two retarded ...

Hello , I m confused by the plethora of information about Humane Genes online, Some say there is a difference between Non-Coding DNA and Junk DNA, some say there is NOT. I read it in rationalwiki Non-coding DNA refers to portions of the genome that dont code for proteins, the Rest are Junk. As it...

On the Perl simulations front, Ive got the program running and used it to do the control simulations. The first controls use random sequences the same lengths and base compositions as the concatenated H. influenzae or N. meningitidis intergenic sequences, run with matrices specifying the corresponding USS or DUS core but with no recombination. These controls tell us what the baseline USS or DUS score is for a genome that hasnt experienced any accumulation. The second controls use the real H. influenzae or N. meningitidis intergenic sequences instead of random sequences, and run for a long time to see how long the sequences take to degenerate to the predetermined baselines (i.e. to become randomized with respect to USS or DUS). The score isnt a very sensitive indicator for this degeneration, as the genome may still contain an excess of the imperfectly matched cores, but Ill be able to tell this from the final analysis done at the end of the run ...

Not quite. What youre leaving out of this is the possibility of multiple levels of selection. In the original edition of The Selfish Gene (1976, p.76), Dawkins argued that the simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. Cavalier-Smith (1977) drew a similar conclusion (before he had read Dawkins), and Doolittle and Sapienza (1980) and Orgel and Crick (1980) [yes, that Crick] independently developed the concept of selfish DNA a few years later. This is an explicitly multi-level selection approach because it specifies that non-coding DNA can be present due to selection within the genome rather than exclusively on the organism (or gene, in Dawkinss case) (see, e.g., Gregory 2004, 2005). (Incidentally, this idea of parasitic DNA dates back at least to 1945, when Gunnar Östergren characterized B chromosomes in this fashion). Of course, they tended to ...

Principal Investigator：GOTO Yuji, Project Period (FY)：2010 - 2012, Research Category：Grant-in-Aid for Young Scientists (B), Research Field：Genetics/Genome dynamics

It is the relationship between the gene and the endo-environment of the organism, which it participates in the creation of, that mediates the activity of the gene. The study of the gene must also include the study of all that might happen the gene, which is a set of possibilities constrained and shaped by the organisms internal environment, which in turn is mediated by its external environment. Furthermore, the expression of the gene is moderated by the non-coding DNA in the chromosomes of the organisms (which may act as an analogue for the systems of organisation between people if we continue to stretch the metaphor) thus we can imagine contrasting mutations in the non-coding DNA with cultural adaptations, and imagine them also diffusing across the boundaries of societies, regulating the activities of people, who are akin to individual genes, in the Neo-Darwinian frame ...

The existence of functional, non-protein-coding DNA is all too frequently portrayed as a great surprise uncovered by genome sequencing projects, both in large media outlets and in scientific publications that should have better quality control in place.

Complete information for LINC02003 gene (RNA Gene), Long Intergenic Non-Protein Coding RNA 2003, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium

Complete information for LINC00908 gene (RNA Gene), Long Intergenic Non-Protein Coding RNA 908, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium

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Conserved Fragments of Transposable Elements In Intergenic Regions: Evidence for Widespread Recruitment of MIR- and L2-derived Sequences Within the Mouse and Human ...

This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ.. ...

This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ.. ...

A new study shows that there are regions of non-coding DNA that may have a connection to cancer growth and progression if altered.

Washington, DC - As members of Congress return to Capitol Hill today, 85 farm and farmer support organizations sent letters to the U.S. Environmental Protection Agency (EPA) and U.S. Department of Agriculture (USDA) urging them to better protect farm families from an unprecedented… Read More. ...

The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important.

We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available,

It is thought that virtually all protein-coding genes in the human genome have already been discovered, yet a significant fraction of genetic variants associated with human disease map to the intergenic space. Furthermore, genome-wide studies of transcription have found that these intergenic regions are pervasively transcribed into different classes of RNA molecules. These include long intervening noncoding RNAs (lincRNAs), which contain at least 200 bases, and similarly to mRNAs, begin with a 5 cap and end with a poly(A) tail. Thousands of lincRNA genes were recently reported in human and mouse and several lines of evidence suggest that many of them are functionally important. For example, lincRNA expression varies across tissues and is commonly dysregulated in human disease, including cancer. Furthermore, the sequences of lincRNA exons were significantly conserved during vertebrate evolution. Accumulating evidence shows that lincRNAs play pivotal regulatory roles in diverse biological ...

The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one genome into another. Usually, a genome is modeled as an ordered sequence of genes, and most of the studies in the genome rearrangement literature consist in shaping biological scenarios into mathematical models. For instance, allowing different genome rearrangements operations at the same time, adding constraints to these rearrangements (e.g., each rearrangement can affect at most a given number of genes), considering that a rearrangement implies a cost depending on its length rather than a unit cost, etc. Most of the works, however, have overlooked some important features inside genomes, such as the presence of sequences of nucleotides between genes, called intergenic regions. In this work, we investigate the problem of computing the distance between two genomes, taking into account both gene order and intergenic sizes. The genome

It has been quite some time since the last update to the Quotes of interest series on junk DNA. Most of the posts have sought to demonstrate that the exhausting cliché that scientists dismissed possible functions for non-coding DNA until recently is false. Therefore, I have provided many quotes indicating that many (if not most) biologists continued to consider possible functions for various non-coding elements throughout the mythical period of neglect. This time, I want to discuss an example in which a particular kind of non-coding sequence was considered as probably non-functional - but because of knowledge about its biology, not because no function could be imagined.. The elements under discussion are endogenous retroviruses (ERVs) which, as the name suggests, are viral-like sequences that exist within the genome. Depending on who you ask, they are either very similar to or are interchangeable with long terminal repeat (LTR) retrotransposons. ERVs make up approximately 8% of the human ...

Title Minute Intergenic Rearrangement as a Cause of Apparent Gene Mutation Author Muller, H.J; Prokofyeva, A.; and Raffel, D. Binding PAPERBACK Publisher Nature, Vol. 135, p. 253, Feb. Publisher Year 1935 Condition Very Good Description Very good condition. First edition. Offprint. Original wrappers. * Genetics. Scie

Are you proposing a thought experiment in which we subtract all the repeat derived sequences (minus the small proportion of bases that regulate gene expression), and most of the the non regulatory intergenic sequences, reducing intron and intergenic sizes by, say 90%, such that we end up with a small number of short chromosomes (say 50 Mb in size - since we know the current division processes can cope with such a size) but keeping the necessary telomeric and centromeric repeats. This would be done with all members of the human species such that all the current copy number polymorphisms and regulatory snps are maintained and all genes are allowed up to 2000bp of regulatory sequences (although we will allow a proportion of genes to have larger regulatory regions). The ultimate result is a human genome that is say, 90% smaller than the current one. You suggest that the current cellular machinery would be able to cope with this change, such that there would be no viability or evolutionary ...

The type of connector spacer you choose will depend on the type of PCB you are using, the materials the PCB and the relevant component is made from, and other considerations like space limitations.. Plastic spacers are cost-effective, non-corrosive and lightweight, and because they do not conduct electricity, they can be used to prevent short circuits. Metal spacers are more durable and resistant to heat, these can be used in applications where electrical conductivity is needed. ...

Daily News Thousands of Mutations Accumulate in the Human Brain Over a Lifetime Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until death.. ...

Daily News How Gaining and Losing Weight Affects the Body Millions of measurements from 23 people who consumed extra calories every day for a month reveal changes in proteins, metabolites, and gut microbiota that accompany shifts in body mass.. ...

Ian Musgrave has a good summary of genes appearing from non-coding DNA (ORFans) on the Pandas Thumb. I have written about ORFans here and here (dudes gotta link to himself sometimes). Ians post is targeted at some claims made by the creationist Paul Nelson, but he focuses more on the science that on the ignorant blowhard.. ...

CNES CNES - CNRS/INSU JOINT PRESS RELEASE: The Swedish Odin science mission, in which France is participating, is operating a 250-kg satellite launche

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The specific name is without the a I.e. cespitosa not caespitosa . It applies to the other photo of C. cespitosa as well. (Sent: [email protected]) ...

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TY - JOUR. T1 - The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. AU - Ranzani, Valeria. AU - Rossetti, Grazisa. AU - Panzeri, Ilaria. AU - Arrigoni, Alberto. AU - Bonnal, Raoul J P. AU - Curti, Serena. AU - Gruarin, Paola. AU - Provasi, Elena. AU - Sugliano, Elisa. AU - Marconi, Maurizio. AU - De Francesco, Raffaele. AU - Geginat, Jens. AU - Bodega, Beatrice. AU - Abrignani, Sergio. AU - Pagani, Massimiliano. PY - 2015/2/17. Y1 - 2015/2/17. N2 - Long noncoding RNAs are emerging as important regulators of cellular functions, but little is known of their role in the human immune system. Here we investigated long intergenic noncoding RNAs (lincRNAs) in 13 subsets of T lymphocytes and B lymphocytes by next-generation sequencing-based RNA sequencing (RNA-seq analysis) and de novo transcriptome reconstruction. We identified over 500 previously unknown lincRNAs and described lincRNA signatures. Expression of linc-MAF-4, ...

Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were

Although unicellular eukaryotes such as yeast have either no introns or very few, metazoans and especially vertebrate genomes have a large fraction of non-coding DNA. For instance, in the human genome only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA.[5] This can provide a practical advantage in omics-aided health care (such as precision medicine) because it makes commercialized whole exome sequencing a smaller and less expensive challenge than commercialized whole genome sequencing. The large variation in genome size and C-value across life forms has posed an interesting challenge called the C-value enigma. Across all eukaryotic genes in GenBank there were (in 2002), on average, 5.48 exons per gene. The average exon encoded 30-36 amino acids.[6] While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long.[7] A single-nucleotide exon has been reported from the Arabidopsis ...

In Bacillus subtilis, expression of the rocG gene, encoding glutamate dehydrogenase, and the rocABC operon, involved in arginine catabolism, requires SigL (sigma(54))-containing RNA polymerase as well as RocR, a positive regulator of the NtrC/NifA family. The RocR protein was purified and shown to bind specifically to the intergenic region located between rocG and the rocABC operon. DNaseI footprinting experiments were used to define the RocR-binding site as an 8 bp inverted repeat, separated by one base pair, forming an imperfect palindrome which is present twice within the rocG-rocABC intergenic region, acting as both a downstream activating sequence (DAS) and an upstream activating sequence (UAS). Point mutations in either of these two sequences significantly lowered expression of both rocG and rocABC. This bidirectional enhancer element retained partial activity even when moved 9 kb downstream of the rocA promoter. Electron microscopy experiments indicated that an intrinsically curved region is

BACKGROUND Long non-coding RNAs (lncRNAs) have a role in physiological and pathological processes, including cancer. The aim of this study was to investigate the expression of the long intergenic non-protein coding RNA 665 (LINC00665) gene and the cell cycle in hepatocellular carcinoma (HCC) using d …

Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052836],Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052836],See cases [RCV000052836 ...

from Zone in With Zon. A Short Walk in the Wondrous, Wacky World of Long-and now Circular-Noncoding RNAs. Im pleased by how much I learn when researching topics for new content, and this was certainly the case for long noncoding RNA (lncRNA), which was briefly mentioned in my last blog post, Ripples from the 2013 TIDES Conference. The topic piqued my interest so I set out to find out more. Plowing through lncRNA (aka lincRNA = large intergenic non-coding RNA) literature I quickly realized that there was an enormous amount of information, and the big challenge would be to capture some intriguing aspects without getting bogged down in technical weeds or being overly simplistic. In what follows there is a super brief introduction to what lncRNAs are and what they do-the latter is controversial-along with an appreciation for why lncRNAs are indeed a structurally and functionally wondrous class of nucleic acids that now encompass circular molecules. Maybe-to borrow from Forrest Gump-lncRNAs are ...

Wind two strands of elastic, eventually it will knot, ultimately it will double up on itself. Separate the strands. From the point of unwinding forces will be directed to different regions and the separation will naturally return to the wound state of the band. Do the same with each of 10 different bands or strings of any type, they will all behave in much the same way. For a given section of DNA being transcribed, the effect of separation will be much the same. For a given gene, there will be sequences that can tolerate force to greater or lesser degrees. For different transcripts, of a gene variation at those sequences may be crucial to the integrity of transcription machinery that separates DNA strands to initiate replication to RNA and for the outcome.. Cellular biology is enormously complex in all regards. The physics of molecular interaction, fluid dynamics, and chemistry combine in a system where cause and effect is near impossible to predict. At the most elementary level we hypothesize ...

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save-buffer) (vc-revert-buffer yes)) These did not work but instead I got an error message about the wrong number of arguments and other junk. How fix ...