Comment on “Linguistic Features of Noncoding DNA Sequences”

1996 ◽  
Vol 76 (11) ◽  
pp. 1978-1978 ◽  
Author(s):  
Richard F. Voss
Keyword(s):  
Dna Sequences ◽  
Linguistic Features ◽  
Noncoding Dna

Linguistic Features of Noncoding DNA Sequences

1994 ◽  
Vol 73 (23) ◽  
pp. 3169-3172 ◽  
Author(s):  
R. N. Mantegna ◽  
S. V. Buldyrev ◽  
A. L. Goldberger ◽  
S. Havlin ◽  
C. K. Peng ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Linguistic Features ◽  
Noncoding Dna

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

1995 ◽  
Vol 51 (5) ◽  
pp. 5084-5091 ◽  
Author(s):  
S. V. Buldyrev ◽  
A. L. Goldberger ◽  
S. Havlin ◽  
R. N. Mantegna ◽  
M. E. Matsa ◽  
...  
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Noncoding Dna ◽  
Range Correlation ◽  
Correlation Properties

scholarly journals Chloroplast Noncoding DNA Sequences Reveal Genetic Distinction and Diversity between Wild and Cultivated Prunus yedoensis

2017 ◽  
Vol 142 (6) ◽  
pp. 434-443
Author(s):  
Eun Ju Cheong ◽  
Myong-Suk Cho ◽  
Seung-Chul Kim ◽  
Chan-Soo Kim
Keyword(s):  
United States ◽  
Dna Sequences ◽  
The United States ◽  
Jeju Island ◽  
Noncoding Dna ◽  
Noncoding Regions ◽  
Naturally Occurring ◽  
Prunus Yedoensis ◽  
History Of ◽  
Ornamental Trees

Cultivated flowering cherries (Prunus subgenus Cerasus), which are one of the most popular ornamental trees around the world, have been developed through artificial hybridizations among wild flowering cherries. Among the hundreds of cultivars of flowering cherries, Prunus ×yedoensis ‘Somei-yoshino’ is the most common and widespread. However, its origin and genetic relationship to wild P. yedoensis, naturally occurring on Jeju Island, South Korea, have long been debated. We used sequence polymorphisms in eight chloroplast DNA (cpDNA) noncoding regions to distinguish wild and cultivated flowering cherries among 104 individuals (55 accessions). We were able to distinguish two distinct groups, one corresponding to wild P. yedoensis collections from Jeju Island and the other collections of cultivated P. ×yedoensis from Korea, Japan, and the United States. The chlorotype diversity of wild P. yedoensis in Jeju Island and cultivated P. ×yedoensis collections in the United States was quite high, suggesting multiple natural hybrid origins and long history of cultivation from different original sources, respectively.

Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 272-277 ◽  
Author(s):  
B. Liu ◽  
J.M. Vega ◽  
G. Segal ◽  
S. Abbo ◽  
M. Rodova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Noncoding Dna ◽  
Genomic Changes

Statistical and linguistic features of noncoding DNA: A heterogeneous «Complex system»

1994 ◽  
Vol 16 (9) ◽  
pp. 1339-1356 ◽  
Author(s):  
H. E. Stanley ◽  
S. V. Buldyrev ◽  
A. L. Goldberger ◽  
S. Havlin ◽  
R. N. Mantegna ◽  
...  
Keyword(s):  
Complex System ◽  
Linguistic Features ◽  
Noncoding Dna

Clustering of Identical Oligomers in Coding and Noncoding DNA Sequences

1999 ◽  
Vol 17 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Rachel H. R. Stanley ◽  
Nikolay V. Dokholyan ◽  
Sergey V. Buldyrev ◽  
Shlomo Havlin ◽  
H. Eugene Stanley
Keyword(s):  
Dna Sequences ◽  
Noncoding Dna

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2020 ◽  
Author(s):  
Richard V. Miller ◽  
Rafik Neme ◽  
Derek M. Clay ◽  
Jananan S. Pathmanathan ◽  
Michael W. Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

AbstractThe germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

scholarly journals Congruity of the Polymorphisms in the Expressed and Noncoding Parts of the Gli-B1 Locus in Common Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1510
Author(s):  
Yulia Popovych ◽  
Sabina Chebotar ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
Laura Pascual ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Evolutionary Significance ◽  
Sequence Length ◽  
Noncoding Dna ◽  
Important Region ◽  
Novel Variants ◽  
Specific Sequences

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 locus. A congruity was established between this polymorphism, allelic sets of the Gli-B1-produced gliadins (especially of the electrophoretic mobility in acid gels of the encoded γ-gliadin) and the presence in the wheat genotype of the Gli-B5b + Rg-1 allelic combination. Six different alleles at the Gli-B1 locus encoding an identical γ-gliadin produced a PCR sequence of about 400 bp (GliB1.1). Nine Gli-B1d-carrying genotypes from four countries produced an identical sequence of about 409 bp (GliB1.2), while three cultivars with Gli-B1h and four with Gli-B1b produced three and two specific sequences, respectively, of slightly different length. Allele Gli-B1j might be the result of recombination between coding and noncoding DNA sequences within the Gli-B1 locus. These observations imply that genetic diversity of the agriculturally important region of chromosome 1B marked by variants of the Gli-B1 locus is rather limited among common wheat cultivars of the 20th century, specifically to eight principal versions. These might have been incorporated into common wheat from diverged genotypes of diploid donor(s), and, due to the scarcity of recombination, subsequently maintained relatively intact. As well as its evolutionary significance, this information is of potential use in wheat breeding and we consider it likely that novel variants of the Gli-B1 locus will be found in hitherto unstudied germplasm.

scholarly journals De NovoEmergence of Peptides That Confer Antibiotic Resistance

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Michael Knopp ◽  
Jonina S. Gudmundsdottir ◽  
Tobias Nilsson ◽  
Finja König ◽  
Omar Warsi ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Comparative Genomics ◽  
Dna Sequences ◽  
De Novo ◽  
Drug Uptake ◽  
Aminoglycoside Resistance ◽  
Noncoding Dna ◽  
Ancestral Gene ◽  
New Genes

ABSTRACTThe origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, andde novofrom noncoding DNA sequences. Comparative genomics has generated strong evidence forde novoemergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement ofde novogene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them inEscherichia colito identify short peptides that could confer a beneficial and selectable phenotypein vivo(in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes.IMPORTANCEDe novogene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics,in vitroselections, or partial randomizations. Here, we describe selection of novel peptidesin vivousing fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence poolsin vivoand support the idea that expression of noncoding sequences could spark the origination of new genes.

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