Nucleosome DNA Bendability Matrix<i>(C. elegans)</i>

Gabdank, Idan; Barash, Danny; Trifonov, Edward N.

doi:10.1080/07391102.2009.10507255

Cited by 69 publications

(65 citation statements)

References 22 publications

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“…S2), on the DNA fragments bound by LutR (regulatory regions of acoA, aprE, czcD, cwlO, glnR, ispA, lip, msmR, pbpE, ppsA, pyrB, rapI, spoIIE, ybfO, ydjM, yhfE, yneN, tapA, bslA, yuaF, yvcA, liaI, bacA, ywfH and yydF genes). A pyrimidine-rich motif such as this one strongly suggests that bending of this DNA region might play a role in the regulatory process (Gabdank et al, 2009). Additional experiments will be …”

Section: Direct Targets Of Lutrmentioning

confidence: 99%

In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase

et al. 2014

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The lutR gene, encoding a product resembling a GntR-family transcriptional regulator, has previously been identified as a gene required for the production of the dipeptide antibiotic bacilysin in Bacillus subtilis. To understand the broader regulatory roles of LutR in B. subtilis, we studied the genome-wide effects of a lutR null mutation by combining transcriptional profiling studies using DNA microarrays, reverse transcription quantitative PCR, lacZ fusion analyses and gel mobility shift assays. We report that 65 transcriptional units corresponding to 23 mono-cistronic units and 42 operons show altered expression levels in lutR mutant cells, as compared with lutR + wild-type cells in early stationary phase. Among these, 11 single genes and 25 operons are likely to be under direct control of LutR. The products of these genes are involved in a variety of physiological processes associated with the onset of stationary phase in B. subtilis, including degradative enzyme production, antibiotic production and resistance, carbohydrate utilization and transport, nitrogen metabolism, phosphate uptake, fatty acid and phospholipid biosynthesis, protein synthesis and translocation, cell-wall metabolism, energy production, transfer of mobile genetic elements, induction of phage-related genes, sporulation, delay of sporulation and cannibalism, and biofilm formation. Furthermore, an electrophoretic mobility shift assay performed in the presence of both SinR and LutR revealed a close overlap between the LutR and SinR targets. Our data also revealed a significant overlap with the AbrB regulon. Together, these findings reveal that LutR is part of the global complex, interconnected regulatory systems governing adaptation of bacteria to the transition from exponential growth to stationary phase.

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Section: Direct Targets Of Lutrmentioning

confidence: 99%

In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase

et al. 2014

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“…The combination of degeneracy and redundancy makes it possible that a great variety of sequences can contribute to nucleosome positioning in the genome. Other matrices have been derived from mononucleosomal DNA based on a probabilistic nucleosome-DNA interaction model (Segal et al 2006) or on the concatenation of a 12-bp consensus palindromic motif derived from Caenorhabditis elegans mononucleosomal DNA (Gabdank et al 2009). These matrices and other computational tools have been used to predict nucleosome positioning on genomic DNA sequences (revised in Teif 2016) whose predictive power varies widely (Liu et al 2014).…”

Section: Wwwgenomeorgmentioning

confidence: 99%

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

et al. 2016

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In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and nontranscribed regions, suggesting the existence of sequence elements that contribute to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is speciesspecific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and noncoding DNA molecules capable of directing their own nucleosomal organization.

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“…This is especially clear in case of eukaryotes where the protein coding sequences comprise only few percents of the genome. One of the first additional codes that drew attention of the sequence research community was, indeed, eukaryotic chromatin code (Trifonov, 1980;Trifonov and Sussman, 1980), the most recent version of which is described in Gabdank et al (2009Gabdank et al ( , 2010 and Trifonov (2010Trifonov ( , 2011. The latest work boils down to a conclusion that all other nucleosome positioning patterns suggested during three decades by various authors match to the universal pattern YRRRRRYYYYYR, of which GAAAATTTTC and AAAAATTTTT are the most representative of generally A + T rich eukaryotic sequences.…”

Section: Introductionmentioning

confidence: 89%