Distribution Density of Nucleotides Within a Desoxyribonucleic Acid Chain

Tamm, Christoph; Shapiro, Herman S.; Lipshitz, Rakoma; Chargaff, Erwin

doi:10.1016/s0021-9258(19)52337-7

Cited by 202 publications

(30 citation statements)

References 29 publications

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“…Following treatment with 100 mM DTT at 25°C for 30 min, the proteins were subjected to SDS-PAGE in an ice-cold electrophoresis chamber. Note that DNA is depurinated during the TCA precipitation, and subsequently digested in alkaline TPS ( Supplementary Figure S5 ) ( 43 ). To estimate the fractional distributions of the proteins, a standard curve for quantitation was calculated from the blot signals from serially diluted samples, whose intensities were measured using ImageJ.…”

Section: Methodsmentioning

confidence: 99%

Local states of chromatin compaction at transcription start sites control transcription levels

Ishihara

Sasagawa

Kameda

et al. 2021

Nucleic Acids Research

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The ‘open’ and ‘compact’ regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.

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Section: Methodsmentioning

confidence: 99%

Local states of chromatin compaction at transcription start sites control transcription levels

Ishihara

Sasagawa

Kameda

et al. 2021

Nucleic Acids Research

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show abstract

“…X i (1) is a random variable representing the length of an Exact Unary Tract starting at the i'th position of the sequence; the superscript (1) denotes the "unarity" of the tract. The general case is Xi(n) for any named "exact n-narity tract".…”

Section: Random Variable X I (1)mentioning

confidence: 99%

“…The general case is Xi(n) for any named "exact n-narity tract". Pr{X i (1) =k (1) the exact unary tract starting at the i' th position (i=0,…,L) is of the length k}…”

Section: Random Variable X I (1)mentioning

confidence: 99%

“…

As previously mentioned, the current work is based on previous research [1][2][3][4][5][6]. The data used in the investigation concerned the human gene p53, as given in genebank.

MethodsA special technique has been derived that is supported by further formalism and was validated by a program [7].

DefinitionsTract: A tract is a sub-sequence within a sequence of events having a mutual property.

Examples:a.

…”

mentioning

confidence: 99%

“…As previously mentioned, the current work is based on previous research [1][2][3][4][5][6]. The data used in the investigation concerned the human gene p53, as given in genebank.…”

mentioning

confidence: 99%

See 2 more Smart Citations

An Analysis of Palindromes and n-nary Tract Frequencies found in a Genomic Sequence

Ophir¹

2013

J Data Mining Genomics Proteomics

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As previously mentioned, the current work is based on previous research [1][2][3][4][5][6]. The data used in the investigation concerned the human gene p53, as given in genebank. MethodsA special technique has been derived that is supported by further formalism and was validated by a program [7]. DefinitionsTract: A tract is a sub-sequence within a sequence of events having a mutual property. Examples:a. A sequence of events, for example, tossing a coin. Each event can have one of two values S (the coin falling on heads) or F (the coin falling on tails) [8].b. A genomic sub-sequence consisting of nucleotides having special properties. An event is associated with one of the nucleotides from a set of nucleotides. c. sub-sequence of a wide spectrum of qualities of a product in a serial mass production.Source-set: Source-Set is a set of elements that builds the sequence.Kernel set: Kernel-Set is a set of elements. The tract is built from elements taken from the Kernel-Set. The Kernel-Set is a subset of a Source-Set. Unary tract:A tract that is composed of one type of elements, i.e., a set of elements from which the tract elements are composed, and which contain one element only. The cardinality of the Kernel-Set of the unary tract is one.Exact unary tract: Exact Unary Tract is a unary tract that cannot be enlarged by exactly one element (one of its neighbors' elements) and remain a unary-tract. Namely, the exact-unary-tract cannot be contained in another unary-tract.Binary tract: Binary Tract is a tract whose Kernel-Set has a cardinality of two.

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The Chemical Basis of Mutation

Le¹

1965

Advances in Enzymology - And Related Areas of Molecular Biology

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Distribution Density of Nucleotides Within a Desoxyribonucleic Acid Chain

Cited by 202 publications

References 29 publications

Local states of chromatin compaction at transcription start sites control transcription levels

Local states of chromatin compaction at transcription start sites control transcription levels

An Analysis of Palindromes and n-nary Tract Frequencies found in a Genomic Sequence

The Chemical Basis of Mutation

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