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Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences.
The high density of PTMs in histones and other signaling molecules results in a large number of potential combinations of marks that regulate chromatin-templated recognition processes.
Thus, the reading process of the "histone code" is a sophisticated, nuanced chromatin language that recognizes combinations of marks rather than single PTMs (Berger, 2007).
Other studies have identified higher number of profiles, both for each chromatin mark and for combinations of marks [ 10, 17], where the final number of states has been determined through various optimizations of a clustering procedure.
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It must be pointed out that the coverage values in Fig. 2 were obtained for the most suitable combinations of marking and releasing enzymes selected from a set of 18 restriction endonucleases.
At the time of Vernam's work, all messages transmitted over AT&T's teleprinter system were encoded in the Baudot Code, a binary code in which a combination of marks and spaces represents a letter, number, or other symbol.
At that time all messages transmitted over AT&T's teleprinter system were encoded in the Baudot Code, a binary code in which a combination of marks and spaces represents a letter, number, or other symbol.
In undifferentiated ES cells this unusual combination of marks is thought to keep genes repressed or expressed at very low levels but poised for later activation.
In this equation, denotes the combination of marks at position t of gene c, extracting for, s = 1,..., 24.
In all the scenarios we studied (individual marks, combination of marks, and non-exonic filtering of ChIP regions), we consistently found that H3K4Me1 significantly peaked at embryonic stages.
With this information, one can better investigate whether a chromatin mark (or combination of marks) plays a causal role or a secondary role in gene silencing.
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Justyna Jupowicz-Kozak
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