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As is well known, genes bearing stronger codon bias are likely to be highly expressed and have housekeeping features [ 3, 45].
So, the genes in the two COGs might present housekeeping features in the fundamental life cycle and essential physiological activities of Neisseria.
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The main achievement of this work is to have proved that it is possible to discover if a gene is housekeeping using simple features of that gene sequence and its surroundings.
The other two promoters (P1A and P1B) lack TATA or CAAT boxes and contain architectural features of housekeeping promoters.
The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs.
A feature of housekeeping genes is that, in comparison to tissue-specific genes, they evolve on average more slowly [ 4].
One can envision several ways for testing these possibilities, such as removing a boundary-associated feature and measuring whether this disrupts topological insulation (as has been shown in one case at the Xist/Tsix locus 13); or else analyzing the effects of placing an ectopic feature (SINE, housekeeping gene, transgene, …) within a TAD on proper long-range regulation.
The promoter region displays the typical features of a housekeeping gene: a high G+C content and the absence of canonical TATA and CAAT boxes consistent with the multiple transcription initiation sites determined by primary extension analysis.
A canonical promoter has features typical of housekeeping genes, while a cryptic promoter in the 5'-UTR and coding region of spastin seems to provide tissue-specificity.
Microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes.
The first column lists various features analyzed for housekeeping genes (second column), hypervariable genes (third column) and the whole genome (fourth column).
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