Local chromatin structure affects multiple stages of transcription, including the accessibility of sequence-specific DNA-binding transcription factors to promoters, enhancers and other genomic regulatory regions.
Not only structural targets may be of effect, also accessibility of sequence targets may depend on global or local mRNA structures.
With wider accessibility of these sequencing systems, there has been an increase in the use of sequencing-based expression profiling methods; these have several advantages, such as the opportunity to detect all expressed genes and to determine their absolute abundances without hybridization biases.
It has also been demonstrated that nucleosome occupancy affects the accessibility of DNA sequence motifs to transcriptional regulators; as a consequence different DNA sequences can display different nucleosome occupancy levels [ 1, 4, 7].
Given the accessibility of genome sequences there is an increasing need for comparative genomics tools that can handle large numbers of sequences.
We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.
We give an overview of FISH probe design, covering issues of affinity and specificity of probes, probe backbone options, cellular targets, and accessibility of target sequences.
Another mechanism underlying the modification of chromatin structure relies on the activity of the SWI/SNF-related ATP-dependent chromatin remodeling complexes that control the accessibility of DNA sequences to transcription factors.
By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes.
sa(i) and sa(j) are the predicted residue solvent accessibility of query sequence and that of the template structure, respectively.
