Coding DNA.
This is DNA which can be related to a cell function or a phenotype at the level of the organism. It is usually thought of, either as coding for a protein or some functional element in the cell, or as playing a role in expression of a gene or circuit of genes.
cis-acting sequences:
The sequences just 5' of the start site of transcription are the most important
for the initiation of transcription. This is where the transcription complex
is built. In general, this region is called the promoter.
For eukaryotes, several sequences same to be conserved among many genes.
One such sequences is the TATA box. The sequence is located about 30 bases
upstream (-30) from the transcription start site and is the one sequence
required for any significant transcription to occur. Other sequences add
in transcription but are not always part of promoter. The two most found
are the CCAAT box (called the CAT box) and the GC box. Because mutants
of these three sequences only express mRNAs at low levels, these are considered
the most important sequences of the basic transcription complex. [Phillip
McClean, "Control of gene expression in eukaryotes, North Dakota State
Univ. 1997]
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/geneexpress/eukaryex3.htm
enhancers: A cis- acting
sequence that increases the utilization of (some) eukaryotic promoters,
and can function in either orientation and in any location (upstream or
downstream) relative to the promoter. Eukaryotes and eukaryotic viruses.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
splice sites / splice junctions: Boundaries between exons and intron, there are two varieties:
Alternative splicing often occurs when a gene must be expressed in different tissues, but not necessarily at the same time or under the same circumstances. This process generates transcripts that may be unique to (or enriched in) specific tissues. Presumably this could provide a mechanism for differential expression in various tissues.
Pharmaceutical companies have also recognized an opportunity for an additional level of drug specificity that is generally not available in targeting proteins. They hope to make drugs that bind to the region of RNA unique to the desired tissue and which would not affect the RNA in other tissues. An analogous opportunity for specificity at the protein level might be post- translational modifications of proteins that are tissue specific. In practice, however, this is variation in proteins has been difficult to exploit or even understand due to the lack of good analytical tools to sort out tissue- specific protein modifications. In contrast, finding alternative transcript forms in RNA is accomplished by straightforward sequencing of cDNA libraries obtained from different tissues. The potential to find alternative transcript forms is one of the unappreciated strategic advantages of RNA as a drug target. [http://www.ibisrna.com/darpa_ii/overview.html]
Alternative initiation: Transcription of genes with promoters containing a TATA box or initiator element begins at a well-defined initiation site. However, transcription of many protein-coding genes has been shown to begin at any one of multiple possible sites over an extended region, often 20 - 200 base pairs in length. As a result, such genes give rise to mRNAs with multiple alternative 5' ends. These genes, which generally are transcribed at low rates (e.g., genes encoding the enzymes of intermediary metabolism, often called "housekeeping genes"), do not contain a TATA box or an initiator. Most genes of this type contain a CG-rich stretch of 20 - 50 nucleotides within approximately 100 base pairs upstream of the start-site region. A transcription factor called SP1 recognizes these CG-rich sequences.
The dinucleotide CG is statistically underrepresented in vertebrate
DNAs, and the presence of CG-rich regions just upstream from start sites
is a distinctly nonrandom distribution. Such CpG
islands can be identified by their susceptibility to restriction
enzymes (e.g., HpaII) that have CG in their recognition sequences. The
presence of a CpG island in a newly cloned DNA fragment suggests that it
may contain a transcription-initiation region. [Alison
Stewart "The human gene map initiative" Genome Digest 2 (2) : 1-4]
http://www.gene.ucl.ac.uk/hugo/london.htm
trans-acting factors: Trans- acting factors functionally have two domains.
plus strand DNA:
in retroviruses, the DNA strand whose sequence codes for protein products
minus strand DNA: in
retroviruses, the complementary DNA strand
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