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:

1. the border going from exon to intron is called a donor site or a 5' site;
2. the border separating intron from exon is called an acceptor site or a 3' site.

• cis-splicing:     The joining together, after removal of the intron, of two segments of the same RNA molecule separated by an intron.  Splicing of messenger RNA precursors (pre- mRNAs) is a requisite step in the generation of virtually all mature mRNAs. This process requires the coordinated interaction of several small nuclear ribonucleoprotein particles (snRNPs) and many protein factors that assemble to form an enzymatic complex known as the spliceosome. Components of the spliceosome recognize the exon- intron boundaries at the 5' and 3' splice sites, excise the intron and ligate the adjoining exons.

Intronn, Inc.  "Background cis- and trans- splicing" 1999] http://www.intronn.com/r&t/background.htm
http://calspace.ucsd.edu/origins/Glossary/C.htm
 
• trans- splicing: Splicing between two independently transcribed pre- mRNAs is termed trans-splicing. This has been described in trypanosomes, nematodes, flatworms, and plant mitochondria. In vitro trans-splicing has been used as a model system to examine the mechanism of splicing. Trans-splicing of pre-mRNAs in human cells has been postulated to account for some rare events, but is unlikely to be of major significance in humans.
• One type of trans- splicing is the "spliced leader" type (primarily found in protozoans such as trypanosomes and in lower invertebrates such as nematodes) which results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs.
• Another type of trans- splicing is the "discontinuous group II introns" type (found in plant/ algal chloroplasts and plant mitochondria) which results in the joining of two independently transcribed coding sequences. Both are mechanistically similar to conventional nuclear pre- mRNA cis-splicing.

• alternative splicing: A single gene can contain numerous exons and introns, and the exons can be spliced together in different ways. For example, if a gene contains 10 exons, one version of the mRNA transcribed from that gene might contain exons 1-9. Another version of the mRNA might contain exons 1-8, and exon 10. This is called alternative splicing, and can produce different forms of a protein from the same gene. The different versions of mRNA produced from a single gene are called splice variants or isoforms or alternative transcripts.  [http://www.ncbi.nlm.nih.gov/Class/MLACourse/Genetics/gene.html]



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.

• One domain is required for the factor to bind to DNA
• the second domain is required for the activation of transcription.

plus strand DNA:    in retroviruses, the DNA strand whose sequence codes for protein products
minus strand DNA: in retroviruses, the complementary DNA strand