Sequence repeats

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

Individual copies of integrated mobile elements may either be degenerate relics or 

Species Repeat Repeat type in genome3 Transcribed Reference 

Species-specific repeat Species-specific repeat Species-specific repeat Species-specific repeat 

477-489 base repeat 186 base, genus-specific, polymorphic, tandem repeat 269 base, species-specific, dispersed tandem repeat 158 base, species-specific tandem and dispersed repeat 53 base, species-specific tandem repeat 

---

Fig. 3. Example of cniciform formation from an inverted-repeat sequence of DNA which occurs in the plasmid ColEl. The bolded bases are paired with...

There are several rules appHed to control charts to spot a lack of randomness. The most obvious is a point outside the control limits. A trend such as a mn, where at least seven consecutive data points are either above or below the average line, or a trend of seven consecutive points either increasing or decreasing in value, also indicates an out of control situation (29). A lack of randomness is also apparent from a pattern in which there is a repeated sequence of points cycling between rising then falling, or when points tend to cluster around the center line or near the control limits. 

Process— The combination of people, equipment, materials, methods, and environment that produce output (product or service). A repeatable sequence of activities with measurable inputs and outputs. 

FIGURE 17.17 All axial view of the two-stranded, a-helical coiled coll of a myosin tall. Hydrophobic residues a and d of the seven-resldne repeat sequence align to form a hydrophobic core. Residues b, c, and f face the outer surface of the colled coll and are typically Ionic. 

Oxidation Involves a Repeated Sequence of Four Reactions... 

Linear chain polymers with repeating sequences of hard and soft segments Possibility of formation of liquid crystal polymers and thermoplastic elastomers... 

The extracellular domain of cadherins consists of a variable number of a repeated sequence of about 110 amino acids. This sequence is termed the cadherin repeat and resembles in overall structure, but not in sequence, the Ig like domains. The cadherin repeat is the characteristic motive common to all members of the cadherin superfamily. Classical and desmosomal cadherins contain five cadherin repeats, but as many as 34 repeats have been found in the FAT cadherin (see below). Cadherins are calcium-dependent cell adhesion molecules, which means that removal of Ca2+, e.g., by chelating agents such as EDTA, leads to loss of cadherin function. The Ca2+-binding pockets are made up of amino acids from two consecutive cadherin repeats, which form a characteristic tertiary structure to coordinate a single Ca2+ion [1]. 

It is believed that many transcription factors bind DNA as dimers ( dimeric transcription factors) in either the same or opposite orientation. The DNA sites therefore can look like two direct repeat sequences or like palindromes. The interaction of the subunits with each other must obviously be specific and be mediated by dimerization domains. Specificity and stability of the dimers (dimeric transcription factors) is mostly promoted by hydrophobic or ionic inteiphases, e.g. a... 

All elastic proteins contain distinct domains, of which at least one is made up of elastic repeat sequences, and they all contain cross-links between residues in either the nonelastic or elastic domains [9]. Previously, the Drosophila CGI5920 gene was tentatively identified as one encoding a resUin-like protein [31]. To prepare recombinant resilin, we chose to express the first exon of the Drosophila CG15920 gene [29], which encodes an N-terminal domain in the native protein comprising 17 copies of the putative elastic repeat motif GGRPSDSYGAPGGGN [31]. 

Fig. 18 CG15920 gene sequence and primary structure. The consensus repeat sequences are also represented. The highlighted regions correspond to the signal sequence, R R chitin-binding domain, and the elastomeric domains containing repeat motifs A and B. Reproduced from [182, 188] with permission from Elsevier, copyright Elsevier 2001, 2010...

Some very unusual nucleotide bonding has been discovered in so-called triplet repeat sequences [23], Two neighboring bases in one strand complex with a single base of the opposite strand in a complex, which is called triad DNA. This type of bonding requires three bases, but unlike triplexes the three bases are within only two DNA strands. 

Trinucleotide sequences that increase in number (microsateUite instability) can cause disease. The unstable p(CGG) repeat sequence is associated with the fragile X syndrome. Other trinucleotide repeats that undergo dynamic mutation (usually an increase) are associated with Huntington s chorea (CAG), myotonic dystrophy (CTG), spinobulbar muscular atrophy (CAG), and Kennedy s disease (CAG). 

Besides unequal crossover and transposition, a third mechanism can effect rapid changes in the genetic material. Similar sequences on homologous or nonhomol-ogous chromosomes may occasionally pair up and eliminate any mismatched sequences between them. This may lead to the accidental fixation of one variant or another throughout a family of repeated sequences and thereby homogenize the sequences of the members of repetitive DNA families. This latter process is referred to as gene conversion. 

It is now known that each codon consists of a sequence of three nucleotides ie, it is a triplet code (see Table 38—1). The deciphering of the genetic code depended heavily on the chemical synthesis of nucleotide polymers, particularly triplets in repeated sequence. 

Exonuclease An enzyme that cleaves nucleotides from either the 3 or 5 ends of DNA or RNA. Fingerprinting The use of RFLPs or repeat sequence DNA to establish a unique pattern of DNA fragments for an individual. 

Microsatellite repeat sequences Dispersed or group repeat sequences of 2-5 bp repeated up to 50 times. May occur at 50-100 thousand locations in the genome. 

Another group of orphan receptors that as yet have no known ligand bind as homodimers or monomers to direct repeat sequences. 

Several collagen types do not form fibrils in tissues (Table 48—2). They are characterized by interruptions of the triple hehx with stretches of protein lacking Gly-X-Y repeat sequences. These non-Gly-X-Y sequences result in areas of globular structure interspersed in the triple hehcal structure. 

Repeat sequences probably constitute more than 50% of the genome. 

Repeat Sequences Probably Constitute More Than 50% of the Human Genome... 

---