Zea mays chloroplast ribosomal RNA genes are part of a 22,000 base pair inverted repeat

Zea mays chloroplast rDNA exists in two identical units. Each unit contains one sequence for the 16, 23 and 5S rRNAs in the order given. The 16 and 23S sequences in each unit are separated by a 2100 base pair (bp) spacer. The DNA sequence for 5S RNA is closely linked to that for the 23S RNA. Within the above unit, the three RNAs are transcribed from a single DNA strand. The two rDNA units on the circular chloroplast DNA molecule are separated from each other by 18,500 bp in one direction and by 106,100 bp in the other direction. The two rDNA units have an inverted orientation with respect to each other. Each rDNA unit is part of a 22,000 bp sequence which is repeated with inverted orientation.     

Constitutive and heat-inducible heat shock element binding activities of heat shock factor in a group of filamentous fungi

This study represents the initial characterization of the heat shock factor (HSF) in filamentous fungi. We demonstrate that HSFs from Beauveria bassiana, Metarhizium anisopliae, Tolypocladium nivea, Paecilomyces farinosus, and Verticillium lecanii bind to the heat shock element (HSE) constitutively (non-shocked), and that heat shock resulted in increased quantities and decreased mobility of HSF-HSE complexes. The monomeric molecular mass of both heat-induced and constitutive HSFs was determined to be 85.8 kDa by UV-crosslinking and the apparent molecular masses of the native HSF-HSE complexes as determined by pore exclusion gradient gel electrophoresis was 260 and 300 kDa, respectively. Proteolytic band clipping assays using trypsin and chymotrypsin revealed an identical partial cleavage profile for constitutive and heat-induced HSF-HSE complexes. Thus, it appears that both constitutive and heat-inducible complexes are formed by trimers composed of the same HSF molecule which undergoes conformational changes during heat shock. The mobility difference between the complexes was not abolished by enzymatic dephosphorylation and deglycosylation, indicating that the reduced mobility of the heat-induced HSF is probably due to a post-translational modification other than phosphorylation or glycosylation.     

The intragenomic polymorphism of a partially inverted repeat (PIR) in Gallus gallus domesticus, potential role of inverted repeats in satellite DNAs evolution

We report here the molecular characterization of the basic repeating unit of a novel repetitive family, partially inverted repeat (PIR), previously identified from chicken genome. This repetitive DNA family shares a close evolutionary relationship with XhoI/EcoRI repeats and chicken nuclear-membrane-associated (CNM) repeat. Sequence analyses reveal the 1430 bp basic repeating unit can be divided into two regions: the central region ( approximately 1000 bp) and the flanking region ( approximately 430 bp). Within the central region, a pair of repeats (86 bp) flanks the central core ( approximately 828 bp) in inversed orientation. Due to the tandem array feature shared by the repeating units, the inverted repeats fall between the central core and flanking region. Southern blot analyses further reveal the intragenomic polymorphism of PIR, and the molecular size of repeating units ranges from 1.1 kb to 1.6 kb. The identified monomer variants may result from multiple crossing-over events, implying the potential roles of inverted repeats in satellite DNAs variation.     

Segmental amplification in a satellite DNA: Restriction enzyme analysis of the major satellite ofMacropus rufogriseus

The 1.708 g/cc satellite DNA of the red necked wallaby is shown to consist of a number of related families of sequences arranged in tandem arrays. Particular families are subpopulations of other families; their distribution supports a model of successive amplification events during the generation of the satellite. In each amplification episode one 2,500 bp unit is multiplied into a tandemly repeated array of that unit (segmental amplification). The 1.708 g/cc sequences can be detected in related kangaroo species in much reduced amount, and with changes to the long order periodicity of the repeat units.     

Large inverted duplications are associated with gene amplification

Amplified DNA can be found in arrays of large repeated units, with each repeat unit containing a marker gene and surrounding DNA sequences. Amplified DNA sequences from established cell lines were assessed for the presence of repeat units in the form of inverted duplications. Inverted duplicated DNA was detected by virtue of its concentration-independent resistance to S1 hydrolysis after denaturation and rapid renaturation. Using this assay, inverted duplications were detected in amplified DNA (both DM and HSR configurations) containing the myc gene (16-50 copies/cell) in four human tumor cell lines and in amplified DNA containing the CAD gene (30-200 copies/cell) in three PALA-resistant BHK cell lines. The widespread association of inverted duplications with amplified DNA must bear on the amplification mechanism.