The development of a 120 basepair repetitive DNA sequence in Chironomus thummi is correlated to the duplication of defined chromosomal segments

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

BACKGROUND

The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.

RESULTS

The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.

CONCLUSIONS

We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.

Somatic breakpoints, distribution of repetitive DNA and non-LTR retrotransposon insertion sites in the chromosomes of Chironomus piger Strenzke (Diptera, Chironomidae)

Structural aberrations, their frequency and distribution as well as distribution of the tandem repetitive minisatellite DNA clusters of Alu and Hinf elements and two retroelements, the LINE NLRCth1 and the SINE CTRT1, were analyzed in the genome of the chironomid C. piger Strenzke larvae from a Bulgarian population. A consistent somatic variability in the structure of the polytene chromosomes was detected, showing that the C. piger genome is more actively rearranging than supposed before. Breakpoints were concentrated in proximal parts of chromosomes significantly more often than in distal parts. By FISH analysis we could detect only one locus containing Alu elements and 38 Hinf cluster loci which appear to be dispersed equally all over the chromosomes. The retrotransposons NLRCth1 and CTRT1 are present only in a few loci, but highly variant among different individuals. The mean number of NLRCth1 sites per individual was 18.4 +/- 2.09 and of CTRT1 was 54.8 +/- 8.42. A third of breakpoint locations were close to or coincide with a locus occupied by a retroelement (either NLRCth1 or CTRT1). Nineteen percent of breakpoints coincided with Hinf repetitive DNA elements. Some breakpoints were identical in the two sibling species C. piger and C. riparius Meigen (syn.: C. thummi thummi) and are considered as conserved hot spots of chromosome breakage.

Inherited and somatic cytogenetic variability in Palearctic populations of Chironomus riparius Meigen 1804 (Diptera, Chironomidae)

Inter- and intracytogenetic variability was analyzed in 13 natural Palearctic populations of Chironomus riparius Meigen 1804 (syn. Chironomus thummi) by examining hereditary and somatic aberrations (mainly inversions) of the salivary gland polytene chromosomes. In total, 77 different types of inherited inversion sequences and 184 different types of somatic inversions were found. The median percent frequency of inherited inversions was 1.4% and karyotypic divergence between populations was very low. Most hereditary inversions were endemic and always in a heterozygous state. Only six inversion sequences, each of them shared by two very distant populations, may be considered a relic of very ancient ancestral inversions. Unlike inherited inversions, occurrence of somatic aberrations seems to increase with the overall rise in the level of heavy metal pollution of the sediments from which larvae were sampled. In contrast with what occurs in populations of other chironomid species, populations of C. riparius do not seem to undergo a process of cytogenetic differentiation.

High mobility group proteins cHMG1a, cHMG1b, and cHMGI are distinctly distributed in chromosomes and differentially expressed during ecdysone dependent cell differentiation

The mammalian high mobility group proteins HMGI/Y and HMG1/2 are thought to play an architectural role in assembly of nucleoprotein structures. Counterparts to these proteins have recently been found in the cells of the Dipteran insect Chironomus. In this report we investigate the distribution of three abundant HMG proteins in interphase giant chromosomes of the midge, Chironomus. By means of the indirect immunofluorescence technique the cHMG1b and cHMGI proteins were localized in chromosomal puffs, suggesting their involvement in the organization of transcriptionally active chromatin. In contrast, the highly abundant protein cHMG1a was rather uniformly distributed in the chromosomes. The cHMGI protein, but not cHMG1a or cHMG1b, was detected in nucleoli, which may indicate a role in the transcription of ribosomal genes. The regions of the interphase chromosomes containing AT-rich DNA did not contain higher levels of the cHMGI and cHMG1b proteins. A correlation between the specific location of these proteins in chromatin and their synthesis and turnover rates was observed.

Structural and functional consequences of mutations within the hydrophobic cores of the HMG1-box domain of the Chironomus high-mobility-group protein 1a

The high-mobility-group protein 1 box domain (HMG1-BD) is a structural element found in several DNA-binding proteins in eukaryotic cells. Its structure is dominated by three alpha-helices. The spatial arrangement of these helices into an L-shaped molecule is maintained by a number of apolar residues organized into a main and a secondary hydrophobic core. To analyze the significance of these residues for proper folding, conformational stability, and ability to bind and bend DNA, we have mutated the highly conserved Trp14 of the Chironomus HMG1a protein and have synthesized a series of N-terminally truncated forms. The observed alterations in DNA-binding and DNA-bending characteristics were correlated with structural consequences, as revealed by CD spectroscopy, limited trypsin digestion, and transverse urea gradient gel electrophoresis. Mutation of the Trp14 residue (Chironomus [W14A]HMG1a) and deletion of the seven N-terminal residues, respectively, which are members of the main and the secondary core of Chironomus HMG1a, both resulted in a substantial unfolding of the protein. Unexpectedly, these mutants still retained their ability to bind and bend DNA. Conformational analysis of wild-type cHMG1a and [W14A]cHMG1a showed that the proteins unfold at 2-4 M urea. In contrast, their DNA complexes persisted even at 6-8 M of the denaturant. Multiple contacts between the HMG1-BD and the DNA are probably responsible for the unusual stability of the complexes.

The sex determining region of Chironomus thummi is associated with highly repetitive DNA and transposable elements

The dominant male sex determiner in chromosome III of the midge Chironomus thummi thummi is closely linked to a large cluster of tandem-repetitive DNA elements, the Cla elements, which are otherwise highly repetitive and distributed over more than 200 sites on all chromosomes. Chromosome III displays a hemizygous cluster of Cla elements in males but not in females. The chromosomal location of this hemizygous Cla element cluster is in the region of the male determiner M as localized by cytogenetic analysis. With Cla elements as hybridization probe, it was possible to clone a large part of the sex determining region. Molecular analysis of the DNA of males and females in this region displayed a number of differences between the two sexes. One striking difference is an unusual transposable element associated with the male sex determining region. The sex determining region also contains several other tandem-repetitive DNA elements in addition to the Cla elements. They are interspersed with single copy DNA. The accumulation of repetitive elements in the sex determining region interpreted as the result of a lack of recombination between the male/female heteromorphic region, although recombination in the other sections of chromosome III occurs.

The organization, localization and nucleotide sequence of the histone genes of the midge Chironomus thummi

Several histone gene repeating units containing the genes for histones H1, H2A, H2B, H3 and H4 were isolated by screening a genomic DNA library from the midge Chironomus thummi ssp. thummi. The nucleotide sequence of one complete histone gene repeating unit was determined. This repeating unit contains one copy of each of the five histone genes in the order and orientation mean value of H3 H4 mean value of H2A H2B H1 mean value of. The overall length is 6262 bp. The orientation, nucleotide sequence and inferred amino acid sequence as well as the chromosomal arrangement and localization are different from those reported for Drosophila melanogaster. The codon usage also shows marked differences between Chironomus and Drosophila. Thus the histone gene structure reported for Drosophila is not typical of all insects.

Photoaffinity labelling of the purine-cytosine permease of Saccharomyces cerevisiae

8-Azidoadenine was used as a photoaffinity reagent to characterize the purine-cytosine permease of Saccharomyces cerevisiae. It is a potent competitive inhibitor of cytosine uptake and irradiation of the cells incubated with the label induced the irreversible inactivation of cytosine uptake. Addition of excess cytosine prevented this labelling which was restricted to the outer face of the plasma membrane since it was not accumulated by the cells. In the strain with the amplified purine-cytosine permease gene the maximum cytosine uptake rate was increased 4-5-fold relative to wild type without a modification of the Michaelis constant of uptake (Kt); no uptake could be measured in the deleted strain. The relative amounts of specific labelling determined for the cells and for membrane preparations were 0, 1 and 4 for the null, the wild-type and the amplified strains, respectively. One major band specifically labelled by [3H]azidoadenine, corresponding to a polypeptide with an apparent molecular mass of 45 kDa, was observed in the wild type, amplified in the strain carrying the multicopy plasmid and not detected in the deleted strain. Therefore this polypeptide corresponds to the purine-cytosine permease.

New foldback transposable element TFB1 found in histone genes of the midge Chironomus thummi

A new Foldback transposable element (TFB1) has been found in the histone H1-H3 intergenic region in the midge Chironomus thummi thummi. TFB1 has long terminal inverted repeats, composed of short, degenerate subrepeats and is flanked by nine or ten base-pair "target site" duplications. TFB1 is present in at least two adjacent histone gene units in Ch. th. thummi, indicating a homogenization of histone gene repeats. The copy number and chromosomal distribution of TFB1 are different in the closely related subspecies Ch. th. thummi and Ch. th. piger. showing that amplification, elimination and transposition of TFB1 have occurred recently during evolution.

A new transposable element in Chironomus thummi

A 1.7 kb long transposable element called TECth1 was found in the 3' flanking region of a Chironomus thummi Balbiani ring gene. As shown by sequence comparison with a second copy, TECth1 is characterized by a perfect terminal inverted repeat of 17 bp flanked by a duplicated target site of 8 bp, four internal imperfect inverted repeats of 17 to 26 bp and terminal regions of about 0.25 kb with a high number of short direct repeats of the consensus sequence ACTTT or permutated and mutated forms such as TTTAC or ACTAT. The terminal inverted repeats and the 8 bp target site duplication are reminiscent of Drosophila P and hobo elements but no long open reading frame starting with ATG is present, suggesting that the two TECth1 copies studied represent deletion derivatives of a longer element coding for its own transposase. In situ hybridization revealed about 75 labelled sites distributed over all chromosomes with the Balbiani ring locus most strongly labelled. Fifty percent of the sites are specific for a given individual, and these variable sites are often heterozygous for the element.

The purine-cytosine permease gene of Saccharomyces cerevisiae: primary structure and deduced protein sequence of the FCY2 gene product

A 2.1 kb DNA segment carrying the purine-cytosine permease gene (FCY2) of Saccharomyces cerevisiae was sequenced, the primary structure of the protein (533 amino acids) deduced and a folding pattern in the membrane is proposed for the permease protein. Expression of the FCY2 gene product requires a functional secretory pathway and is reduced in mnn9, a mutant strain deficient in outer chain glycosylation. The FCY2 gene was mapped on the right arm of chromosome V close to the HIS1 gene.

A blotting procedure which preserves specific protein-DNA interactions

A quick, quantitative, and nonselective electrophoretic transfer of proteins from acetic acid-urea gels onto nitrocellulose, which preserves their ability to interact specifically with DNA, is achieved when exposure to dodecyl sulfate ions is avoided and a special type of nitrocellulose is used which contains cellulose phosphate ester. Filter-adsorbed histone H1 and other nuclear proteins from an insect, Chironomus thummi, were tested for binding of an AT-rich DNA sequence from the heterochromatin of the same organism under competitive conditions. On the blots, histone H1 exhibited the dependency of DNA binding on NaCl concentration and the preference for AT-rich DNA or poly[d(A-T)] found in quantitative filter-binding studies. By stepwise alteration of the NaCl molarity and competing Escherichia coli DNA concentration, respectively, in the binding buffer, two minor protein fractions could be identified in the heterogeneous extracts, one of which bound preferentially to AT-rich DNA, and the other bound to this sequence at up to 500 mM NaCl. Exposure to dodecyl sulfate led to a disappearance of the ability of these proteins to interact specifically with DNA. While nondenaturing transfer by diffusion (L. Levinger and A. Varshavsky (1982) Proc. Natl. Acad. Sci. USA 79, 7152) is a procedure that requires about 2 days, the present technique of gentle protein transfer for DNA binding studies requires only 2 to 3 h.

Cotransposition of a highly repetitive DNA element with flanking sequences in the genome of the midge Chironomus thummi

A family of highly repetitive DNA elements, the Cla-elements, is present in the genomes of the two sibling species Chironomus th. thummi and Ch. th. piger. These Cla-elements are organized in large tandem repetitive clusters as well as occurring as interspersed monomeric elements, in both subspecies. The analysis of a monomeric Cla-element and several kilobases of its flanking sequences from Ch. th. piger revealed that the short Cla-elements are cotransposed together with adjacent DNA. We found the same association of Cla-elements with specific flanking DNA in clones obtained from the rDNA of Ch. th. thummi and from nonribosomal Cla-DNA of Ch. th. piger. The Cla-element-flanking DNA is clearly also repetitive, but mainly of interspersed organization.

Identification of a polytene chromosome band containing a male sex determiner of Chironomus thummi thummi

Hybrid males of Chironomus thummi piger female x Ch. th. thummi male crosses were backcrossed with females of both parental stocks. Fourth-instar larvae of these backcrosses showed sex specific differences in the pairing behavior of region D3d-g in chromosome arm F of salivary gland chromosome III. Analysis of the banding pattern of region D3d-g after RB and quinacrine staining demonstrated that in piger female x thummi male hybrid males a single selectively stained band occurs within this region in the heterozygous condition at map position D3e1. This band could only be found in the thummi chromosome partner, it is heterochromatic and contains AT-rich DNA. In female hybrid larvae, however, such a selectively stained band is present in neither the thummi nor the piger chromosome region D3d-g. From these results it is concluded that the selectively stained band D3e1 represents the male sex determiner of our Ch. th. thummi stock and that the male is the heterogametic sex.

Clustered and interspersed repetitive DNA sequence family of Chironomus. The nucleotide sequence of the Cla-elements and of various flanking sequences

The nucleotide sequence of more than 30 cloned members of the clustered and interspersed repetitive Cla-sequence family present in the genome of various chironomids has been determined. In four cloned Cla-element clusters, the 5' and 3'-flanking sequences including the junctions between the Cla-element clusters and the flanking sequences were also sequenced. The repetitive Cla-elements, which are able to transpose under certain circumstances, have a monomer length ranging from 110 to 119 base-pairs, are very A + T-rich (greater than 80% A + T) and display numerous palindromic sequences. The Cla-elements are organized in small (4 elements) to medium-sized (greater than 30 elements) tandem repetitive clusters, which are dispersed over more than 200 sites of the chromosomes of Chironomus thummi thummi, including the non-transcribed spacer of the ribosomal DNA repeating unit. The tandem repetitive Cla-elements show anomalous behaviour during high-percentage polyacrylamide gel electrophoresis, indicating a bent or globular conformation. The flanking sequences are also repetitive, but the sequenced parts did not reveal any tandem repetitive arrangement. Near the junctions of the Cla-element clusters and the flanking sequences, short duplications are found, ranging from 5 to 12 bases, present in both sides of the Cla-element clusters. The Cla-elements might be involved in the hybrid dysgenesis phenomenon that is observed after crossings between the two subspecies Ch. th. thummi and Ch. th. piger.

Cloning and analysis of ribosomal DNA of Chironomus thummi piger and Chironomus thummi thummi. The nontranscribed spacer of Ch. th. thummi contains a highly repetitive DNA sequence

The ribosomal DNAs from Ch. thummi piger and Ch. th. thummi were cloned and analysed by a variety of restriction endonucleases. Comparison of rDNA clones from the two subspecies revealed a considerable length difference: the length of the analysed rDNA cistrons is approximately 9.0 kb for Ch. th. piger and approximately 14.5 kb for Ch. th. thummi. The nearly 5 kb additional DNA in Ch. th. thummi is clearly located within the non-transcribed spacer region, and consists of AT-rich, repetitive DNA elements. These elements with a basic repeat length of approximately 120 bp, are arranged tandemly in stretches of up to about 50 identical copies, which are characterized by a cleavage site for ClaI restriction endonuclease. They are found only in the Ch. th. thummi rDNA clones and not in the Ch. th. piger clones. Southern hybridizations between cloned ribosomal DNA and "centromeric" highly repetitive DNA have shown that the ribosomal repetitive Cla-elements are closely related to a highly repetitive DNA sequence family, which is present in various chromosomal sites particularly the centromeres. Sequence analysis has revealed more than 90% homology between the ribosomal Cla-elements and the "centromeric" Cla-elements.--Since it is clear from cytological investigations that Ch. th. piger with the small rDNA repeating unit is the phylogenetically older subspecies, we postulate a transposition of Cla-elements into the nucleolar DNA during the evolution of Ch. th. thummi.