Insertion and excision of Caenorhabditis elegans transposable element Tc1

1988 ◽  
Vol 8 (2) ◽  
pp. 737-746
Author(s):  
D Eide ◽  
P Anderson
Keyword(s):  
Amino Acid ◽  
Caenorhabditis Elegans ◽  
Transposable Element ◽  
Dna Sequences ◽  
Germ Line ◽  
Consensus Sequence ◽  
Somatic Cells ◽  
Chain Gene ◽  
Imprecise Excision ◽  
Insertion Sites

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

scholarly journals Insertion and excision of Caenorhabditis elegans transposable element Tc1.

1988 ◽  
Vol 8 (2) ◽  
pp. 737-746 ◽  
Author(s):  
D Eide ◽  
P Anderson
Keyword(s):  
Amino Acid ◽  
Caenorhabditis Elegans ◽  
Transposable Element ◽  
Dna Sequences ◽  
Germ Line ◽  
Consensus Sequence ◽  
Somatic Cells ◽  
Chain Gene ◽  
Imprecise Excision ◽  
Insertion Sites

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

Stereotyped patterns of somatic hypermutation in subsets of patients with chronic lymphocytic leukemia: implications for the role of antigen selection in leukemogenesis

Blood ◽  
2008 ◽  
Vol 111 (3) ◽  
pp. 1524-1533 ◽  
Author(s):  
Fiona Murray ◽  
Nikos Darzentas ◽  
Anastasia Hadzidimitriou ◽  
Gerard Tobin ◽  
Myriam Boudjogra ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chronic Lymphocytic Leukemia ◽  
Heavy Chain ◽  
Germ Line ◽  
Somatic Hypermutation ◽  
Lymphocytic Leukemia ◽  
Chain Gene ◽  
Distinctive Features ◽  
Ighv Gene ◽  
Gene Usage

Abstract Somatic hypermutation (SHM) features in a series of 1967 immunoglobulin heavy chain gene (IGH) rearrangements obtained from patients with chronic lymphocytic leukemia (CLL) were examined and compared with IGH sequences from non-CLL B cells available in public databases. SHM analysis was performed for all 1290 CLL sequences in this cohort with less than 100% identity to germ line. At the cohort level, SHM patterns were typical of a canonical SHM process. However, important differences emerged from the analysis of certain subgroups of CLL sequences defined by: (1) IGHV gene usage, (2) presence of stereotyped heavy chain complementarity-determining region 3 (HCDR3) sequences, and (3) mutational load. Recurrent, “stereotyped” amino acid changes occurred across the entire IGHV region in CLL subsets carrying stereotyped HCDR3 sequences, especially those expressing the IGHV3-21 and IGHV4-34 genes. These mutations are underrepresented among non-CLL sequences and thus can be considered as CLL-biased. Furthermore, it was shown that even a low level of mutations may be functionally relevant, given that stereotyped amino acid changes can be found in subsets of minimally mutated cases. The precise targeting and distinctive features of somatic hypermutation (SHM) in selected subgroups of CLL patients provide further evidence for selection by specific antigenic element(s).

scholarly journals Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5' splice sites.

1994 ◽  
Vol 14 (5) ◽  
pp. 3426-3433 ◽  
Author(s):  
B Carr ◽  
P Anderson
Keyword(s):  
Caenorhabditis Elegans ◽  
Splice Site ◽  
General Characteristic ◽  
Chain Gene ◽  
Splice Sites ◽  
Wild Type ◽  
Reading Frame ◽  
Intron Splice ◽  
Mature Mrna ◽  
Imprecise Excision

Imprecise excision of the Caenorhabditis elegans transposon Tc1 from a specific site of insertion within the unc-54 myosin heavy chain gene generates either wild-type or partial phenotypic revertants. Wild-type revertants and one class of partial revertants contain insertions of four nucleotides in the unc-54 third exon (Tc1 "footprints"). Such revertants express large amounts of functional unc-54 myosin despite having what would appear to be frameshifting insertions in the unc-54 third exon. We demonstrate that these Tc1 footprints act as efficient 5' splice sites for removal of the unc-54 third intron. Splicing of these new 5' splice sites to the normal third intron splice acceptor removes the Tc1 footprint from the mature mRNA and restores the normal translational reading frame. Partial revertant unc-54(r661), which contains a single nucleotide substitution relative to the wild-type gene, is spliced similarly, except that the use of its new 5' splice site creates a frameshift in the mature mRNA rather than removing one. In all of these revertants, two alternative 5' splice sites are available to remove intron 3. We determined the relative efficiency with which each alternative 5' splice site is used by stabilizing frameshifted mRNAs with smg(-) genetic backgrounds. In all cases, the upstream member of the two alternative sites is used preferentially (> 75% utilization). This may reflect an inherent preference of the splicing machinery for the upstream member of two closely spaced 5' splice sites. Creation of new 5' splice sites may be a general characteristic of Tc1 insertion and excision events.

Activation of a transposable element in the germ line but not the soma of Caenorhabditis elegans

Nature ◽  
1987 ◽  
Vol 328 (6132) ◽  
pp. 726-728 ◽  
Author(s):  
John Collins ◽  
Bonnie Saari ◽  
Philip Anderson
Keyword(s):  
Caenorhabditis Elegans ◽  
Transposable Element ◽  
Germ Line

Characterization of the hypothetical proteins of Human Papillomavirus DNA consensus sequence

2021 ◽  
Vol 16 (7) ◽  
pp. 197-202
Author(s):  
Suruchi Jamkhedkar
Keyword(s):  
Genetic Algorithm ◽  
Human Papillomavirus ◽  
Amino Acid ◽  
High Risk ◽  
Amino Acid Sequence ◽  
Drug Development ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Software Tool ◽  
Molecular Techniques

The diagnosis of HPV infection is generally carried out using immunological and molecular techniques based on high risk to probable high-risk HPV strains. The aim of this work is to generate a global representation of HPV strains for diagnosis and drug development. In this work, all the complete genomic DNA sequences of registered Human Papillomavirus (HPV) strains available in NCBI GenBank were used to obtain a consensus sequence of HPV using the Genetic Algorithm. The consensus DNA sequence was translated using the ExPASy software tool. In all, six longest amino acids frames were selected from the six translated frames. The amino acid sequence identity was carried out using the BLAST tool. The six amino acid sequences were identified as E1, E2, E6, E7, L1 and L2. The homology modeling method (Modeller Software Tool) was used to determine the secondary structure of these six identified primary amino acid sequence. The percentage of similarity ranged from 24% in L2 to 100% in E7 and L1. The functions of these structural domains were also determined from PDB databank, InterProScan and CATH. Hence the consensus sequence built using a genetic algorithm is representative of the HPV genome which can be used for diagnostics and drug development purposes.

scholarly journals Extrachromosomal DNA transformation of Caenorhabditis elegans.

1985 ◽  
Vol 5 (12) ◽  
pp. 3484-3496 ◽  
Author(s):  
D T Stinchcomb ◽  
J E Shaw ◽  
S H Carr ◽  
D Hirsh
Keyword(s):  
Molecular Weight ◽  
Caenorhabditis Elegans ◽  
High Molecular Weight ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Germ Line ◽  
C Elegans ◽  
Linear Molecules ◽  
Foreign Dna ◽  
And Function

DNA was introduced into the germ line of the nematode Caenorhabditis elegans by microinjection. Approximately 10% of the injected worms gave rise to transformed progeny. Upon injection, supercoiled molecules formed a high-molecular-weight array predominantly composed of tandem repeats of the injected sequence. Injected linear molecules formed both tandem and inverted repeats as if they had ligated to each other. No worm DNA sequences were required in the injected plasmid for the formation of these high-molecular-weight arrays. Surprisingly, these high-molecular-weight arrays were extrachromosomal and heritable. On average 50% of the progeny of a transformed hermaphrodite still carried the exogenous sequences. In situ hybridization experiments demonstrated that approximately half of the transformed animals carried foreign DNA in all of their cells; the remainder were mosaic animals in which some cells contained the exogenous sequences while others carried no detectable foreign DNA. The presence of mosaic and nonmosaic nematodes in transformed populations may permit detailed analysis of the expression and function of C. elegans genes.

Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 657-665 ◽  
Author(s):  
Guy Drouin
Keyword(s):  
Dna Sequences ◽  
Germ Line ◽  
Somatic Cells ◽  
Repeated Sequences ◽  
Cyclopoid Copepod ◽  
Embryonic Cells ◽  
Repeated Dna ◽  
Chromatin Diminution ◽  
Mesocyclops Edax ◽  
Tandemly Repeated Dna

Chromatin diminution, i.e., the loss of selected chromosomal regions during the differentiation of early embryonic cells into somatic cells, has been described in taxa as varied as ciliates, copepods, insects, nematodes, and hagfish. The nature of the eliminated DNA has been extensively studied in ciliate, nematode, and hagfish species. However, the small size of copepods, which makes it difficult to obtain enough DNA from early embryonic cells for cloning and sequencing, has limited such studies. Here, to identify the sequences eliminated from the somatic cells of a copepod species that undergoes chromatin diminution, we randomly amplified DNA fragments from germ line and somatic line cells of Mesocyclops edax, a freshwater cyclopoid copepod. Of 47 randomly amplified germ line clones, 45 (96%) contained short, tandemly repeated sequences composed of either 2 bp CA-repeats, 8 bp CAAATAGA-repeats, or 9 bp CAAATTAAA-repeats. In contrast, of 83 randomly amplified somatic line clones, only 47 (57%) contained such short, tandemly repeated sequences. As previously observed in some nematode species, our results therefore show that there is partial elimination of chromosomal regions containing (CAAATAGA and CAAATTAAA) repeated sequences during the chromatin diminution observed in the somatic cells of M. edax. We speculate that chromatin diminution might have evolved repeatedly by recruitment of RNAi-related mechanisms to eliminate nonfunctional tandemly repeated DNA sequences from the somatic genome of some species.Key words: chromatin diminution, Mesocyclops edax, copepod, satellite DNA, hetorochromatin.

Extrachromosomal DNA transformation of Caenorhabditis elegans

1985 ◽  
Vol 5 (12) ◽  
pp. 3484-3496
Author(s):  
D T Stinchcomb ◽  
J E Shaw ◽  
S H Carr ◽  
D Hirsh
Keyword(s):  
Molecular Weight ◽  
Caenorhabditis Elegans ◽  
High Molecular Weight ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Germ Line ◽  
C Elegans ◽  
Linear Molecules ◽  
Foreign Dna ◽  
And Function

DNA was introduced into the germ line of the nematode Caenorhabditis elegans by microinjection. Approximately 10% of the injected worms gave rise to transformed progeny. Upon injection, supercoiled molecules formed a high-molecular-weight array predominantly composed of tandem repeats of the injected sequence. Injected linear molecules formed both tandem and inverted repeats as if they had ligated to each other. No worm DNA sequences were required in the injected plasmid for the formation of these high-molecular-weight arrays. Surprisingly, these high-molecular-weight arrays were extrachromosomal and heritable. On average 50% of the progeny of a transformed hermaphrodite still carried the exogenous sequences. In situ hybridization experiments demonstrated that approximately half of the transformed animals carried foreign DNA in all of their cells; the remainder were mosaic animals in which some cells contained the exogenous sequences while others carried no detectable foreign DNA. The presence of mosaic and nonmosaic nematodes in transformed populations may permit detailed analysis of the expression and function of C. elegans genes.

Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V

1989 ◽  
Vol 9 (2) ◽  
pp. 566-577
Author(s):  
M S Sachs ◽  
H Bertrand ◽  
R L Metzenberg ◽  
U L RajBhandary
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Chromosomal Mapping ◽  
Cytochrome Oxidase Subunit ◽  
Hydrophobic Domain ◽  
Oxidase Subunit ◽  
V Gene

The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.

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