Biomedical subjects

L Podemski

Publications and source records attributed to L Podemski.

8 recordsLinked to original sources

PubMed2001

Characterization of the adenosine deaminase-related growth factor (ADGF) gene family in Drosophila.

A novel family of growth factors, with sequence similarity to adenosine deaminase, has been identified in various organisms including flesh fly, tsetse fly, sand fly, mollusk and human. The human homologue, CECR1, is a candidate gene for the genetic disorder cat eye syndrome. Here, we describe six members of this growth factor family in Drosophila and two in vertebrates. The six Drosophila genes, named adenosine deaminase-related growth factors (ADGF), are found at three different chromosomal locations, with one singleton, two in an inverted orientation, and three in a tandem arrangement. These genes show distinct patterns of expression as measured by RT-PCR and Northern blots, indicating gene-specific function. The presence of six ADGF genes in the Drosophila genome suggests that gene duplication and divergence has been important for these growth factors in insect development. Phylogenetic analysis of the 14 extant ADGF-like gene products shows there are at least three major groups, two of which are found in Drosophila. The third appears specific to the vertebrate line. Seven gene duplications are inferred among the ADGF-like genes, most of which occurred long before the origin of Drosophila. Our analysis predicts the existence of several other unsampled ADGF-like genes, both within the species examined here, and in other related invertebrates.

Amino Acid Sequence↗

PubMed2001

Whole arm inversions of chromosome 4 in Drosophila species.

Inversions of genetic segments during the evolution of Drosophila are well documented in the X chromosome and most autosomes, but little attention has been paid to chromosome 4, the smallest autosome or "dot chromosome" present in many Drosophila species. From our previous mapping we have defined probes that mark proximal, intermediate, and distal locations of chromosome 4 in D. melanogaster. In situ hybridizations on salivary gland polytene chromosomes with these probes show that the whole right arm, including genes within cytological region 101EF-102F, is inverted relative to D. simulans. We also used these probes to determine the orientation of the arm of the dot chromosome in nine species of Drosophila, including eight from the melanogaster subfamily. To account for the observed whole arm inversions of chromosome 4 in five of the nine species examined, we propose that three inversion events have occurred during the evolution of these species. These whole arm inversions may explain some of the unusual features of this chromosome.

Animals↗

PubMed2000

A physical map of the polytenized region (101EF-102F) of chromosome 4 in Drosophila melanogaster.

Chromosome 4, the smallest autosome ( approximately 5 Mb in length) in Drosophila melanogaster contains two major regions. The centromeric domain ( approximately 4 Mb) is heterochromatic and consists primarily of short, satellite repeats. The remaining approximately 1.2 Mb, which constitutes the banded region (101E-102F) on salivary gland polytene chromosomes and contains the identified genes, is the region mapped in this study. Chromosome walking was hindered by the abundance of moderately repeated sequences dispersed along the chromosome, so we used many entry points to recover overlapping cosmid and BAC clones. In situ hybridization of probes from the two ends of the map to polytene chromosomes confirmed that the cloned region had spanned the 101E-102F interval. Our BAC clones comprised three contigs; one gap was positioned distally in 102EF and the other was located proximally at 102B. Twenty-three genes, representing about half of our revised estimate of the total number of genes on chromosome 4, were positioned on the BAC contigs. A minimal tiling set of the clones we have mapped will facilitate both the assembly of the DNA sequence of the chromosome and a functional analysis of its genes.

Animals↗

PubMed1999

The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster.

The banded portion of chromosome 4 (the "dot" chromosome) in Drosophila melanogaster displays some properties of beta-heterochromatin, which is normally found within the centric domain of the chromosomes. The nature and distribution of repetitive elements on chromosome 4 could play a role in the establishment of this unusual chromatin configuration. We describe here one such element: a short, interspersed repetitive sequence named DINE-1. Determination of a consensus sequence for the element reveals that there are two conserved regions (A and B) separated by a highly variable spacer. The conserved sequences are approximately 400 bp long but degenerate at both ends, opening the possibility that a yet-to-be-discovered mother element may be present in the genome. DINE-1 bears few of the properties of the mammalian short interspersed elements (SINEs) to which it bears a superficial resemblance in size. It does not appear to be the product of reverse transcription and lacks any polymerase III promoter consensus. The elements are not flanked by target site duplications and their termini lack direct or inverted repeats, suggesting that they themselves are not transposable. Our analysis of cosmid clones from chromosome 4, and elsewhere in the genome, revealed that the euchromatic locations of DINE-1 are almost exclusively confined to chromosome 4. In situ hybridization of a DINE-1 probe to polytene chromosomes confirmed the preferential distribution along 4, in addition to its presence in the centric heterochromatin. This unusual genomic distribution of bias toward chromosome 4 is also seen in the sibling species, D. simulans, whose dot chromosomes exhibit poorly resolved polytene bands and lack crossing over during meiosis like those of D. melanogaster. However, the dot chromosome of D. virilis, which exhibits a well-defined banded structure on polytene chromosomes and can cross over, has only a single, discrete site of DINE-1 element hybridization. The presence of DINE-1 within these regions suggests a role in the heterochromatic nature of chromosome 4 in D. melanogaster and supports the contention that repeats accumulate in regions of diminished crossing over.

Animals↗

PubMed1999

Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences.

Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing approximately 5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus (ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met-hepatocyte growth factor receptor. The other cosmid contains only the two short 5'-most exons from the zinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the beta-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome.

Amino Acid Sequence↗

PubMed1998

Observations on template switching during DNA replication through long inverted repeats.

The bacterial Tn5 transposon consists of a pair of long inverted repeats flanking a central region that carries genes for antibiotic resistance. An analysis of DNA replication through Tn5 by two-dimensional gel electrophoresis has revealed two interesting features: (i) a spike representing X-shaped molecules, and (ii) a spot representing a barrier on the arc of Y-shaped replication intermediates. The electrophoretic behavior of various restriction fragments derived from this region indicates that the X molecules contain two linear Tn5 fragments joined together by a cross connection (Holliday junction). However, their formation is recA independent. The junction seems to connect the right inverted repeat of one fragment to the left inverted repeat of the other. The structure of the X molecules suggests that they could be formed by template switching when synthesis of the leading strand enters the right inverted repeat. One possible mechanism is that switching occurs at the center of a transient cruciform structure. A similar switching event, occurring when synthesis of the leading strand enters the left inverted repeat, could give rise to the barrier. These results imply that the inviability of palindromic DNA, which has previously been attributed to the slowing down of replication, may actually be caused by frequent template switching.

Bacterial Proteins↗

PubMed1997

Use of ordered deletions in genome sequencing.

Previous attempts to use the non-random approach for sequencing long DNA fragments have met with little success. As a result, nearly all genomic sequencing is done by the random (shotgun) approach, and the economy promised by the non-random approach has so far not materialized. Here we describe a simple system based on the use of ordered deletions that can be incorporated in the common strategies for genome sequencing. Long genomic fragments are cloned in the pAL-F cosmid and fragmented by digestion with specific restriction endonucleases. The digests are religated to subclone individual restriction fragments. The subclones are then subdivided by overlapping deletions and used for sequencing. We present the nucleotide sequences of two cosmid inserts from chromosome IV of Drosophila (containing the ci gene and the 5' end of the zfh-2 gene) that were determined by this method. This is the first report of successful sequencing of long genomic fragments by the use of overlapping deletions. Our calculations show that, with the present approach, sequence data can be acquired at a rate comparable to the shotgun approach but with significantly reduced numbers (approximately 30%) of sequencing runs. Hence, the use of ordered deletions should allow significant savings in both the amount and cost of sequencing work.

Animals↗

PubMed1995

The revised nucleotide sequence of Tn5.

A re-examination of the IS50 sequence revealed nine single-bp changes from the original published sequence. The changes account for four replacements in the deduced amino-acid sequences of the Tn5 transposase and inhibitor protein. Both IS50L and IS50R are 1534 bp in length, and the total length of Tn5, therefore, is 5820 bp.

Amino Acid Sequence↗