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T G Fanning

Publications and source records attributed to T G Fanning.

At least 37 records · Page 2Linked to original sources
PubMed1992

Active LINE-1 retrotransposons in human testicular cancer.

An antibody to the protein encoded by the first open reading frame of the human LINE-1 (L1Hs) element was used to examine immunohistochemically 59 formalin-fixed, human testicular germ cell tumors. Six tumors were positive for L1Hs expression. In all cases the L1Hs-positive cells were epithelial and most had the very characteristic, undifferentiated appearance of embryonal carcinoma or yolk sac tumor cells. One L1Hs-positive tumor had metastasized to the lung and lymph nodes and the metastatic cells also expressed L1Hs. This is the first observation of widespread retrotransposon expression in human tissue. These observations raise the possibility that L1Hs-encoded proteins may function as oncoproteins in some cancers.

DNA Transposable Elements↗
PubMed1990

Translation of LINE-1 DNA elements in vitro and in human cells.

The LINE-1 (L1) family of interspersed DNA sequences found throughout the human genome (L1 Homo sapiens, L1Hs) includes active transposable elements. Current models for the mechanism of transposition involve reverse transcription of an RNA intermediate and utilization of element-encoded proteins. We report that an antiserum against the polypeptide encoded by the L1Hs 5' open reading frame (ORF1) detects, in human cells, an endogenous ORF1 protein as well as the ORF1 product of an appropriate transfecting recombinant vector. The endogenous polypeptide is most abundant in teratocarcinoma and choriocarcinoma cells, among those cell lines tested; it appears to be a single species of approximately 38 kDa. In contrast, RNAs synthesized in vitro from cDNAs representing full-length, polyadenylylated cytoplasmic L1Hs RNA yield, upon in vitro translation, ORF1 products of slightly different sizes. This is consistent with the fact that the various cDNAs are different and represent transcription of different genomic L1Hs elements. In vitro studies additionally suggest that translation of ORF1 is initiated at the first AUG codon. Finally, in no case was an ORF1-ORF2 fusion protein detected.

Animals↗
PubMed1989

Molecular evolution of centromere-associated nucleotide sequences in two species of canids.

The major centromeric satellite nt sequences present in the domestic dog (Canis familiaris) and in the grey fox (Urocyon cineroargenteus) have been examined. The dog satellite monomer is 737 bp long and contains 51% G + C; the grey fox satellite monomer is 880 b long and contains 54% G + C. The two satellites share three regions of 78, 92 and 314 bp with 70-80% sequence similarity. Sequence data from 16 monomers of dog satellite and 19 monomers of grey fox satellite demonstrate that the substitution spectra are different in the two canid species. For example, substitutions involving G or C residues are much more common in the grey fox satellite than in the domestic dog satellite despite their similar G + C contents.

Animals↗
PubMed1989

The Callimico goeldii (Primates, Platyrrhini) genome: karyology and middle repetitive (LINE-1) DNA sequences.

Callimico goeldii (Goeldi's marmoset) is a neotropical primate with 2n = 47,X1X2Y in the male, and 2n = 48,X1X1X2X2 in the female, due to a Y-autosome translocation. Karyological comparisons of Callimico, Callithrix jacchus and Cebus apella suggest that Callimico is a member of the Callitrichidae. Isozyme data and restriction mapping of LINE-1 repetitive elements in these species and in a variety of other neotropical primates confirm these findings and supply strong evidence for including Callimico in the Callitrichidae.

Animals↗
PubMed1989

Satellite DNA sequences in the neotropical marmoset Callimico goeldii (Primates, Platyrrhini).

Two families of tandemly repeated satellite DNAs were isolated from the neotropical primate Callimico goeldii (Goeldi's marmoset). One satellite, CgoA, is over 70% A + T and has a monomer length of 338 bp. The other satellite, CgoB, is 50% A + T and has a monomer length of 916 bp. Both CgoA and CgoB hybridize strongly with Callimico DNA, but not with the DNA of other new and old world primates. Based upon a neutral substitution rate of 1.5 X 10(-9)/site per year for primates, sequence data from 15 CgoA monomers indicate that the tandem array is at least 30 million years old. Since no other neotropical primate has amplified CgoA sequences, the data suggest that the ancestor of Callimico separated from the other neotropical primates at least 30 million years ago. This value is about fourfold larger than the value of 7-9 million years derived from immunological data by Sarich and Cronin (1980). Possible reasons for this discrepancy are discussed.

Animals↗
PubMed1988

Unit-length line-1 transcripts in human teratocarcinoma cells.

We have characterized the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-1 (L1) RNA present in a human teratocarcinoma cell line, NTera2D1, by primer extension and by analysis of cloned cDNAs. The bulk of the RNA begins (5' end) at the residue previously identified as the 5' terminus of the longest known primate genomic L1 elements, presumed to represent "unit" length. Several of the cDNA clones are close to 6 kilobase pairs, that is, close to full length. The partial sequences of 18 cDNA clones and full sequence of one (5,975 base pairs) indicate that many different genomic L1 elements contribute transcripts to the 6.5-kilobase cytoplasmic poly(A)+ RNA in NTera2D1 cells because no 2 of the 19 cDNAs analyzed had identical sequences. The transcribed elements appear to represent a subset of the total genomic L1s, a subset that has a characteristic consensus sequence in the 3' noncoding region and a high degree of sequence conservation throughout. Two open reading frames (ORFs) of 1,122 (ORF1) and 3,852 (ORF2) bases, flanked by about 800 and 200 bases of sequence at the 5' and 3' ends, respectively, can be identified in the cDNAs. Both ORFs are in the same frame, and they are separated by 33 bases bracketed by two conserved in-frame stop codons. ORF 2 is interrupted by at least one randomly positioned stop codon in the majority of the cDNAs. The data support proposals suggesting that the human L1 family includes one or more functional genes as well as an extraordinarily large number of pseudogenes whose ORFs are broken by stop codons. The cDNA structures suggest that both genes and pseudogenes are transcribed. At least one of the cDNAs (cD11), which was sequenced in its entirety, could, in principle, represent an mRNA for production of the ORF1 polypeptide. The similarity of mammalian L1s to several recently described invertebrate movable elements defines a new widely distributed class of elements which we term class II retrotransposons.

Amino Acid Sequence↗
PubMed1988

Chromosomal localization of satellite DNA sequences among 22 species of felids and canids (Carnivora).

In situ hybridization was carried out using cloned satellite DNAs from the domestic cat and domestic dog as probes to metaphase chromosomes from 12 species of felids and 10 species of canids. Autoradiographic silver grains along metaphase chromosomes were counted and analyzed with regard to the mean number of grains per cell in each species, their chromosomal location, and their presence or absence on specific autosomes or sex chromosomes, where known. Among the felids and canids there was a 7.6- and 8.9-fold statistically significant difference, respectively, in the mean number of grains per cell between the species having the minimum and maximum values. Among the felids, most grains occurred on the telomeres of D- and E-group chromosomes, although departures from this general pattern also occurred. For example, the Asian golden cat and the Bornean bay cat showed substantial labeling at the centromeric region of chromosome A1, and a number of species showed some labeling at the short-arm telomeres of B-group chromosomes. Among the canids, about 90% of all grains were located at autosomal centromeres, and grains were absent from the sex chromosomes. Grains are usually distributed at chromosomal locations that stain C-band positive; however, certain C-band-positive regions without grains probably do not contain the particular satellites studied here.

Animals↗
PubMed1988

Evolution of heterochromatin-associated satellite DNA loci in felids and canids (Carnivora).

Cloned satellite DNAs that hybridize primarily to C-band-positive regions of felid and canid chromosomes were used to probe the organization of satellite families in the genomes of 16 species of felids and 15 species of canids. Southern-blot and quantitative dot-blot experiments demonstrated that satellite families within the great cats (panthera lineage) vary considerably in regard to amount and/or sequence mismatch and vary some-what in regard to restriction patterns. Satellite families within the canids appeared to be more uniform in regard to both amount/sequence and restriction patterns, although some canid species did differ significantly from the consensus in both respects. Even though intrafamilial satellite restriction patterns were generally similar, every species could be shown to have a unique, characteristic pattern.

Animals↗
PubMed1987

Origin and evolution of a major feline satellite DNA.

A major satellite DNA has been cloned from the domestic cat (Felis catus) and characterized. The satellite monomer, termed FA-SAT, is 483 base-pairs in size, 64% G + C, and represents about 1 to 2% of the cat genome. A consensus sequence based upon partial sequence data from 21 independently isolated clones demonstrates: (1) FA-SAT is not composed of a series of shorter repeats, although about 25 copies, primarily imperfect, of the hexanucleotide TAACCC appear in the sequence; (2) there are many more CpG dinucleotides present in FA-SAT than expected for a random sequence of its size; and (3) 61% of all base substitutions in FA-SAT involve the replacement of G and C residues by A and T residues, indicating that FA-SAT is rapidly becoming A + T-rich. FA-SAT-related sequences are found in many mammals, where they appear to be scattered throughout the genome and not tandemly arranged as in the cat. An FA-SAT-related sequence was cloned from the domestic dog genome and sequenced, and shown to contain multiple copies of the same TAACCC hexanucleotide found in the cat satellite.

Animals↗
PubMed1985

Characterization of an endogenous retrovirus-repetitive DNA chimera in the mouse genome.

We found that an endogenous mouse mammary tumor provirus, GR-MTV-8, is embedded within a member of the BAM HI family of long interspersed repetitive mouse DNAs. GR-MTV-8 appears to be transcriptionally silent at its normal chromosomal position in the mouse genome. The provirus is transcriptionally active, however, when cloned and transfected into mouse cells (Kennedy et al., Nature (London) 295:622-624, 1982). We propose that the transcriptional inactivity of GR-MTV-8 in situ is due to an inhibitory effect, possibly involving DNA methylation, attributable to the flanking BAM HI element.

Animals↗
PubMed1985

Analysis of tissue-specific methylation patterns of mouse mammary tumor virus DNA by two-dimensional Southern blotting.

We used a two-dimensional Southern blotting procedure to analyze the tissue-specific methylation patterns of the five endogenous mouse mammary tumor viruses in the GR/A mouse strain. Our findings suggest that in certain tissues (brain, kidney, and liver) all proviruses are extensively methylated. In other tissues (spleen, placenta, and testes) all proviruses are hypomethylated to some degree. In these tissues individual proviruses display both quantitative and qualitative differences in methylation. We interpret the general patterns of tissue-specific hypomethylation in terms of a "hitch-hiker" model: mouse mammary tumor virus proviral methylation patterns reflect the tissue-specific activity of neighboring sequences. The observation that certain sites on particular proviruses are differentially methylated in a tissue-specific fashion may reflect tissue-specific differences in the makeup or conformation, or both, of proviral-containing chromatin.

Animals↗
PubMed1984

Mouse mammary tumor virus: specific methylation patterns of proviral DNA in normal mouse tissues.

The methylation state of endogenous mouse mammary tumor virus (MuMTV) proviral DNA was examined in normal mouse tissues. DNAs from various tissues were cleaved with the methylation-sensitive enzymes HhaI and HpaII and analyzed by Southern blotting. Tissue-specific MuMTV proviral DNA methylation patterns were found in the BALB/c, C3H, C57BL, GR/A, and GR-Mtv-2- mouse strains. MuMTV proviral DNA was hypomethylated in DNAs from the spleens and testes of all strains examined. The GR/A mouse strain, which was most thoroughly studied, also showed hypomethylation of MuMTV proviral DNA in bone marrow and placental tissues. Analysis of RNAs extracted from GR/A liver, mammary tumor, testes, placenta, and spleen tissues demonstrated that MuMTV proviral hypomethylation need not reflect significant proviral transcription.

Cell Transformation, Viral↗
PubMed1983

Homology between the KpnI primate and BamH1 (M1F-1) rodent families of long interspersed repeated sequences.

The KpnI and BamH1 (or M1F-1) families are the predominant sets of long interspersed repeated DNA sequences (LINEs) in primates and rodents, respectively. Recently, the sequences of several cloned subsegments from each family were determined in different laboratories. These sequences have now been compared and found to be homologous over at least 1400 bp. The data suggest that the two LINE families had a common progenitor and have been conserved in similar abundance although in divergent forms in the two mammalian orders.

Animals↗
PubMed1983

Size and structure of the highly repetitive BAM HI element in mice.

The BAM HI family of long interspersed DNAs in mice represent as much as 0.5% of the mouse genome. Cloned mouse DNA fragments which contain BAM HI/non-BAM HI junction sequences have been analyzed by restriction mapping and DNA sequencing. It has been found that BAM HI elements: (i) are approximately 7 kilobase pairs in size, (ii) are not bracketed by long repeated sequences analogous to the terminal repeats of proviruses and (iii) contain a poly-dA track at one end. The data strongly suggest that BAM HI elements arose by a process involving RNA intermediates. The beginning of the element, opposite the poly-dA track, contains a 22 base pair sequence exhibiting 65% homology to a ubiquitous mammalian sequence which may play a role in DNA replication (1). The poly-dA end of the element contains BAM5 and R sequences, both of which have been described previously (2,3).

Animals↗
PubMed1982

Characterization of a highly repetitive family of DNA sequences in the mouse.

A large proportion (0.5-1%) of total mouse DNA is cleaved by Bam HI into fragments whose size is about 500 base pairs. A cloned member of this repetitive family of DNA sequences (BAM5 family) was sequenced by the dideoxy chain termination procedure and shown to contain 507 base pairs. The sequence exhibited no unusual or remarkable features. Repetitive sequences complementary to the cloned BAM5 fragment were found in rat DNA, but not in feline or human DNA. Restriction mapping suggested that many BAM5 sequences were components of much larger repetitive DNAs which were scattered throughout the mouse genome. The BAM5 sequences within the larger repetitive DNAs did not appear to be arranged tandemly or as members of scrambled tandem repeats. RNA homologous to the cloned BAM5 sequence was detected in cultured mouse cells, but not in cultured rat cells.

Animals↗
PubMed1982

Methylation and amplification of mouse mammary tumor virus DNA in normal, premalignant, and malignant cells of GR/A mice.

The methylation and amplification of mouse mammary tumor virus (MuMTV) proviral DNA was investigated in normal, premalignant, and malignant tissues of GR/A mice. The proviral methylation pattern was examined with the restriction enzyme HhaI, which fails to cleave methylated DNA. MuMTV proviral DNA from liver, kidney, and heart was highly methylated. Proviral DNA was somewhat undermethylated in mammary gland cells from virgin and lactating mice and extensively undermethylated in cells from premalignant outgrowths, pregnancy-dependent tumors, and pregnancy-independent tumors. The restriction enzyme SacI was used to detect additional proviruses in the same cells. No additional proviral copies of MuMTV were detected in liver, kidney, or heart cells or in mammary gland cells from virgin mice. Some mammary gland cells from lactating mice appeared to contain additional copies of the endogenous, highly oncogenic GT-MTV-2 provirus. Premalignant outgrowth, pregnancy-dependent tumor, and pregnancy-independent tumor cells contained an average of two to three additional copies per cell of the GT-MTV-2 provirus. Thus, neoplasia in GR/A mice was directly associated with quantized increases in MuMTV proviral DNA undermethylation and GR-MTV-2 proviral DNA amplification. Restriction enzyme analysis suggested that premalignant outgrowths and pregnancy-dependent tumors both consisted largely of heterogenous cell populations, although some evidence of clonal dominance was detected.

Animals↗
PubMed1982

Identification of a unique mouse mammary tumor virus in the BALB/cNIV mouse strain.

We examined the genetic structure, in terms of restriction endonuclease recognition sites, of the milk-transmitted, low-oncogenic mouse mammary tumor virus (MuMTV) of the BALB/cNIV mouse strain. An analysis with EcoRI documented the presence of acquired cNIV proviruses in the mammary tumor DNAs of BALB/cNIV animals. A comparison of tumor DNAs digested with PstI showed that both the cNIV MuMTV and C3Hf MuMTV proviruses lacked the 4.3- and 1.1-kilobase pair fragments characteristic of C3H MuMTV patterns. An examination of mammary tumor and normal, nonmammary tissue DNAs with BamHI supported the idea that the cNIV MuMTV is identical to the C3Hf MuMTV and demonstrated that these two low-oncogenic proviruses are identical to the high-oncogenic C3H MuMTV provirus with respect to a pair of BamHI sites which define a 1.3-kilobase pair fragment. For each of the three MuMTV strains, we also mapped DNAs generated in isolated virions by reverse transcription of their genomic RNAs. Our results showed that cNIV and C3Hf MuMTV are distinct entities by virtue of an additional PstI site within the cNIV long terminal repeat sequence. Another unique feature of cNIV MuMTV revealed by the analysis of virion-generated DNAs was the existence of a family of genomes within the cNIV population. We concluded that cNIV is distinct from its presumptive C3Hf MuMTV predecessor.

Animals↗