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M F Singer

Publications and source records attributed to M F Singer.

At least 19 recordsLinked to original sources
PubMed1993

Undermethylation of specific LINE-1 sequences in human cells producing a LINE-1-encoded protein.

Nucleotide sequences near the 5' ends of some long interspersed elements-1 (LINE-1) from Homo sapiens (L1Hs) are undermethylated in cell lines which produce a L1Hs-encoded protein. In contrast, these sequences are methylated in cell lines with little or no detectable L1Hs expression. The fact that the 5' end of L1Hs is differentially methylated in cells exhibiting different levels of L1Hs expression suggests that the methylation state of this region plays a role in L1Hs expression.

Blotting, Southern↗
PubMed1992

Studies on p40, the leucine zipper motif-containing protein encoded by the first open reading frame of an active human LINE-1 transposable element.

Full-length human LINE-1 retrotransposons encode p40 proteins with varying electrophoretic mobilities under denaturing conditions. The p40 expressed from the first open reading frame in the LINE-1 copy designated L1.2A co-electrophoreses with the endogenous p40 in human teratocarcinoma cells. This finding is consistent with previous data indicating that L1.2A is an active element. The amino acid sequence in the central region of the L1.2A p40 accounts, at least in part, for its characteristic mobility. This region includes sequences which can, in principle, form a leucine zipper.

Amino Acid Sequence↗
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↗
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↗
PubMed1987

Genomic organization of low copy number sequences that are associated with deca-satellite DNA in the monkey genome.

A previously described segment of African green monkey DNA (cloned in phage lambda MkA) contains deca-satellite linked to DNA sequences that are estimated to occur once per genome. Sequences homologous to the low copy number sequences in lambda MkA are also associated with species-specific satellite DNAs in the human and mouse genomes. A second clone, lambda Mk8, contains a monkey DNA region that is colinear and homologous to a portion of the low copy number sequences in lambda MkA, but no satellite sequences. The two cloned segments are markedly different starting at a point proximal to the satellite DNA region in lambda MkA. DNA-blotting experiments indicate that lambda Mk8 but not lambda MkA represents the typical genomic organization and that the low copy number segments occur only once per haploid genome. The data suggest that rearrangements such as deletions or inversions occurring in monkey cells account in part for the structure of lambda MkA. Additional rearrangements may have occurred during cloning in E. coli. This unique chromosomal region may be particularly susceptible to recombination.

Animals↗
PubMed1986

Analysis of LINE-1 family sequences on a single monkey chromosome.

The structure of LINE-1 (L1Ca) family members present on African green monkey chromosome CAE-19 is compared with that of the entire set of L1Ca sequences present in the monkey genome. The analysis involved annealing of cloned subsegments of monkey L1 family members to DNA-blots containing restriction endonuclease digests of either total monkey liver DNA or DNA isolated from a monkey/mouse somatic cell hybrid carrying the single monkey chromosome. In addition, L1Ca segments cloned from hybrid cell DNA were characterized by restriction endonuclease mapping and hybridization. The data indicate that, taken as a whole, the set of L1Ca sequences on CAE-19 tends to differ in characteristic ways from the set present in the total monkey genome.

Animals↗
PubMed1986

Isolation of low-copy-number sequences that neighbor satellite DNA in mammals.

To investigate the role of satellite DNA in eukaryotic genomes, we isolated from an African green monkey (Cercopithecus aethiops) genomic library cloned segments containing the previously described deca-satellite linked to low-copy-number genomic sequences. Three such clones were obtained. The low-copy-number sequences in the three clones do not cross-hybridize suggesting that they derive from different genomic loci. The structure of one of the clones, lambda MkA, is described in detail. Subcloned segments containing the low-copy-number sequences from lambda MkA anneal to monkey, human and mouse genomic DNA. The subcloned probes were used to select clones containing homologous sequences from a second, independent monkey library as well as from human and mouse genomic libraries. Several of the newly isolated monkey clones hybridized to probes containing the species-specific deca- and alpha-satellites, confirming the genomic association of the low-copy-number sequence in lambda MkA with satellite DNA. Moreover, several of the human and mouse clones hybridized to species-specific human and mouse satellite DNAs, respectively. These experiments indicate that the low-copy-number sequence in lambda MkA and its association with satellite DNA is conserved in primates and rodents.

Animals↗
PubMed1985

Expression of a cytoplasmic LINE-1 transcript is regulated in a human teratocarcinoma cell line.

The major primate family of highly repeated, long interspersed DNA sequences (LINE-1, previously Kpn I, family) includes several thousand 6-kilobase-pair long units that terminate in an A-rich stretch. Recent evidence indicates that long open reading frames occur in at least some family members. These results suggested that one or more LINE-1 family members might be structural genes. Accordingly, a variety of human cell lines was analyzed for the presence of a cytoplasmic, polyadenylylated RNA homologous to LINE-1 sequences. Such a transcript was detected in a human pluripotent teratocarcinoma cell line (NTera2 clone D1). The RNA is approximately 6.5 kilobases long and is homologous to the LINE-1 strand with the open reading frames. The abundance of the transcript varies markedly with previously described variations in the phenotype of these cells and is highest when the cells display the embryonal carcinoma morphology. This RNA may represent a mRNA transcribed from one or more functional genes in the LINE-1 family.

Cell Line↗
PubMed1984

Continuous reorganization leads to extensive polymorphism in a monkey centromeric satellite.

Previously we reported the existence of a highly polymorphic satellite, deca-satellite, in the African green monkey genome; deca-satellite probe anneals to complex sets of repeated restriction endonuclease fragments that differ from individual to individual in the monkey population. Here we present experiments aimed at clarifying the structure and organization of deca-satellite sequences and investigating the mechanisms that generate the polymorphisms. Deca-satellite represents less than 1% of the monkey genome but the percentage varies from one monkey to another. The core sequence 5'-C-C-G-G within the ten base-pair deca-satellite repeat unit is well conserved and the central 5'-C-G is sometimes but not always methylated. Restriction endonuclease analysis with BamHI and EcoRI defines separate satellite domains that have evolved in an independent manner. In situ hybridization shows deca-satellite to be located at the centromeric regions of some but not all monkey chromosomes. This location is independently confirmed by a high frequency, in monkey libraries, of segments containing junctions between deca-satellite and alpha-satellite, the main monkey centromeric satellite. The total number of metaphase chromosomes that show centromeric grains after in situ hybridization with a deca-satellite probe varies from one monkey to another. Moreover, in situ hybridization to endoreduplicated diplochromosomes showed that deca-satellite is occasionally distributed asymmetrically on one or the other of the two pairs of sister chromatids in one diplochromosome. This indicates that major reorganization of the satellite can occur frequently in somatic cells. We discuss several possible mechanisms by which deca-satellite sequences could be either amplified or deleted during a single replicative cycle. Also, on the basis of the marked fluidity of deca-satellite abundance and organization and other well-known attributes of centromeric satellites, we suggest that the existence and maintenance of centromeric satellite rests on the role of the tandem repeats themselves and not on any particular nucleotide sequence, repeat length or organization.

Animals↗
PubMed1984

Transcription from SV 40-like monkey DNA sequences.

The ability of an African green monkey genomic segment, homologous to the regulatory region of SV40, to promote transcription in monkey cells has been investigated. Genomic transcripts from CV-1 cells hybridize to both strands of this SV40-like segment. Further examination of the promoter potential of the SV40-like segment using expression vectors suggests that the SV40-like region contains at least part of the necessary information for promoting transcription in both directions. In addition, the latter experiments suggest that sequences several hundred nucleotides away in the genome modulate the transcription initiating at multiple sites in the SV40-like segment.

Animals↗