The GenBank sequence database.
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Amino Acid Sequence↗
Biomedical subjects
I Karsch-Mizrachi
Publications and source records attributed to I Karsch-Mizrachi.
RNA interference demonstrates a role for nautilus in the myogenic conversion of Schneider cells by daughterless.
Schneider SL2 cells activate the myogenic program in response to the ectopic expression of daughterless alone, as indicated by exit from the cell cycle, syncytia formation, and the presence of muscle myosin fibrils. Myogenic conversion can be potentiated by the coexpression of DMEF2 and nautilus with daughterless. In RT-PCR assays Schneider cells express two mesodermal markers, nautilus and DMEF2 mRNAs, as well as very low levels of daughterless mRNA but no twist. Full-length RT-PCR products for nautilus and DMEF2 encode immunoprecipitable proteins. We used RNA-i to demonstrate that both endogenous nautilus expression and DMEF2 expression are required for the myogenic conversion of Schneider cells by daughterless. Coexpression of twist blocks conversion by daughterless but twist dsRNA has no effect. Our results indicate that Schneider cells are of mesodermal origin and that myogenic conversion with ectopic expression of daughterless occurs by raising the levels of daughterless protein sufficiently to allow the formation of nautilus/daughterless heterodimers. The effectiveness of RNA-i is dependent upon protein half-life. Genes encoding proteins with relatively short half-lives (10 h), such as nautilus or HSF, are efficiently silenced, whereas more stable proteins, such as cytoplasmic actin or beta-galactosidase, are less amenable to the application of RNA-i. These results support the conclusion that nautilus is a myogenic factor in Drosophila tissue culture cells with a functional role similar to that of vertebrate MyoD. This is discussed with regard to the in vivo functions of nautilus.
Animals↗
GenBank.
The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov
Animals↗
Type IIx myosin heavy chain transcripts are expressed in type IIb fibers of human skeletal muscle.
Several members of the sarcomeric myosin heavy chain (MHC) gene family have been mapped in the human genome but many of them have not yet been identified. In this study we report the identification of two human skeletal MHC genes as fast IIa and IIx MHC based on pattern of expression and sequence homology with the corresponding rat genes in the 3'-translated and untranslated regions. The distribution of these two gene products as well as that of the beta/slow MHC gene was analyzed in human skeletal muscles by in situ hybridization. The distribution of beta/slow, IIa, and IIx MHC transcripts defines three major muscle fiber types expressing a single MHC mRNA, i.e., either beta/slow, IIa, or IIx MHC mRNA, and two populations of hybrid fibers coexpressing beta/slow with IIa or IIa with IIx MHC mRNA. Fiber typing by ATPase histochemistry shows that IIa MHC transcripts are more abundant in histochemical type IIa fibers, whereas IIx MHC transcripts are more abundant in histochemical type IIb fibers.
Adolescent↗
Fast myosin heavy chains expressed in secondary mammalian muscle fibers at the time of their inception.
Mammalian skeletal muscle is generated by two waves of fiber formation, resulting in primary and secondary fibers. These fibers mature to give rise to several classes of adult muscle fibers with distinct contractile properties. Here we describe fast myosin heavy chain (MyHC) isoforms that are expressed in nascent secondary, but not primary, fibers in the early development of rat and human muscle. These fast MyHCs are distinct from previously described embryonic and neonatal fast MyHCs. To identify these MyHCs, monoclonal antibodies were used whose specificity was determined in western blots of MyHCs on denaturing gels and reactivity with muscle tissue at various stages of development. To facilitate a comparison of our results with those of others obtained using different antibodies or species, we have identified cDNAs that encode the epitopes recognized by our antibodies wherever possible. The results suggest that epitopes characteristic of adult fast MyHCs are expressed very early in muscle fiber development and distinguish newly formed secondary fibers from primary fibers. This marker of secondary fibers, which is detectable at the time of their inception, should prove useful in future studies of the derivation of primary and secondary fibers in mammalian muscle development.
Animals↗
The Rb97D gene encodes a potential RNA-binding protein required for spermatogenesis in Drosophila.
Many proteins that bind RNA contain a common RNA-binding domain, the RNP motif. We have been studying two Drosophila RNP motif proteins, Hrb98DE and Hrb87F, which are hnRNA-binding proteins. We report here the characterization of the Rb97D gene, which encodes a protein that is closely related to the Hrb proteins in the RNP motif domain, but has a distinctive proline-rich C-terminal domain. The gene is located at 97D on the right arm of the third chromosome, near the rough gene. Multiple transcripts from the Rb97D gene are present at varying levels throughout development. The transcripts are generated by alternative processing in the coding and 3' untranslated regions, and can encode two protein isoforms. Analysis of a mutant containing a P element inserted into the 5' untranslated region of the gene demonstrates that Rb97D is required for male fertility. Possible models for the function of Rb97D in testes are discussed.
Amino Acid Sequence↗
Three slow myosin heavy chains sequentially expressed in developing mammalian skeletal muscle.
Myosin heavy chain (MyHC) isoforms show a striking diversity of expression patterns during mammalian development. Using a set of monoclonal antibodies that recognize different epitopes on myosin heavy chain isoforms we show that there exist in human and rat skeletal muscle at least three isoforms of slow twitch myosin heavy chain. To facilitate a comparison of our results to others obtained using different antibodies or species, we have identified cDNAs encoding the epitopes recognized by the three slow antibodies. Using these reagents, we show that the onset of expression of three slow MyHC isoforms is temporally distinct during early gestation. This result suggests that a sequence of MyHC transitions plays an important role in determining muscle fiber function at fetal, neonatal, and adult stages.
Animals↗
Two new Drosophila genes related to human hematopoietic and neurogenic transcription factors.
We have identified two new basic domain helix-loop-helix (bHLH) genes in Drosophila melanogaster, DroSCL and DroNHLH. DroSCL was identified because of its homology to the mammalian hematopoietic transcription factor SCL. DroNHLH was similarly identified by homology to NHLH1 and NHLH2, two bHLH genes expressed in the developing mammalian nervous system. A partial DroSCL complementary DNA clone was obtained from an early pupal (5.5-7.5-day) Drosophila library. DroSCL is 73% identical to SCL within the 55-amino acid region of the bHLH domain. A DroNHLH complementary DNA clone was obtained from an early instar (I and II) Drosophila library. Its coding region consists of 162 amino acids and encodes a predicted protein of 18,312 daltons. DroNHLH is 87% identical to NHLH1 and NHLH2 within the bHLH domain. DroSCL and DroNHLH are located on the X chromosome. A 1.7-kilobase DroSCL transcript and a 1.5-kilobase DroNHLH transcript were detected by Northern analysis of total Drosophila RNA. Examination of Drosophila embryos by tissue in situ hybridization reveals restricted expression of both genes in a subset of cells in the developing central nervous system.
Amino Acid Sequence↗
Four sarcomeric myosin heavy chain genes are expressed by human fetal skeletal muscle cells differentiating in culture.
Expression of four sarcomeric myosin heavy chain (MHC) genes was examined in continuously passaged human fetal (18-22 week) skeletal myoblasts and in myoblasts induced to differentiate by low mitogen medium. Although embryonic MHC mRNA predominated at all time points following induction, three additional MHC genes were expressed at lower levels. These consisted of perinatal, slow, and fast skeletal MHC genes. Temporal regulation of MHC gene expression was observed. In myoblasts and early induced cultures, embryonic and fast transcripts were detected, accompanied in later induced cultures by the accumulation of perinatal and slow MHC transcripts. In situ hybridization analysis of uninduced cells revealed that sarcomeric MHC transcripts originated from a small population of spontaneously fused multinucleated cells. Taken together, these observations demonstrate that human fetal myoblasts induced to differentiate in culture execute a developmental program that includes temporally regulated expression of four distinct sarcomeric MHC genes.
Base Sequence↗
Generation of a full-length human perinatal myosin heavy-chain-encoding cDNA.
Vertebrate sarcomeric myosin heavy chains (MHC) are encoded by multigene families whose members show tissue-specific and developmentally-regulated patterns of expression. Molecular genetic studies have allowed the cloning of a small number of complete genes or cDNAs encoding MHC isoforms [see Warrick and Spudich, Annu. Rev. Cell Biol. 3 (1987) 379-421]. Reported here is the isolation and sequence of a 2.6-kb cDNA that encodes the subfragment 1 or head of a human perinatal skeletal MHC. A cDNA sequence encoding the rod portion of this isoform has been previously reported [Feghali and Leinwand, J. Cell Biol. 108 (1989) 1791-1797]. Polymerase chain reaction with fetal skeletal muscle RNA was used to join the two nonoverlapping cDNA sequences to construct a full-length sequence. The gene encoding the perinatal skeletal MHC has been localized to the cluster of skeletal MHC-encoding genes on chromosome 17.
Amino Acid Sequence↗
Expression and DNA sequence analysis of a human embryonic skeletal muscle myosin heavy chain gene.
Vertebrate myosin heavy chains (MHC) are represented by multiple genes that are expressed in a spatially and temporally distinct pattern during development. In order to obtain molecular probes for developmentally regulated human MHC isoforms, we used monoclonal antibodies to screen an expression cDNA library constructed from primary human myotube cultures. A 3.4 kb cDNA was isolated that encodes one of the first MHCs to be transcribed in human skeletal muscle development. A portion of the corresponding gene encoding this isoform has also been isolated. Expression of this embryonic MHC is a hallmark of muscle regeneration after birth and is a characteristic marker of human muscular dystrophies. During normal human development, expression is restricted to the embryonic period of development prior to birth. In primary human muscle cell cultures, devoid of other cell types, mRNA accumulation begins as myotubes form, reaches a peak 2 days later and declines to undetectable levels within 10 days. The expression of the protein encoded by the embryonic skeletal MHC gene follows a similar time course, lagging behind the mRNA by approximately two days. Thus, expression of the human embryonic gene is efficiently induced and then repressed in cultured muscle cells, as it is in muscle tissue. The study of the regulation of a human MHC isoform with a central role in muscle development and in muscle regeneration in disease states is therefore amendable to analysis at a molecular level.
Amino Acid Sequence↗
Complete genomes in WWW Entrez: data representation and analysis.
MOTIVATION: The large amount of genome sequence data now publicly available can be accessed through the National Center for Biotechnology Information (NCBI) Entrez search and retrieval system, making it possible to explore data of a breadth and scope exceeding traditional flatfile views. RESULTS: Here we report recent improvements for completely sequenced genomes from viruses, bacteria, and yeast. Flexible web based views, precomputed relationships, and immediate access to analytical tools provide scientists with a portal into the new insights to be gained from completed genome sequences. AVAILABILITY: Entrez Genomes can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Entrez/Genome/ org.html.
Amino Acid Sequence↗