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RBBP7 is a highly conserved WD-repeat protein that interacts with histone deacetylases and is a component of several co-repressor complexes. The mouse gene Rbbp7 spans ~20 kb, consists of at least 12 exons, and contains a C/T polymorphism in the 3' splice acceptor region of intron 3. We found that Rbbp7 contains a TATA-less promoter with multiple transcription initiation sites. In transient transfection...
α 1 -Proteinase inhibitor (α 1 -PI) is a member of the serpin superfamily of serine proteinase inhibitors, which function in maintaining homeostasis through regulation of numerous proteolytic processes. In laboratory mice (Mus musculus domesticus), α 1 -PI occurs in multiple isoforms encoded by a family of three to five genes that are polymorphic among inbred strains and that...
The cellular repressor of E1A-stimulated genes, CREG, is a secreted glycoprotein that enhances differentiation of pluripotent stem cells. Here we report two novel members of the CREG family, human CREG2 and mouse Creg2 cDNAs. The predicted human and mouse protein sequences exhibit 35% identity with CREG protein. Northern blot analyses demonstrate specific CREG2 and Creg2 transcription in brain-in...
Probing the functional complexity of the human genome will require new gene cloning techniques, not only to discover intraspecies gene homologs and interspecies gene orthologs, but also to identify alternatively spliced gene variants. We report homologous cDNA cloning methods that allow cloning of gene family members, genes from different species, and alternatively spliced gene variants. We cloned...
Fukuyama-type congenital muscular dystrophy (FCMD) is a severe autosomal-recessive muscular dystrophy accompanied by brain malformation. Previously, we identified the gene responsible for FCMD through positional cloning. Here we report the isolation of its murine ortholog, Fcmd. The predicted amino acid sequence of murine fukutin protein encoded by Fcmd is 90% identical to that of its human counterpart...
The multigene family encoding the five classes of replication-dependent histones has been identified from the human and mouse genome sequence. The large cluster of histone genes, HIST1, on human chromosome 6 (6p21-p22) contains 55 histone genes, and Hist1 on mouse chromosome 13 contains 51 histone genes. There are two smaller clusters on human chromosome 1: HIST2 (at 1q21), which contains six genes,...
Inbred mouse strains with age-related hearing loss (AHL) provide valuable models for studying the genetic basis of human presbycusis. Here we report the genetic mapping of a second AHL locus in mice (designated Ahl2) that is a major contributor to the 8- to 10-month difference in hearing loss onset times between NOD/LtJ and C57BL/6J mice. A whole-genome linkage scan of 110 progeny from a (C57BL/6JxNOD/LtJ)xNOD/LtJ...
We cloned the forkhead box C1 (FOXC1) gene, a member of the forkhead/winged-helix transcription factor family, as a transforming growth factor-β1 (TGF-β1) responsive gene. We showed that TGF-β1 upregulated transcription of FOXC1 in several human cancer cell lines. Ectopic expression of FOXC1 cDNA in HeLa cells, which lack both copies of the FOXC1 allele, restores the potential of TGF-β1 to inhibit...
The region of the dystrophin gene containing introns 45-50 is characterized by a high rate of recombination events that give rise to large deletions causing dystrophinopathy. The nucleotide sequence of this intronic region has recently been released in GenBank. With the aim of further understanding the mechanism favoring the occurrence of these deletions, we have characterized the distribution of...
Mutations in the gene MID1 are responsible for the X-linked form of Opitz syndrome, a genetic disorder that primarily affects the development of midline structures. Several mRNA isoforms with variant 5' ends have been reported for MID1, suggesting the presence of alternative transcription initiation sites. However, the genomic organization and expression pattern of the heterogeneous MID1 5'-untranslated...
A significant fraction of the human genome is composed of various types of transposable elements, which are divided into two broad classes based on their mechanism of transposition: via an RNA intermediate (retroelements) or via a DNA intermediate (DNA transposons). The retroelements, which include endogenous retroviruses, are the more prominent group in humans and seem to be restricted to eukaryotes...
We have previously shown that there is a temporal difference in human CRX: gene expression compared with that of mouse Crx. We have now characterized these genes at the genomic and transcriptional levels and here we expand on this earlier report. Human CRX: spans 25 kb and has six exons, and mouse Crx: spans 15 kb and has four exons. We isolated seven human and two mouse mRNAs generated by alternative...
Nesprin-1 and nesprin-2 (also known as Syne-1 and Syne-2,) are large (~3300-residue) vertebrate proteins associated with emerin and lamin A at the nuclear envelope of muscle cells and other cell types. We show that the previously described nesprins are short isoforms of giant proteins comprising an actin-binding amino-terminus connected to a carboxy-terminal klarsicht-related transmembrane domain...
Messenger RNA polyadenylation in male germ cells does not seem to require the AAUAAA polyadenylation signal required in all other cell types. To account for this difference, we found a variant form of the polyadenylation protein, the 64,000 Mr protein of the cleavage stimulation factor (CstF-64), in mouse meiotic and postmeiotic germ cells. This protein is a candidate to alter polyadenylation in those...
Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes...
Amplification of source DNA is a nearly universal requirement for molecular biology applications. The primary methods currently available to researchers are limited to in vivo amplification in Escherichia coli hosts and the polymerase chain reaction. Rolling-circle DNA replication is a well-known method for synthesis of phage genomes and recently has been applied as rolling circle amplification (RCA)...
The mouse tyrosine hydroxylase (Th) gene is located in an evolutionarily conserved imprinted gene cluster on distal chromosome 7. It is associated with a CpG island that spans the promoter of the gene. Using a bisulfite sequencing method we show that the Th promoter is fully methylated in both male and female mouse germ cells and in human spermatozoa, suggesting that it belongs to the newly identified...
Production of transgenic animals is an important technique for studying various biological processes. However, whether the integration of a particular transgene occurs randomly in the mouse genome has not been determined. Analysis by fluorescence in situ hybridization of the integration sites of the 142 EGFP (a mutant of green fluorescent protein) transgenic lines that we produced showed that the...
Human 11p15.5, as well as its orthologous mouse 7F4/F5, is known as the imprinting domain extending from IPL/Ipl to H19. OBPH1 and Obph1 are located beyond the presumed imprinting boundary on the IPL/Ipl side. We determined full-length cDNAs and complete genomic structures of both orthologues. We also investigated their precise imprinting and methylation status. The orthologues resembled each other...
Methylation of cytosines at CpG dinucleotides is essential for mammalian development. MeCP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of proteins that contain a methyl-CpG binding domain (MBD). Except for MBD4, these proteins are involved in gene silencing imposed by methylated DNA. We have identified a human gene that codes for a protein that is 42% identical to MBD3 and 38% identical to MBD2...
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