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At least 1,387 records · Page 77Linked to original sources
PubMed1999

Asymmetric and node-specific nodal expression patterns are controlled by two distinct cis-acting regulatory elements.

The TGFbeta-related molecule Nodal is required for establishment of the anterior-posterior (A-P) and left-right (L-R) body axes of the vertebrate embryo. In mouse, several discrete sites of nodal activity closely correlate with its highly dynamic expression domains. nodal function in the posterior epiblast promotes primitive streak formation, whereas transient nodal expression in the extraembryonic visceral endoderm is essential for patterning the rostral central nervous system. Asymmetric nodal expression in the developing node and at later stages in left lateral plate mesoderm has been implicated as a key regulator of L-R axis determination. We have analyzed the cis-regulatory elements controlling nodal expression domains during early development. We show that the regulatory sequences conferring node-specific expression are contained in an upstream region of the locus, whereas early expression in the endoderm and epiblast and asymmetric expression at later stages on the left side of the body axis are controlled by a 600-bp intronic enhancer. Targeted deletion of a 100-bp subregion of this intronic enhancer eliminates nodal expression in the early epiblast and visceral endoderm and disrupts asymmetric expression in the node and lateral plate mesoderm. Thus, developmentally regulated nodal expression at distinct tissue sites during A-P and L-R axis formation is potentially controlled by common transcriptional activators.

Animals↗
PubMed1999

Neurogenin1 and neurogenin2 control two distinct waves of neurogenesis in developing dorsal root ganglia.

Different classes of sensory neurons in dorsal root ganglia (DRG) are generated in two waves: large-diameter trkC+ and trkB+ neurons are born first, followed by small-diameter trkA+ neurons. All such neurons require either neurogenin (ngn) 1 or 2, two neuronal determination genes encoding basic helix-loop-helix (bHLH) transcription factors. ngn2 is required primarily if not exclusively for the generation of trkC+ and trkB+ neurons, whereas the generation of most or all trkA+ neurons requires ngn1. Comparison with previous lineage tracing data in the chick suggests that this dichotomy reflects a requirement for the two ngns in distinct sensory precursor populations. The neurogenesis defect in ngn2(-/-) embryos is transient and later compensated by ngn1-dependent precursors, suggesting that feedback or competitive interactions between these precursors may control the proportion of different neuronal subtypes they normally produce. These data reveal remarkable parallels in the roles of bHLH factors during neurogenesis in the DRG, and myogenesis in the neighboring myotome.

Animals↗
PubMed2002

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including the Xist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5' of Xist that was recently shown to attract histone modification early after the onset of X inactivation.

Animals↗
PubMed2001

Evolutionarily conserved sequences on human chromosome 21.

Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide arrays as a rapid approach for comparing human sequences with the DNA of multiple species whose sequences are not presently available. High-density arrays representing approximately 22.5 Mb of nonrepetitive human chromosome 21 sequence were synthesized and then hybridized with mouse and dog DNA to identify sequences conserved between humans and mice (human-mouse elements) and between humans and dogs (human-dog elements). Our data show that sequence comparison of multiple species provides a powerful empiric method for identifying actively conserved elements in the human genome. A large fraction of these evolutionarily conserved elements are present in regions on chromosome 21 that do not encode known genes.

Animals↗
PubMed1998

Alternative gene form discovery and candidate gene selection from gene indexing projects.

Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index classes if and only if they share a common progenitor gene. Accurate gene indexing facilitates gene expression studies, as well as inexpensive and early gene sequence discovery through assembly of ESTs that are derived from genes that have not been sequenced by classical methods. We extend, correct, and enhance the information obtained from index groups by splitting index classes into subclasses based on sequence dissimilarity (diversity). Two applications of this are highlighted in this report. First it is shown that our method can ameliorate the damage that artifacts, such as chimerism, inflict on index integrity. Additionally, we demonstrate how the organization imposed by an effective subpartition can greatly increase the sensitivity of gene expression studies by accounting for the existence and tissue- or pathology-specific regulation of novel gene isoforms and polymorphisms. We apply our subpartitioning treatment to the UniGene gene indexing project to measure a marked increase in information quality and abundance (in terms of assembly length and insertion/deletion error) after treatment and demonstrate cases where new levels of information concerning differential expression of alternate gene forms, such as regulated alternative splicing, are discovered. [Tables 2 and 3 can be viewed in their entirety as Online Supplements at http://www.genome.org.]

Alternative Splicing↗
PubMed2003

Discovering novel cis-regulatory motifs using functional networks.

We combined functional information such as protein-protein interactions or metabolic networks with genome information in Saccharomyces cerevisiae to predict cis-regulatory motifs in the upstream region of genes. We developed a new scoring metric combining these two information sources and used this metric in motif discovery. To estimate the statistical significance of this metric, we used brute-force randomization, which shows a consistent well-behaved trend. In contrast, real data showed complex nonrandom behavior. With conservative parameters we were able to find 42 degenerate motifs (that touch 40% of yeast genes) based on 647 original patterns, five of which are well known. Some of these motifs also show limited spatial position in the promoter, indicative of a true motif. We also tested the metric on other known motifs and show that this metric is a good discriminator of real motifs. As well as a pragmatic motif discovery method, with many applications beyond this work, these results also show that interacting proteins are often coordinated at the level of transcription, even in the absence of obvious coregulation in gene expression data sets.

Amino Acid Motifs↗
PubMed1994

Leafy Cotyledon Mutants of Arabidopsis.

We have previously described a homeotic leafy cotyledon (lec) mutant of Arabidopsis that exhibits striking defects in embryonic maturation and produces viviparous embryos with cotyledons that are partially transformed into leaves. In this study, we present further details on the developmental anatomy of mutant embryos, characterize their response to abscisic acid (ABA) in culture, describe other mutants with related phenotypes, and summarize studies with double mutants. Our results indicate that immature embryos precociously enter a germination pathway after the torpedo stage of development and then acquire characteristics normally restricted to vegetative parts of the plant. In contrast to other viviparous mutants of maize (vp1) and Arabidopsis (abi3) that produce ABA-insensitive embryos, immature lec embryos are sensitive to ABA in culture. ABA is therefore necessary but not sufficient for embryonic maturation in Arabidopsis. Three other mutants that produce trichomes on cotyledons following precocious germination in culture are described. One mutant is allelic to lec1, another is a fusca mutant (fus3), and the third defines a new locus (lec2). Mutant embryos differ in morphology, desiccation tolerance, pattern of anthocyanin accumulation, presence of storage materials, size and frequency of trichomes on cotyledons, and timing of precocious germination in culture. The leafy cotyledon phenotype has therefore allowed the identification of an important network of regulatory genes with overlapping functions during embryonic maturation in Arabidopsis.

Journal Article↗
PubMed1990

Mycoplasma pneumoniae DNA gyrase genes.

We have identified a clone from a lambda EMBL3 library containing a 19kb insert of Mycoplasma pneumoniae DNA which includes the genes that encode both subunits of DNA gyrase. The gyrB gene and the 5' end of the gyrA gene have been subcloned into M13. The gyrB gene is 1953bp in length and overlaps the gyrA gene by a single base. The nucleotide sequence of these subclones has significant homology to previously reported gyrase genes. In terms of the size of the gyrB gene and its proximity to the gyrA gene, M. pneumoniae is more similar to Bacillus subtilis than to Escherichia coli.

Amino Acid Sequence↗
PubMed1992

Heterogeneous Expression Patterns of Mammalian Potassium Channel Genes in Developing and Adult Rat Brain.

Voltage-gated K+ channels in the mammalian brain are functionally heterogeneous. Mechanisms which may underlie heterogeneity are the expression of multiple K+ channel subunit genes, alternative splicing and the formation of heteromultimers from different subunits. To examine the molecular basis of regional and cell-specific K+ channel expression in rat brain in situ hybridization techniques were used. The transcript distribution patterns of 11 cloned mammalian K+ channel genes encoding both slow- and fast-inactivating K+ channels from four different gene families were examined at different stages of development. The results show that each subunit-specific messenger RNA (mRNA) is independently expressed and is characterized by an individual expression pattern. In the hippocampal formation transcripts of RCK2, RCK3, RCK4, RCK5, Raw3 and rat Shal genes are heterogeneously expressed and regulated during postnatal development. RCK1, Raw1, Raw2 and DRK1 mRNAs, on the other hand, are present in the hippocampus throughout postnatal life. The expression patterns of the 11 genes partially overlap, suggesting the formation of different heteromultimeric K+ channel complexes.

Journal Article↗
PubMed1989

Two species of the phosphoprotein mRNA with differently edited reading frames discovered in measles virus infected Vero cells. Brief report.

One cDNA clone representing the phosphoprotein mRNA sequence of the Edmonston strain of measles virus contained 4 G nucleotides at a particular position. Two other clones contained 3 G nucleotides at the same position. Otherwise the nucleotide sequence were identical. The mRNA with 3 G nucleotides codes for the 70 kD phosphoprotein. The mRNA with 4 G nucleotides may code for a putative new peptide with 231 aminoterminal amino acids in common with the P protein whereas the 68 carboxyterminal amino acids are different from any amino acid sequence of the phosphoprotein. Thus the consequence of the insertion of one additional G is a translational shift to a shorter open reading frame. There are several indications that the observation is of biological significance.

Animals↗
PubMed2025

Genome sequencing and population genetics provide insights into local adaptation of Opisthopappus species on cliff environments of Taihang Mountains.

Local adaptation represents a pivotal theme in evolutionary biology. The Opisthopappus genus, comprising Opisthopappus longilobus and O. taihangensis, thrives on the cliffs of the Taihang Mountains. During their evolutionary history, two species are hypothesized to have locally adapted to their cliff habitats. In the present study, we employed a combined approach of whole-genome sequencing of O. taihangensis and population genomic analysis from both species to gain deeper insights into their patterns of local adaptation. Our results revealed that the expansive genome of O. taihangensis (3010.18 Mb), a consequence of a whole-genome duplication (WGD) event, coupled with a high proportion of repetitive sequences (82.70%), was postulated as one of its adaptive strategies. A clear differentiation between O. taihangensis and O. longilobus was observed, with the two species diverging approximately 17.57 million years ago (Mya), with O. longilobus serving as the ancestor. Since their divergence, limited gene flow was observed between the two species. Post-divergence, the effective population sizes of both species expanded, yet underwent a dramatic reduction at approximately 0.07 Mya. Furthermore, a total of 798 adaptive genes were identified, of which 207 overlapped with expanded genes, and eight genes were found to be under positive selection. These genes primarily regulated the growth and development of both species via pathways such as oxidation-reduction and ubiquitin-proteasome, enabling them to withstand climate changes. These findings provide profound insights into the local adaptation of Opisthopappus species to the cliff environments and offer valuable clues for further exploring the local adaptation among various cliff-dwelling organisms.

Adaptation, Physiological↗
PubMed2003

Human chromosome 7: DNA sequence and biology.

DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.

Animals↗
PubMed2001

Analysis of the capsule biosynthetic locus of Mannheimia (Pasteurella) haemolytica A1 and proposal of a nomenclature system.

A 16-kbp DNA region that contains genes involved in the biosynthesis of the capsule of Mannheimia (Pasteurella) haemolytica A1 has been characterized. The gene cluster can be divided into three regions like those of the typical group II capsule biosynthetic clusters in gram-negative bacteria. Region 1 contains four genes (wzt, wzm, wzf, and wza) which code for an ATP-binding cassette transport apparatus for the secretion of the capsule materials across the membranes. The M. haemolytica A1 wzt and wzm genes were able to complement Escherichia coli kpsT and kpsM mutants, respectively. Further, the ATP binding activity of Wzt was demonstrated by its affinity for ATP-agarose, and the lipoprotein nature of Wza was supported by [(3)H]palmitate labeling. Region 2 contains six genes; four genes (orf1/2/3/4) code for unique functions for which no homologues have been identified to date. The remaining two genes (nmaA and nmaB) code for homologues of UDP-N-acetylglucosamine-2-epimerase and UDP-N-acetylmannosamine dehydrogenase, respectively. These two proteins are highly homologous to the E. coli WecB and WecC proteins (formerly known as RffE and RffD), which are involved in the biosynthesis of enterobacterial common antigen (ECA). Complementation of an E. coli rffE/D mutant with the M. haemolytica A1 nmaA/B genes resulted in the restoration of ECA biosynthesis. Region 3 contains two genes (wbrA and wbrB) which are suggested to be involved in the phospholipid modification of capsular materials.

ATP-Binding Cassette Transporters↗
PubMed1986

Genetic organization of plasmid R1162 DNA involved in conjugative mobilization.

DNA involved in the mobilization of broad-host-range plasmid R1162 was localized to a region of 2.7 kilobases within coordinates 3.4 to 6.1 kilobases on the R1162 map. By examining the transfer properties of plasmids containing cloned fragments of DNA from within this region, we showed that at least four trans-active products and a cis-active site (oriT) were involved in mobilization. A cloned DNA fragment of 155 base pairs was capable of providing full oriT activity. This fragment was located within 600 base pairs of DNA containing the origin of replication of R1162, and its nucleotide sequence and that of neighboring DNA were determined. Activation of oriT required R1162-encoded, trans-acting products. Deletions which resulted in the loss of one or more of these had a variable effect on transfer efficiency and indicated the presence of both essential and nonessential Mob products. Regions encoding these products flanked oriT and in one case appeared to overlap a gene essential for plasmid replication. The implications of these findings with respect to the broad host range of R1162 are discussed.

Base Sequence↗
PubMed2005

Regulation of finP transcription by DNA adenine methylation in the virulence plasmid of Salmonella enterica.

DNA adenine methylase (Dam(-)) mutants of Salmonella enterica serovar Typhimurium contain reduced levels of FinP RNA encoded on the virulence plasmid. Dam methylation appears to regulate finP transcription, rather than FinP RNA stability or turnover. The finP promoter includes canonical -10 and -35 modules and depends on the sigma(70) factor. Regulation of finP transcription by Dam methylation does not require DNA sequences upstream from the -35 module, indicating that Dam acts at the promoter itself or downstream. Unexpectedly, a GATC site overlapping with the -10 module is likewise dispensable for Dam-mediated regulation. These observations indicate that Dam methylation regulates finP transcription indirectly and suggest the involvement of a host factor(s) responsive to the Dam methylation state of the cell. We provide evidence that one such factor is the nucleoid protein H-NS, which acts as a repressor of finP transcription in a Dam(-) background. H-NS also restrains transcription of the overlapping traJ gene, albeit in a Dam-independent fashion. Hence, the decreased FinP RNA content found in Dam(-) hosts of S. enterica appears to result from H-NS-mediated repression of finP transcription.

Adenine↗
PubMed2006

Unusual naturally occurring humoral and cellular mutated epitopes of hepatitis B virus in a chronically infected argentine patient with anti-HBs antibodies.

Serum hepatitis B virus (HBV) DNA was extracted from a chronically infected patient with cocirculation of hepatitis B surface antigen (HBsAg) and anti-HBs antibodies. Direct PCR and clone-derived sequences of the S and overlapped P genes were obtained. DNA sequences and phylogenetic analysis ascribed this isolate to genotype A (serotype adw2). Five of six HBV DNA clones exhibited point mutations inside and outside the major hydrophilic region, while the sixth clone exhibited a genotype A "wild-type" amino acid sequence. Observed replacements included both humoral and/or cellular (major histocompatibility complex class I [MHC-I] and MHC-II) HBV mutated epitopes, such as S45A, P46H, L49H, C107R, T125A, M133K, I152F, P153T, T161S, G185E, A194T, G202R, and I213L. None of these mutants were individually present within a given clone. The I213L replacement was the only one observed in the five clones carrying nonsynonymous mutations in the S gene. Some of the amino acid substitutions are reportedly known to be responsible for the emergence of immune escape mutants. C107R replacement prevents disulfide bonding, thus disrupting the first loop of the HBsAg. Circulation of some of these mutants may represent a potential risk for the community, since neither current hepatitis B vaccines nor hyperimmune hepatitis B immune globulin are effectively prevent the liver disease thereto associated. Moreover, some of the recorded HBsAg variants may influence the accuracy of the results obtained with currently used diagnostic tests.

Adult↗