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PubMed1997

Changes in expression of neurohypophysial hormone genes during spawning migration in chum salmon, Oncorhynchus keta.

We analyzed changes in the hypothalamic levels of vasotocin (VT) and isotocin (IT) mRNA in chum salmon during spawning migration to the Ishikari river. The fish were caught at Atsuta, a fisherman's village facing the Ishikari bay, and at Chitose, an upstream branch of the Ishikari river. The former are referred to as sea water (SW) fish, and the latter as freshwater (FW) fish. The levels of VT and IT mRNA in the forebrains were determined by quantitative Northern blot analysis using single-stranded DNA with the same mRNA sequences as the standards. Levels of VT mRNA were higher in the FW males than the FW females, although no such difference was seen in the SW fish. Changes in the levels of VT mRNA were markedly different in males and females. In the males, no significant differences were seen in the levels of VT-I and VT-II mRNA between the SW and FW fish. However, in the females, the levels of VT mRNA in the FW fish were significantly lower than those in the SW fish. Changes in the levels of IT-I and IT-II mRNA were essentially similar in the males and females. These results suggest that the control of VT gene expression is different in males and females during spawning migration, although the neuroendocrine mechanism is not known.

Actins↗

PubMed2006

[Expression of alpha 1 anti-trypsin in proximal tubular epithelial cell line].

OBJECTIVE: To investigate the expression and regulation of alpha 1 anti-trypsin (AAT) in tubular epithelial cells. METHODS: The expression of AAT in tubular epithelial cell line HKC was detected with indirect immunofluorescence assay and confirmed by reverse transcription polymerase chain reaction (PCR) in transcription level respectively, and PCR product was sequenced. In order to observe the response of HCK to LPS, the different concentrations of LPS (0, 0.5, 1.0, 2.0 microg/ml) were used in the research and the regulation of AAT in HKC was semi-quantitatively detected with Western Blot and Real-Time PCR respectively. RESULTS: Indirect immunofluorescence staining showed that AAT was positive in HKC, but negative in renal interstitial fibroblast. By PCR, a significant messenger RNA band of AAT was found in HKC, but not in renal interstitial fibroblast. DNA sequencing indicated that the sequence of PCR product is consistent with AAT mRNA sequence in Gene Bank. Real-time PCR showed that the expression of AAT mRNA was up-regulated (fluorescence intensity ratio is 3.43 +/- 0.88 versus 1.22 +/- 0.20; P < 0.01) in HKC stimulated with 2.0 microg/ml LPS for 4 h, and Western Blot showed that the synthesis of AAT significantly increased (band density ratio is 0.88 +/- 0.12 versus 0.59 +/- 0.05; P < 0.01) in HKC stimulated with 2.0 microg/ml LPS for 8 h, as compared with unstimulated HKC. 0.5, 1.0 g/ml of LPS has no effect on the expression of AAT mRNA and AAT protein in HKC. CONCLUSIONS: HKC express AAT and the expression can be up-regulated by LPS.

Cell Line↗

PubMed1997

Thrombopoietin is synthesized by bone marrow stromal cells.

We have previously characterized stromal progenitor cells contained in fetal bone marrow by fluorescence-activated cell sorting (FACS) using the differential expression of CD34, CD38, and HLA-DR, and found that a small number were contained within the CD34(+) cell fraction. In the present study, the frequency of stromal progenitors in both the CD34+ and CD34- subpopulations from samples of fetal and adult bone marrow was approximately one in 5,000 of the mononuclear cell fraction. Using multiparameter single-cell sorting, one in 20 fetal bone marrow cells with the CD34+, CD38-, HLA-DR-, CDw90+ phenotype were clonogenic stromal progenitors, whereas greater than one in five single cells with the CD34-, CD38-, HLA-DR-, CDw90+ phenotype formed stromal cultures. We found that cultures initiated by hematopoietic and stromal progenitors contained within the CD34+ fraction of bone marrow cells formed mixed hematopoietic/stromal cell cultures that maintained the viability of the hematopoietic progenitor cells for 3 weeks in the absence of added hematopoietic cytokines. We characterized some of the hematopoietic cytokines synthesized by stromal cultures derived from either CD34+ or CD34- bone marrow cells using reverse transcriptase-polymerase chain reaction (RT-PCR) amplification of interleukin-3 (IL-3), stem cell factor (SCF), CD34, Flt3/Flk2 ligand (FL), and thrombopoietin (TPO) mRNA sequences. We found ubiquitous expression of TPO mRNA in greater than 90% of stromal cultures initiated by either CD34+ or CD34- cells, and variable expression of SCF, FL, and CD34 mRNA. In particular, SCF and CD34 mRNA were detected only in stromal cultures initiated by CD34+ bone marrow cells, although the differences between CD34+ and CD34- stromal cells were not statistically significant. IL-3 mRNA was not found in any stromal cultures. An enzyme-linked immunosorbent assay (ELISA) of soluble SCF and TPO present in culture supernatants demonstrated that biologically significant amounts of protein were secreted by some cultured stromal cells: eight of 16 samples of conditioned media from stromal cultures initiated by fetal and adult bone marrow contained more than 32 pg/mL SCF (in the linear range of the ELISA), with a median value of 32 pg/mL (range, 9 to 230), while 13 of 24 samples of conditioned media had more than 16 pg/mL TPO (in the linear range of the ELISA), with a median of 37 pg/mL (range, 16 to 106). Our data indicate that stromal cultures initiated by single bone marrow cells can make FL, SCF, and TPO. Local production of early-acting cytokines and TPO by stromal cells may be relevant to the regulation of hematopoietic stem cell self-renewal and megakaryocytopoiesis in the bone marrow microenvironment.

Adult↗

PubMed1983

cDNA clone spanning the alpha-gamma subunit junction in the precursor of the murine fourth complement component (C4).

cDNA clones carrying parts of murine fourth complement component (C4, serum substance protein) mRNA sequences have been identified by differential hybridization to mRNA from a high C4-producing strain, B10.WR, and a congeneic low C4 strain, B10.BR, followed by hybrid-selected translation and DNA sequence analysis. One clone, pMLC4/w7-2, encodes an open amino acid reading frame that includes four tandem arginine residues immediately preceding a sequence 85% homologous with the NH2-terminal sequence of the human C4 gamma-chain. The amino acid composition of the predicted sequence upstream of the tandem arginines matches quite closely with the composition of a similar sized peptide at the COOH terminus of the human C4 alpha chain. The latter result raises questions regarding the nature and extent of plasma-mediated postsynthetic processing of the C4 alpha-chain COOH terminus. The results also demonstrate that strain differences in plasma C4 levels (low C4 vs. high C4) reflect differences in steady-state levels of liver C4 mRNA in these strains.

Amino Acid Sequence↗

PubMed2005

Formation of an alphaCP1-KH3 complex with UC-rich RNA.

The alphaCP family of proteins [also known as poly(C)-binding or heterogeneous nuclear ribonucleoprotein E proteins] are involved in the regulation of messenger RNA (mRNA) stability and translational efficiency. They bind via their triple heterologous nuclear ribonucleoprotein K homology (KH) domain structures to C-rich mRNA, and are thought to interact with other mRNA-binding proteins as well as provide direct nuclease protection. In particular, alphaCP1 and alphaCP2 have been shown to bind to a specific region of androgen receptor (AR) mRNA, resulting in its increased stability. The roles of each of the KH motifs in the binding affinity and the specificity is not yet understood. We report the beginning of a systematic study of each of the alphaCP KH domains, with the cloning and expression of alphaCP1-KH2 and alphaCP1-KH3. We report the ability of alphaCP1-KH3, but not alphaCP1-KH2, to bind the target AR mRNA sequence using an RNA electrophoretic mobility gel shift assay. We also report the preparation of an alphaCP1-KH3/AR mRNA complex for structural studies. (1)H-(15)N heteronuclear single quantum correlation NMR spectra of (15)N-labelled alphaCP1-KH3 verified the integrity and good solution behaviour of the purified domain. The titration of the 11-nucleotide RNA target sequence from AR mRNA resulted in a rearrangement of the (1)H-(15)N correlations, demonstrating the complete binding of the protein to form a homogeneous protein/RNA complex suitable for future structural studies.

Amino Acid Motifs↗

PubMed1978

Analysis of the 3'-terminal nucleotide sequence of vesicular stomatitis virus N protein mRNA.

The sequence of 205 nucleotides adjacent to the poly(A) tract at the 3'-terminus of the mRNA encoding the N polypeptide of vesicular stomatitis virus has been determined by copying with reverse transcriptase and using 2', 3'-dideoxynucleoside triphosphates as specific chain terminators. The method appears highly suitable for sequence determination in any purified mRNA. An examination of the sequence did not locate without ambiguity the limit of polypeptide coding RNA. The hexanucleotide AAUAAA, previously found in all poly(A)-containing eukaryote mRNAs, is not present, although the sequence immediately adjacent to the 3'-terminal poly(A) has a high content of A+U.

Base Sequence↗

PubMed1996

A functional analysis of protooncogene Vav's role in adult human hematopoiesis.

The Vav protooncogene is expressed almost exclusively in hematopoietic cells, but its role in regulating adult human hematopoietic cell development remains uncertain. To analyze Vav function in adult blood cell formation, we used antisense (AS) oligodeoxynucleotides (ODN) to disrupt its expression in normal and malignant human hematopoietic cells. Bone marrow or peripheral blood mononuclear cells (MNC) were obtained from consenting normal donors and patients with acute or chronic myelogenous leukemia (AML and CML, respectively) and polycythemia vera (PV). Adherent and T-cell-depleted (A-T-) MNC or CD34+ MNC were exposed to unmodified sense, antisense, or scrambled sequence ODN corresponding to codons 2-7 of Vav's mRNA sequence. Cells were then assayed for Vav mRNA expression by reverse transcription-polymerase chain reaction and Vav protein expression by Western binding. After showing that Vav-targeted AS ODN could specifically diminish Vav mRNA and protein expression, we assessed the ability of Vav-deficient cells to form myeloid and erythroid colonies in methyl-cellulose cultures. When normal CD34+ MNC were exposed to Vav AS ODN, no effect on colony-forming unit-granulocyte-macrophage (CFU-GM) or CFU-megakaryocyte colony formation was observed. In contrast erythroid colony growth was inhibited by a mean +/- SD of 62% +/- 16%. In patients with hematopoietic malignancies. Vav-targeted AS ODN inhibited CFU-GM colony formation in a sequence-specific and dose-dependent manner in 1 of 3 AML, 13 of 17 CML, and 2 of 2 PV patients. At the highest concentration used, the Vav AS ODN inhibited CFU-GM colony formation from 66% to 81% when compared with control cell colony growth. Burst-forming unit-erythroid (BFU-E) colony-formation was also assessed in 7 PV patients. The Vav-targeted AS ODN inhibited BFU-E colony formation in all by a mean +/- SD of 81% +/- 4%. These findings suggest that Vav function may not be easily complemented in a significant subset of normal adult erythroid progenitor cells and may also be necessary for myeloid progenitor cell growth in a variety of hematopoietic malignancies.

Adult↗

PubMed1983

Isolation and characterization of the human apolipoprotein A-I gene.

We have recently shown that an inherited polymorphism occurring in the human apolipoprotein A-I (apo A-I) gene is related to decreased high density lipoprotein and apo A-I levels in the plasma of two patients with severe premature atherosclerosis. Analysis of the molecular basis of this polymorphism and its possible effects on apo A-I gene expression requires direct comparison of both normal and polymorphic apo A-I alleles. Here we report the isolation and characterization of the normal human apo A-I gene and we show that the gene is interrupted by three intervening sequences, IVS-1, IVS-2, and IVS-3, occurring in the 5' noncoding region of apo A-I mRNA, the mRNA sequence coding for the signal peptide of apo A-I, and the sequence coding for the mature protein, respectively. In addition, the nucleotide sequence analysis of the apo A-I gene allowed determination of the complete amino acid sequence of the primary translation product of apo A-I mRNA. This amino acid sequence consists of 267 residues including a 24-residue-long amino-terminal extension (preprosegment). Finally, we show that the apo A-I gene contains six 66-base-pair-long tandemly repeated DNA segments, which suggests that the gene may have evolved by intragenic duplication events.

Apolipoprotein A-I↗

PubMed1981

Sequence determination and analysis of the 3' region of chicken pro-alpha 1(I) and pro-alpha 2(I) collagen messenger ribonucleic acids including the carboxy-terminal propeptide sequences.

Three pro-alpha 1 collagen cDNA clones, pCg1, pCg26, and pCg54, and two pro-alpha 2 collagen cDNA clones, pCg 13 and pCg45, were subjected to extensive DNA sequence determination. The combined sequences specified the amino acid sequences for chicken pro-alpha 1 and pro-alpha 2 type I collagens starting at residue 814 in the collagen triple-helical region and continuing to the procollagen C-termini as determined by the first in-phase termination codon. Thus, the sequences of 272 pro-alpha 1 C-terminal, 260 pro-alpha 2 C-terminal, 201 pro-alpha 1 helical, and 201 pro-alpha 2 helical amino acids were established. In addition, the sequences of several hundred nucleotides corresponding to noncoding regions of both procollagen mRNAs were determined. In total, 1589 pro-alpha 1 base pairs and 1691 pro-alpha 2 base pairs were sequenced, corresponding to approximately one-third of the total length of each mRNA. Both procollagen mRNA sequences have a high G+C content. The pro-alpha 1 mRNA is 75% G+C in the helical coding region sequenced and 61% G&C in the C-terminal coding region while the pro-alpha 2 mRNA is 60% and 48% G+C, respectively, in these regions. The dinucleotide sequence pCG occurs at a higher frequence in both sequences than is normally found in vertebrate DNAs and is approximately 5 times more frequent in the pro-alpha 1 sequence than in the pro-alpha 2 sequence. Nucleotide homology in the helical coding regions is very limited given that these sequences code for the repeating Gly-X-Y tripeptide in a region where X and Y residues are 50% conserved. These differences are clearly reflected in the preferred codon usages of the two mRNAs.

Amino Acid Sequence↗

PubMed1979

Evidence for the protection of specific RNA sequences in globin messenger ribonucleoprotein particles.

Purified 15 S globin mRNA-protein (mRNP) complexes obtained by EDTA dissociation of duck reticulocytes polyribosomes were digested with the calcium dependant Staphylococcus aureus nuclease (EC 3. 1. 4. 7.). 25% of the globin mRNA sequences were resistant to extensive nuclease digestion as determined by TCA precipitation of the digested 15 S particles labelled in vivo with tritiated uridine. Polyacrylamide gel electrophoresis of the RNA from nuclease digested 15 S particles showed that the protected oligoribonucleotides were distributed into two distinct size classes of 25,000 and 12,000 MW. Comparison between in vitro iodine-labelled 9 S globin mRNA extracted from Staphylococcal nuclease digested 15 S mRNP particles was carried out by fingerprinting. Mapping of T1 ribonuclease digests by high-voltage electrophoresis and homochromatography showed that specific oligoribonucleotides were protected against nuclease attack by proteins of the 15 S mRNP.

Animals↗

PubMed1978

Sequence organization of the beta-globin mRNA precursor.

The sequence organization of the beta-globin mRNA precursor has been determined directly by analyzing the resistant fragments from the RNase A digestion of the precursor RNA-globin cDNA hybrid. Three fragments are obtained which proves that the beta-globin mRNA sequence in its precursor is split into three discontinuous segments. The two intervening sequences in the beta-globin gene are therefore transcribed and removed during mRNA maturation.

Base Sequence↗

PubMed1982

Estradiol regulates the transcription of the prolactin gene.

The effect of estradiol on prolactin gene transcription in pituitaries from ovariectomized, female rats has been investigated. Analysis of the multiple prolactin mRNA species present in pituitary cells demonstrated that estradiol increases the concentration of all the large, potential nuclear precursors of prolactin mRNA. To further examine possible estradiol effects on prolactin mRNA synthesis, nuclei were isolated from rat pituitaries and allowed to continue RNA synthesis in vitro in the presence of [alpha-32P]UTP. Newly synthesized prolactin mRNA sequences were quantitated by hybridization of [32P]RNA to immobilized plasmid DNA containing prolactin cDNA sequences. After 24 h of estradiol treatment, prolactin mRNA synthesis was increased 4-fold. Estradiol effects on prolactin gene transcription were detected as early as 20 min after injection of the steroid. These findings suggest that estradiol increases prolactin mRNA levels by increasing the transcription of the prolactin gene.

Animals↗

PubMed2001

RefSeq and LocusLink: NCBI gene-centered resources.

Thousands of genes have been painstakingly identified and characterized a few genes at a time. Many thousands more are being predicted by large scale cDNA and genomic sequencing projects, with levels of evidence ranging from supporting mRNA sequence and comparative genomics to computing ab initio models. This, coupled with the burgeoning scientific literature, makes it critical to have a comprehensive directory for genes and reference sequences for key genomes. The NCBI provides two resources, LocusLink and RefSeq, to meet these needs. LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for fruit fly, human, mouse, rat and zebrafish. RefSeq provides reference sequence standards for genomes, transcripts and proteins; human, mouse and rat mRNA RefSeqs, and their corresponding proteins, are discussed here. Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation. Additional information about LocusLink and RefSeq is available at http://www.ncbi.nlm.nih.gov/LocusLink/.

Animals↗

PubMed1986

Motoneurone survival factor produced by muscle increases in parallel with messenger RNA sequences homologous to beta NGF-cDNA.

Motoneurone survival in culture is enhanced by growth factors present in embryonic rat muscles and denervated adult muscles: extracts from mature muscle and 2-day denervated mature muscle do not produce survival effects whereas extracts from embryonic muscle and 4-day denervated mature muscle produce maximum survival effects. Here we show, using dot hybridization of mRNA with a 32P-labelled cDNA probe for beta-nerve growth factor (beta NGF), that mRNA sequences homologous to beta NGF appear in muscle in parallel with increased motoneurone survival activity. RNA gel blot hybridizations show that embryonic mRNA contains a sequence in the same molecular weight range as the mRNA for beta NGF.

Animals↗

PubMed1985

Cloned DNA sequences that determine mRNA stability of bacteriophage phi X174 in vivo are functional.

The stability of two species of phi X174 polycistronic mRNA in vivo can be altered by mutating sequences existing immediately upstream of a termination site. The wild type phage contains an mRNA stabilizing sequence ((+) sequence), while the same sequence mutated by insertion ((-) sequence) reduces the stability of the mRNAs. These two sequences were cloned at the 3' ends of gene D or gene B of phi X174 in a pBR322 derivative plasmid. The cloned sequences were functional. The (+) sequence stabilized gene B or gene D mRNA; half-lives of these mRNAs were 7 to 8 min. When the (+) sequence is eliminated ((o) sequence) or replaced with the (-) sequence, the half-lives of the mRNA were reduced to about 1 to 2 min. The stabilization of mRNAs caused an increased production of these proteins.

Bacteriophage phi X 174↗

PubMed1984

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species.

Amino Acid Sequence↗

PubMed1993

Isolation of an Arabidopsis cDNA sequence encoding a 22 kDa calcium-binding protein (CaBP-22) related to calmodulin.

Complementary DNA sequences were isolated from a library of cloned Arabidopsis leaf mRNA sequences in lambda gt10 that encoded a 21.7 kDa polypeptide (CaBP-22), which shared 66% amino acid sequence identity with Arabidopsis calmodulin. The putative Ca(2+)-binding domains of CaBP-22 and calmodulin, however, were more conserved and shared 79% sequence identity. Ca2+ binding by CaBP-22, which was inferred from its amino acid sequence similarity with calmodulin, was demonstrated indirectly by Ca(2+)-induced mobility shifting of in vitro translated CaBP-22 during SDS-polyacrylamide gel electrophoresis. CaBP-22 is encoded by a ca. 0.9 kb mRNA that was detected by northern blotting of leaf poly(A)+ RNA; this mRNA was slightly larger than the 809 bp CaBP-22 cDNA insert, indicating that the deduced amino acid sequence of CaBP-22 is near full-length. CaBP-22 mRNA was detected in RNA fractions isolated from leaves of both soil-grown and hydroponically grown Arabidopsis, but below the limits of detection in RNA isolated from roots, and developing siliques. Thus, CaBP-22 represents a new member of the EF-hand family of Ca(2+)-binding proteins with no known animal homologue and may participate in transducing Ca2+ signals to a specific subset of response elements.

Amino Acid Sequence↗

PubMed1981

Nucleotide sequence of the 26S mRNA of Sindbis virus and deduced sequence of the encoded virus structural proteins.

The nucleotide sequence of intracellular 26S mRNA of Sindbis virus has been determined by direct sequence analysis of the cDNA made to this RNA with reverse transcriptase. From this, the amino acid sequences of the encoded virus structural proteins, which include a basic capsid protein and two integral membrane glycoproteins, have been deduced. The features of these proteins as related to their functions are discussed. We suggest that three proteases are required to produce these proteins from their polyprotein precursor: a viral protease, which functions in the cytosol to release the capsid protein, signalase, which makes two cleavages to separate the glycoproteins; and a protease of the Golgi complex that cleaves after double basic residues, to process the precursor form of one of the glycoproteins.

Amino Acid Sequence↗