Characterization of a mouse multigene family that encodes zinc finger structures

The Drosophila segmentation gene Krüppel encodes multiple tandemly repeated units predicted to form DNA-binding zinc fingers. We have isolated 23 bacteriophages, containing nonoverlapping inserts from a mouse genomic DNA library, on the basis of cross-hybridization under nonstringent conditions to a probe corresponding to the Krüppel finger region. Nucleotide sequence analysis of six phage DNAs indicated that they all contained regions with similarity to Krüppel and potentially encoded zinc finger domains. Within these regions, the level of similarity to Krüppel was particularly high between successive fingers. Northern (RNA) blotting analysis suggested that the mouse sequences belonged to different genes, the expression of some of which was modulated during cell differentiation and development. Hybridization experiments suggested that the similarity between some of the genes extended outside of the finger regions. In conclusion, our data suggest that the mouse genome contains a large family of evolutionarily related genes encoding possible trans-acting factors. These genes are likely to play a regulatory role at the transcriptional level.

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Characterization of the expressed gene and several processed pseudogenes for the mouse ribosomal protein L30 gene family.

Molecular and Cellular Biology ◽

10.1128/mcb.4.11.2518 ◽

1984 ◽

Vol 4 (11) ◽

pp. 2518-2528 ◽

Cited By ~ 109

Author(s):

L M Wiedemann ◽

R P Perry

Keyword(s):

Ribosomal Protein ◽

Basic Protein ◽

Recombinant Dna ◽

Consensus Sequence ◽

Nucleotide Sequence Analysis ◽

Dna Library ◽

Polyadenylic Acid ◽

Genes Encoding ◽

Processed Pseudogenes

Five cloned genes encoding the mouse ribosomal protein L30 were isolated from a recombinant DNA library and characterized by restriction mapping and nucleotide sequence analysis. Only one of these genes has introns and is expressed; the others are inactive processed pseudogenes. The expressed gene consists of five exons and four introns spanning 2,723 nucleotides. Transcripts of this gene are processed into the mature L30 mRNA by pathways that exhibit both constraints and flexibility with regard to the order of intron excision. The L30 mRNA which is 457 to 468 nucleotides in length excluding the polyadenylic acid tail, exhibits some microheterogeneity at its 3' end and encodes a basic protein of 115 amino acids. The 5' portion of the rpL30 gene has some novel features which are remarkably similar to the previously characterized mouse rpL32 gene. These include homologous sequences in the -60 to -340 region, the absence of a good TATA consensus sequence, and the presence of a palindromic pyrimidine sequence that spans the cap site.

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Characterization of the expressed gene and several processed pseudogenes for the mouse ribosomal protein L30 gene family

Molecular and Cellular Biology ◽

10.1128/mcb.4.11.2518-2528.1984 ◽

1984 ◽

Vol 4 (11) ◽

pp. 2518-2528

Author(s):

L M Wiedemann ◽

R P Perry

Keyword(s):

Ribosomal Protein ◽

Basic Protein ◽

Recombinant Dna ◽

Consensus Sequence ◽

Nucleotide Sequence Analysis ◽

Dna Library ◽

Polyadenylic Acid ◽

Genes Encoding ◽

Processed Pseudogenes

Five cloned genes encoding the mouse ribosomal protein L30 were isolated from a recombinant DNA library and characterized by restriction mapping and nucleotide sequence analysis. Only one of these genes has introns and is expressed; the others are inactive processed pseudogenes. The expressed gene consists of five exons and four introns spanning 2,723 nucleotides. Transcripts of this gene are processed into the mature L30 mRNA by pathways that exhibit both constraints and flexibility with regard to the order of intron excision. The L30 mRNA which is 457 to 468 nucleotides in length excluding the polyadenylic acid tail, exhibits some microheterogeneity at its 3' end and encodes a basic protein of 115 amino acids. The 5' portion of the rpL30 gene has some novel features which are remarkably similar to the previously characterized mouse rpL32 gene. These include homologous sequences in the -60 to -340 region, the absence of a good TATA consensus sequence, and the presence of a palindromic pyrimidine sequence that spans the cap site.

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Eimeria species: studies using rRNA and rDNA probes

Parasitology ◽

10.1017/s0031182000079671 ◽

1990 ◽

Vol 101 (1) ◽

pp. 1-6 ◽

Cited By ~ 12

Author(s):

J. Ellis ◽

J. Bumstead

Keyword(s):

Genomic Dna ◽

Southern Hybridization ◽

Eimeria Species ◽

Small Subunit ◽

Rrna Genes ◽

Rdna Probe ◽

Dna Library ◽

Rdna Sequences ◽

Genomic Dna Library

SUMMARYrRNA and a heterologous cloned rDNA probe have been used to detect the rRNA genes of Eimeria species which infe the chicken, and has allowed the isolation and preliminary characterization of cloned rDNA sequences from a genomic DNA library of Eimeria tenella. It is demonstrated that rRNA and rDNA probes can be used to identify individual Eimeria species by the restriction fragment patterns detected after Southern hybridization. In addition, studies have shown that the large and small subunit rRNAs are expressed throughout sporulation.

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A Trypanosoma cruzi Zinc Finger protein that controls expression of epimastigote specific genes and affects metacyclogenesis

10.1101/2020.07.07.189688 ◽

2020 ◽

Author(s):

Thais Silva Tavares ◽

Fernanda Lins Brandão Mügge ◽

Viviane Grazielle-Silva ◽

Bruna Mattioly Valente ◽

Wanessa Moreira Goes ◽

...

Keyword(s):

Gene Expression ◽

Trypanosoma Cruzi ◽

Zinc Finger ◽

Rna Binding ◽

Environmental Changes ◽

Zinc Finger Protein ◽

Negative Regulator ◽

Transcriptional Level ◽

Control Of Gene Expression ◽

Genes Encoding

SummaryTrypanosoma cruzi has three biochemically and morphologically distinct developmental stages that are programed to rapidly respond to environmental changes the parasite faces during its life cycle. Unlike other eukaryotes, Trypanosomatid genomes contain protein coding genes that are transcribed into polycistronic pre-mRNAs and control of gene expression relies on mechanisms acting at the post-transcriptional level. Transcriptome analyses comparing epimastigote, trypomastigote and intracellular amastigote stages revealed changes in gene expression that reflect the parasite adaptation to distinct environments. Several genes encoding RNA binding proteins (RBP), known to act as key post-transcriptional regulatory factors, were also differentially expressed. We characterized one T. cruzi RBP (TcZH3H12) that contains a zinc finger domain, and whose transcripts are upregulated in epimastigotes compared to trypomastigotes and amastigotes. TcZC3H12 knockout epimastigotes showed decreased growth rates and increased capacity to differentiate into metacyclic trypomastigotes. Comparative transcriptome analysis revealed a TcZC3H12-dependent expression of epimastigote specific genes encoding amino acid transporters and proteins associated with differentiation (PAD), among others. RNA immunoprecipitation assays showed that transcripts from the PAD family interact with TcZC3H12. Taken together, these findings suggest that TcZC3H12 positively regulates the expression of genes involved in epimastigote proliferation and also acts as a negative regulator of metacyclogenesis.

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Molecular characterization of BrRZFPs genes encoding C3HC4 type RING zinc finger protein under abiotic stress from Chinese cabbage (Brassica rapa L.)

Journal of Plant Biotechnology ◽

10.5010/jpb.2013.40.2.102 ◽

2013 ◽

Vol 40 (2) ◽

pp. 102-110

Author(s):

Yu Jin Jung ◽

Kye Dong Lee ◽

Yong Gu Cho ◽

Ill Sup Nou ◽

Kwon Kyoo Kang

Keyword(s):

Abiotic Stress ◽

Zinc Finger ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Zinc Finger Protein ◽

Finger Protein ◽

Ring Zinc Finger ◽

Genes Encoding ◽

Ring Zinc Finger Protein

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Isolation and characterization of genes differentially expressed during conidiation of Neurospora crassa.

Molecular and Cellular Biology ◽

10.1128/mcb.5.4.849 ◽

1985 ◽

Vol 5 (4) ◽

pp. 849-855 ◽

Cited By ~ 77

Author(s):

V Berlin ◽

C Yanofsky

Keyword(s):

Neurospora Crassa ◽

Cdna Probe ◽

Genomic Sequences ◽

Dna Library ◽

Isolation And Characterization ◽

Polyadenylated Rna ◽

Length Polymorphisms ◽

Genomic Dna Library ◽

Asexual Cycle

A Neurospora crassa genomic DNA library was screened with a cDNA probe enriched in sequences expressed in conidiating cultures. Clones were isolated that preferentially hybridized to this probe versus a second cDNA probe complementary to polyadenylated RNA isolated from mycelia. Twelve clones contained unique sequences that hybridized to 22 transcripts, 19 of which accumulated preferentially in conidiating cultures. Eight transcripts were present in higher levels in conidiating cultures than in mycelia. Eleven transcripts were detected only in conidiating cultures and first appeared at different times during the asexual cycle. We mapped genomic sequences homologous to the 11 clones by conventional crosses using restriction fragment-length polymorphisms as genetic markers. The sequences homologous to genes expressed preferentially in conidiating cultures are distributed on six of the seven chromosomes. Clones that map to the same chromosome are linked. No recombination occurred between genomic sequences homologous to three clones, suggesting that the genes contained in these clones may constitute a gene cluster.

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Molecular cloning and characterization of the complementary DNA and gene coding for the B-chain of subcomponent C1q of the human complement system

Biochemical Journal ◽

10.1042/bj2310729 ◽

1985 ◽

Vol 231 (3) ◽

pp. 729-735 ◽

Cited By ~ 62

Author(s):

K B M Reid

Keyword(s):

Nucleotide Sequencing ◽

Chain Gene ◽

Amino Acid Residues ◽

Cdna Insert ◽

Coding Sequence ◽

Dna Library ◽

Gene Coding ◽

Liver Cdna Library ◽

Genomic Dna Library

Plasmid clones containing cDNA coding for the B-chain of human Clq were isolated from a liver cDNA library. The longest cDNA insert isolated contained all the coding sequence for amino acid residues B1 to B226 plus a 3′ non-translated region of 264 nucleotides that extended into the poly(A) tail, thus accounting for 950 nucleotides of the mRNA. The B-chain mRNA was estimated by Northern-blot analysis to be 1.46 kb (kilobases) long, which indicated that approx. 500 bases were not accounted for in the cDNA clone. A cosmid clone containing the C1q-B chain gene was isolated from a human genomic DNA library. The precise 5′ limit of gene was not established, but from the data available it appears that the gene is approx. 2.6 kb long. The coding sequence for residues B1 to B226 in the gene is interrupted by one intron, of 1.1 kb, which is located within the codon coding for glycine at position B36. This glycine residue is located in the middle of the triple-helical regions found in C1q at exactly the position where there is an unusual structural feature, i.e. a bend in each of the helical regions brought about by the interruption of the Gly-Xaa-Yaa repeating triplet sequences in the A- and C-chains and the presence of an ‘extra’ triplet in the B-chain. Nucleotide sequencing of the 5′ end of the gene indicates the presence of a predominantly hydrophobic stretch of 29 amino acids, immediately before residue B1, which could serve as a signal peptide.

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CHARACTERIZATION OF THE GENE FOR HUMAN HISTIDINE-RICH GLYCOPROTEIN

10.1055/s-0038-1643599 ◽

1987 ◽

Author(s):

T Koide

Keyword(s):

Blot Hybridization ◽

Southern Blot Hybridization ◽

Single Chain ◽

Structural Domains ◽

Dna Library ◽

Genomic Dna Library ◽

Human Genomic ◽

Considerable Homology ◽

Amino Acid Segment

Human histidine-rich glycoprotein (HRG) is a single-chain glycoprotein in plasma which is considered to modulate a coagulation and fibrinolysis system with the ability to bind to heparin, plasminogen, fibrinogen, thrombospondin, etc. Recently we have elucidated the primary structure of HRG by determining the nucleotide sequence of its cDNA, and showed that HRG is composed of several different types of internal repeats, each one of which shows considerable homology with the functional and/or structural domains of other proteins including high molecular weight kininogen, antithrombin III, cystatins, and proline-rich protein and peptide. Thus, the multifunctional property of HRG was suggested to be due to its multi-domain structure. In the present studies, a human genomic DNA library, cloned in the bacteriophage vector Charon 4A, was screened for HRG gene using a full-length cDNA coding for human IMI as a probe. A total of 7 clones were isolated from 6 × 105 phage and each was plaque purified. The entire HRG gene is represented in 3 genomic inserts with overlapping sequences that carry human DNA spanning 30 kb. Overlapping gene fragments were subcloned into pUC9 and characterized by Southern blot hybridization using 5’ and 3’ end probes isolated from human HRG cDNA and by DNA sequencing. These studies have shown that the gene for human HRG spans about 9 kb and consists of at least 5 exons and 4 introns. The putative histidine-rich region consisted of 12 tandemly repeated sequences of a 5 amino acid segment and 2 proline-rich regions contiguous to it are likely to be involved within one exon.

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