Cotransfer of circular and linear prokaryotic and eukaryotic DNA sequences into mouse cells.

A 1.6-kilobase DNA segment of the genomic human interferon beta 1 (IF-beta 1) gene was inserted into each of two possible orientations at the single HindIII site of a recombinant plasmid pBPV69T, consisting of the 69% transforming region of the bovine papilloma virus type 1 (BPV-1) and a modified SalI-SalI fragment of plasmid pBR322. After cleavage of the pBR322 sequences from this recombinant, BPV69T-IF-beta 1 hybrid DNAs were transfected onto C127 mouse cells by the standard calcium precipitation technique. Mouse cells transformed by this hybrid DNA produced low levels of human IF-beta 1 constitutively and responded to induction with either inactivated Newcastle disease virus or polyriboinosinic acid-polyribocytidylic acid. The BPV69T-IF-beta 1 hybrid DNA was nonintegrated in the transformed mouse cells but had acquired DNA sequences as a result of the transfection. Accurate transcripts of the IF-beta 1 mRNA were detected in cells only after induction. When the IF-beta 1 gene was oriented in the plasmid in the same direction of transcription as the BPV-1 genome, transcription was promoted from within the BPV-1 sequences. These results indicate that the regulatory sequences responsible for the inducible expression of the human IF-beta 1 gene are present in the 1.6-kilobase genomic segment and that these sequences can function in a free extrachromosomal state linked to BPV-1 sequences.

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Mbd1 Is Recruited to both Methylated and Nonmethylated CpGs via Distinct DNA Binding Domains

Molecular and Cellular Biology ◽

10.1128/mcb.24.8.3387-3395.2004 ◽

2004 ◽

Vol 24 (8) ◽

pp. 3387-3395 ◽

Cited By ~ 115

Author(s):

Helle F. Jørgensen ◽

Ittai Ben-Porath ◽

Adrian P. Bird

Keyword(s):

Dna Sequences ◽

Methylation Status ◽

Dna Binding Domains ◽

Cpg Sites ◽

Binding Domains ◽

Mouse Cells ◽

Cpg Dinucleotide ◽

Promoter Dna ◽

Mbd Proteins

ABSTRACT MBD1 is a vertebrate methyl-CpG binding domain protein (MBD) that can bring about repression of methylated promoter DNA sequences. Like other MBD proteins, MBD1 localizes to nuclear foci that in mice are rich in methyl-CpG. In methyl-CpG-deficient mouse cells, however, Mbd1 remains localized to heterochromatic foci whereas other MBD proteins become dispersed in the nucleus. We find that Mbd1a, a major mouse isoform, contains a CXXC domain (CXXC-3) that binds specifically to nonmethylated CpG, suggesting an explanation for methylation-independent localization. Transfection studies demonstrate that the CXXC-3 domain indeed targets nonmethylated CpG sites in vivo. Repression of nonmethylated reporter genes depends on the CXXC-3 domain, whereas repression of methylated reporters requires the MBD. Our findings indicate that MBD1 can interpret the CpG dinucleotide as a repressive signal in vivo regardless of its methylation status.

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Autonomous replicating sequences from mouse cells which can replicate in mouse cells in vivo and in vitro.

Molecular and Cellular Biology ◽

10.1128/mcb.7.1.1 ◽

1987 ◽

Vol 7 (1) ◽

pp. 1-6 ◽

Cited By ~ 18

Author(s):

H Ariga ◽

T Itani ◽

S M Iguchi-Ariga

Keyword(s):

Dna Replication ◽

Dna Sequences ◽

Simian Virus 40 ◽

Simian Virus ◽

T Antigen ◽

Copy Numbers ◽

Mouse Cells ◽

Simplex Virus

We have already reported that the cloned mouse DNA fragment (pMU65) could replicate in a simian virus 40 T antigen-dependent system in vivo and in vitro (H. Ariga, Z. Tsuchihashi, M. Naruto, and M. Yamada, Mol. Cell. Biol. 5:563-568, 1985). The plasmid p65-tk, containing the thymidine kinase (tk) gene of herpes simplex virus and the BglII-EcoRI region of pMU65 homologous to the simian virus 40 origin of DNA replication, was constructed. The p65-tk persisted episomally in tk+ transformants after the transfection of p65-tk into mouse FM3Atk- cells. The copy numbers of p65-tk in FM3Atk+ cells were 100 to 200 copies per cell. Furthermore, the p65-tk replicated semiconservatively, and the initiation of DNA replication started from the mouse DNA sequences when the replicating activity of p65-tk was tested in the in vitro DNA replication system developed from the FM3A cells. These results show that a 2.5-kilobase fragment of mouse DNA contains the autonomously replicating sequences.

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Less than 40% of the simian virus 40 large T-antigen-coding sequence is required for transformation

Molecular and Cellular Biology ◽

10.1128/mcb.4.8.1661-1663.1984 ◽

1984 ◽

Vol 4 (8) ◽

pp. 1661-1663

Author(s):

L Sompayrac ◽

K J Danna

Keyword(s):

Dna Sequences ◽

Deletion Mutant ◽

Simian Virus 40 ◽

Simian Virus ◽

Large Deletion ◽

T Antigen ◽

Large T Antigen ◽

Wild Type ◽

Coding Sequence ◽

Mouse Cells

F8dl is a simian virus 40 early-region deletion mutant that lacks the simian virus 40 DNA sequences between 0.168 and 0.424 map units. Despite this large deletion, cloned F8dl DNA transforms Fisher rat F111 cells and BALB/3T3 clone A31 mouse cells as efficiently as does cloned simian virus 40 wild-type DNA. These results indicate that less than 40% of the large T-antigen-coding sequence is required for efficient transformation.

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Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors

Bioinformatics ◽

10.1093/bioinformatics/17.1.13 ◽

2001 ◽

Vol 17 (1) ◽

pp. 13-15 ◽

Cited By ~ 32

Author(s):

A. A. Mironov ◽

P. S. Novichkov ◽

M. S. Gelfand

Keyword(s):

Dna Sequences ◽

Gene Recognition ◽

Eukaryotic Dna

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Gene amplification in methotrexate-resistant mouse cells. IV. Different DNA sequences are amplified in different resistant lines

Nucleic Acids Research ◽

10.1093/nar/10.21.6597 ◽

1982 ◽

Vol 10 (21) ◽

pp. 6597-6618 ◽

Cited By ~ 12

Author(s):

Ruggero Caizzi ◽

Christopher J. Bostock

Keyword(s):

Gene Amplification ◽

Dna Sequences ◽

Resistant Mouse ◽

Resistant Lines ◽

Mouse Cells

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Identification of Protein Coding Regions in the Eukaryotic DNA Sequences Based on Marple Algorithm and Wavelet Packets Transform

Abstract and Applied Analysis ◽

10.1155/2014/402567 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14 ◽

Cited By ~ 7

Author(s):

Guangchen Liu ◽

Yihui Luan

Keyword(s):

Dna Sequences ◽

Structure Prediction ◽

Critical Role ◽

Wavelet Packets ◽

Protein Coding ◽

Gene Structure Prediction ◽

Coding Regions ◽

Eukaryotic Gene ◽

Benchmark Datasets ◽

Eukaryotic Dna

The identification of protein coding regions (exons) plays a critical role in eukaryotic gene structure prediction. Many techniques have been introduced for discriminating between the exons and the introns in the eukaryotic DNA sequences, such as the discrete Fourier transform (DFT) based techniques, but these DFT-based methods rapidly lose their effectiveness in the case of short DNA sequences. In this paper, a novel integrated algorithm based on autoregressive spectrum analysis and wavelet packets transform is presented to improve the efficiency and accuracy of the coding regions identification. The experimental results show that the new algorithm outperforms the conventional DFT-based approaches in improving the prediction accuracy of protein coding regions distinctly by testing GENSCAN65, HMR195, and BG570 benchmark datasets.

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De novo assembly and delivery to mouse cells of a 101 kb functional human gene

Genetics ◽

10.1093/genetics/iyab038 ◽

2021 ◽

Author(s):

Leslie A Mitchell ◽

Laura H McCulloch ◽

Sudarshan Pinglay ◽

Henri Berger ◽

Nazario Bosco ◽

...

Keyword(s):

Dna Sequences ◽

Large Scale ◽

De Novo ◽

Human Gene ◽

Embryonic Stem ◽

Building Blocks ◽

Functional Study ◽

Dna Assembly ◽

Functional Evaluation ◽

Mouse Cells

Abstract Design and large-scale synthesis of DNA has been applied to the functional study of viral and microbial genomes. New and expanded technology development is required to unlock the transformative potential of such bottom-up approaches to the study of larger mammalian genomes. Two major challenges include assembling and delivering long DNA sequences. Here we describe a workflow for de novo DNA assembly and delivery that enables functional evaluation of mammalian genes on the length scale of 100 kilobase pairs (kb). The DNA assembly step is supported by an integrated robotic workcell. We demonstrate assembly of the 101 kb human HPRT1 gene in yeast from 3 kb building blocks, precision delivery of the resulting construct to mouse embryonic stem cells, and subsequent expression of the human protein from its full-length human gene in mouse cells. This workflow provides a framework for mammalian genome writing. We envision utility in producing designer variants of human genes linked to disease and their delivery and functional analysis in cell culture or animal models.

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Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

Frontiers in Microbiology ◽

10.3389/fmicb.2021.664560 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kai Song

Keyword(s):

Dna Sequences ◽

Viral Genome ◽

Metagenomic Data ◽

Viral Sequence ◽

Genome Sequences ◽

Sequence Identification ◽

Viral Genes ◽

Eukaryotic Dna ◽

Viral Sequences

Metagenomes can be considered as mixtures of viral, bacterial, and other eukaryotic DNA sequences. Mining viral sequences from metagenomes could shed insight into virus–host relationships and expand viral databases. Current alignment-based methods are unsuitable for identifying viral sequences from metagenome sequences because most assembled metagenomic contigs are short and possess few or no predicted genes, and most metagenomic viral genes are dissimilar to known viral genes. In this study, I developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data. VirMC uses Markov chains to model sequence signatures and construct a scoring model using a likelihood test to distinguish viral and bacterial sequences. Compared with the other two state-of-the-art viral sequence-prediction methods, VirFinder and PPR-Meta, my proposed method outperformed VirFinder and had similar performance with PPR-Meta for short contigs with length less than 400 bp. VirMC outperformed VirFinder and PPR-Meta for identifying viral sequences in contaminated metagenomic samples with eukaryotic sequences. VirMC showed better performance in assembling viral-genome sequences from metagenomic data (based on filtering potential bacterial reads). Applying VirMC to human gut metagenomes from healthy subjects and patients with type-2 diabetes (T2D) revealed that viral contigs could help classify healthy and diseased statuses. This alignment-free method complements gene-based alignment approaches and will significantly improve the precision of viral sequence identification.

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