Strategies for rapid and accurate DNA sequencing

Chissoe, Stephanie L.; Wang, Yunfang; Clifton, Sandra W.; Ma, Nien-Tung; Sun, Hei-Jen; Lobsinger, Judy S.; Kenton, Steve; White, James D.; Roe, Bruce A.

doi:10.1016/s1046-2023(05)80164-1

Cited by 29 publications

(13 citation statements)

References 16 publications

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“…The sheared DNA was ethanol precipitated, its ends were repaired using the End-It Repair Kit (Epicentre), and it was subjected to size selection by agarose gel electrophoresis to obtain 2-to 4-kb fragments (10,44). These fragments were cloned into the vector pUC18 that had been cleaved with SmaI and was then phosphatase-treated.…”

Section: Methodsmentioning

confidence: 99%

“…Plasmid DNA from the strain 1885MEE library was purified by alkaline lysis in a 96-well format on a Beckman Biomek 2000 automated robotics workstation, using a typical sodium dodecyl sulfate (SDS)-NaOH lysis protocol (10). The final ethanol-precipitated templates (in a 96-well plate) were each dissolved in 100 l of double-distilled H 2 O. DNA from random clones was analyzed by gel electrophoresis to determine the size of the insert.…”

Section: Methodsmentioning

confidence: 99%

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Partial Analysis of the Genomes of Two Nontypeable Haemophilus influenzae Otitis Media Isolates

et al. 2004

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In 1995, The Institute for Genomic Research completed the genomic sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. This sequence, though extremely useful in understanding the basic biology of H. influenzae, has yet to provide significant insight into our understanding of disease caused by nontypeable H. influenzae (NTHI), because serotype d strains are not generally pathogens. In contrast, NTHI strains are frequently mucosal pathogens and are the primary pathogens of chronic otitis media as well as a significant cause of acute otitis media in children. Thus, it is of great importance to further understand their biology. We used a DNA-based microarray approach to identify genes present in a clinical isolate of NTHI that were absent from strain Rd. We also sequenced the genome of a second NTHI isolate from a child with chronic otitis media to threefold coverage and then used an array of bioinformatics tools to identify genes present in this NTHI strain but absent from strain Rd. These methods were complementary in approach and results. We identified, in both strains, homologues of H. influenzae lav, an autotransported protein of unknown function; tnaA, which encodes tryptophanase; as well as a homologue of Pasteurella multocida tsaA, which encodes an alkyl peroxidase that may play a role in protection against reactive oxygen species. We also identified a number of putative restriction-modification systems, bacteriophage genes and transposon-related genes. These data provide new insight that complements and extends our ongoing analysis of NTHI virulence determinants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Partial Analysis of the Genomes of Two Nontypeable Haemophilus influenzae Otitis Media Isolates

et al. 2004

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“…2) were subjected to complete DNA sequence analysis (32,33) and have GenBank accession nos AC068907 and AC069562, respectively. BAC sequences were annotated by subjecting the working draft sequences to BLAST searches (http:// www.ncbi.nih.gov/BLAST) after masking repetitive sequences (ftp.genome.washington.edu/cgi-bin/RepeatMasker).…”

Section: Bac Sequencingmentioning

confidence: 99%

The gene for the muted (mu) mouse, a model for Hermansky-Pudlak syndrome, defines a novel protein which regulates vesicle trafficking

Zhang

2002

Human Molecular Genetics

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The muted (mu) mouse is a model for Hermansky-Pudlak Syndrome (HPS), an inherited disorder of humans causing hypopigmentation, hemorrhaging and early death due to lung abnormalities. The mu gene regulates the synthesis of specialized mammalian organelles such as melanosomes, platelet dense granules and lysosomes. Further, balance defects indicate that it controls the synthesis of otoliths of the inner ear. The mu gene has been identified by a positional/candidate approach involving large mouse interspecific backcrosses. It encodes a novel ubiquitously expressed transcript, specifying a predicted 185 amino acid protein, whose expression is abrogated in the mu allele which contains an insertion of an early transposon (ETn) retrotransposon. Expression is likewise expected to be lost in the mu J allele which contains a deletion of a single base pair within the coding region. The presence of structurally aberrant melanosomes within the eyes of mutant mice together with localization of the muted protein within vesicles in both the cell body and dendrites of transfected melan-a melanocytes emphasizes the role of the mu gene in vesicle trafficking. The mu gene is present only in mice and humans among analyzed genomes. As is true for several other recently identified mouse HPS genes, the mu gene is absent in lower eukaryotes. Therefore, the mu gene is a member of the novel gene set that has evolved in higher eukaryotes to regulate the synthesis/function of highly specialized subcellular organelles such as melanosomes and platelet dense granules.

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“…Large-scale genomic sequencing was performed as described previously (Chissoe et al 1991;Bodenteich et al 1994;Kedra et al 1997). Repetitive sequences were filtered out from genomic sequence using REPEAT MASTER server (ftp.genome.…”

Section: Sequencing and Informaticsmentioning

confidence: 99%

Duplications on Human Chromosome 22 Reveal a Novel Ret Finger Protein-Like Gene Family with Sense and Endogenous Antisense Transcripts

Seroussi¹,

Kedra²,

Pan³

et al. 1999

Genome Res.

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Analysis of 600 kb of sequence encompassing the beta-prime adaptin (BAM22) gene on human chromosome 22 revealed intrachromosomal duplications within 22q12-13 resulting in three active RFPL genes, two RFPL pseudogenes, and two pseudogenes of BAM22. The genomic sequence of BAM221 shows a remarkable similarity to that of BAM22. The cDNA sequence comparison of RFPL1, RFPL2, and RFPL3 showed 95%-96% identity between the genes, which were most similar to the Ret Finger Protein gene from human chromosome 6. The sense RFPL transcripts encode proteins with the tripartite structure, composed of RING finger, coiled-coil, and B30-2 domains, which are characteristic of the RING-B30 family. Each of these domains are thought to mediate protein-protein interactions by promoting homo-or heterodimerization. The MID1 gene on Xp22 is also a member of the RING-B30 family and is mutated in Opitz syndrome (OS). The autosomal dominant form of OS shows linkage to 22q11-q12. We detected a polymorphic protein-truncating allele of RFPL1 in 8% of the population, which was not associated with the OS phenotype. We identified 6-kb and 1.2-kb noncoding antisense mRNAs of RFPL1S and RFPL3S antisense genes, respectively. The RFPL1S and RFPL3S genes cover substantial portions of their sense counterparts, which suggests that the function of RFPL1S and RFPL3S is a post-transcriptional regulation of the sense RFPL genes. We illustrate the role of intrachromosomal duplications in the generation of RFPL genes, which were created by a series of duplications and share an ancestor with the RING-B30 domain containing genes from the major histocompatibility complex region on human chromosome 6.

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Strategies for rapid and accurate DNA sequencing

Cited by 29 publications

References 16 publications

Partial Analysis of the Genomes of Two Nontypeable Haemophilus influenzae Otitis Media Isolates

Partial Analysis of the Genomes of Two Nontypeable Haemophilus influenzae Otitis Media Isolates

The gene for the muted (mu) mouse, a model for Hermansky-Pudlak syndrome, defines a novel protein which regulates vesicle trafficking

Duplications on Human Chromosome 22 Reveal a Novel Ret Finger Protein-Like Gene Family with Sense and Endogenous Antisense Transcripts

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