High Throughput Fingerprint Analysis of Large-Insert Clones

Marra, Marco A.; Kucaba, Tamara A.; Dietrich, Nicole; Green, Eric D.; Brownstein, Buddy; Wilson, Richard K.; McDonald, Ken; Hillier, LaDeana W.; Mcpherson, John Douglas; Waterston, Robert H.

doi:10.1101/gr.7.11.1072

Cited by 375 publications

(295 citation statements)

References 14 publications

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“…Sequencing was initiated using bacterial arti®cial chromosomes (BACs) that had been placed onto the physical map of chromosome 2 by hybridization to YACs and genetic markers. Subsequently, BAC end sequences and BAC ®ngerprint data 13 allowed extension from these initial seed points and completion of the entire chromosome. A total of 257 BAC and P1 clones (including 5 BACs completed by other groups) were sequenced to produce over 24 Mb of ®nished sequence, which has been assembled as two contigs terminating in blocks of 180-bp repeats.…”

Section: Features Of Chromosomementioning

confidence: 99%

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Lin¹,

Kaul²,

Rounsley³

et al. 1999

Nature

673

378

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Section: Features Of Chromosomementioning

confidence: 99%

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Lin¹,

Kaul²,

Rounsley³

et al. 1999

Nature

673

378

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“…Either end sequencing or ®ngerprinting of PCR-screened PAC/BAC clones was conducted. The ®ngerprint data from both the RGP and Monsanto clones were integrated for contig analysis automatically or manually by using FPC V4.7 at a Sulston score cutoff of 1e À8 ± 1e À12 and a tolerance of 2±5 (Marra et al, 1997;Soderlund et al, 2000;Sulston et al, 1989). PAC/BAC clones comprising the MTP were selected for sequencing.…”

Section: Map Constructionmentioning

confidence: 99%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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“…The positional transgenesis approach, knock-in, inserts transgene into mouse genome at a specific location, such as Rosa26 and HPRT locus, while random transgenesis, which usually uses bacterial artificial chromosome (BAC), integrates the transgene at a random location. These days, the BAC transgenic approach has been widely used owing to its advantages, including ease of use and the availability of large library [32][33][34][35][36][37]. However, endogenous gene expression can be altered because the delivery of BAC may contain coding regions or promoters of other genes [20,38].…”

Section: Genetic Identitymentioning

confidence: 99%

Selective Manipulation of Neural Circuits

Park

Carmel

2016

Neurotherapeutics

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Unraveling the complex network of neural circuits that form the nervous system demands tools that can manipulate specific circuits. The recent evolution of genetic tools to target neural circuits allows an unprecedented precision in elucidating their function. Here we describe two general approaches for achieving circuit specificity. The first uses the genetic identity of a cell, such as a transcription factor unique to a circuit, to drive expression of a molecule that can manipulate cell function. The second uses the spatial connectivity of a circuit to achieve specificity: one genetic element is introduced at the origin of a circuit and the other at its termination. When the two genetic elements combine within a neuron, they can alter its function. These two general approaches can be combined to allow manipulation of neurons with a specific genetic identity by introducing a regulatory gene into the origin or termination of the circuit. We consider the advantages and disadvantages of both these general approaches with regard to specificity and efficacy of the manipulations. We also review the genetic techniques that allow gain-and loss-of-function within specific neural circuits. These approaches introduce light-sensitive channels (optogenetic) or drug sensitive channels (chemogenetic) into neurons that form specific circuits. We compare these tools with others developed for circuit-specific manipulation and describe the advantages of each. Finally, we discuss how these tools might be applied for identification of the neural circuits that mediate behavior and for repair of neural connections.

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High Throughput Fingerprint Analysis of Large-Insert Clones

Cited by 375 publications

References 14 publications

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Physical maps and recombination frequency of six rice chromosomes

Selective Manipulation of Neural Circuits

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