Utilization of FISH in positional cloning: an example on 13q22.

Abstract:

:In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have facilitated this process substantially. Here we summarize a strategy that combines a spectrum of FISH techniques [metaphase, interphase, mechanically stretched chromosomes (MSCs), and fiber-FISH on free chromatin] for the construction and characterization of a high-resolution physical map for a positional cloning project. The chromosomal region 13q22, containing the locus of the variant form of the neuronal ceroid lipofuscinosis (vLINCL, CLN5) disease, serves here as an example for this process. We used metaphase FISH to exclude positionally a candidate gene, to refine the locus to 13q22, and to analyze the possible chimerism of the YACs in the region. Both metaphase and interphase FISH techniques were applied to determine the low-resolution distances between the restricting markers. FISH using MSCs confirmed the centromeric-telomeric order of the clones and facilitated the estimation of the size of the gaps between the clones. Finally, fiber-FISH was found to be the method of choice for the construction of an accurate high-resolution map of the contig established over the restricted region. Thus, FISH techniques in combination with genetic mapping data enabled the refinement of the initial 4-cM region to a high-resolution map of only 400 kb in length. Here the FISH strategy replaced the need for many laborious traditional physical mapping methods, e.g., pulsed-field gel electrophoresis.

journal_name

Genome Res

journal_title

Genome research

authors

Laan M,Isosomppi J,Klockars T,Peltonen L,Palotie A

doi

10.1101/gr.6.10.1002

subject

Has Abstract

pub_date

1996-10-01 00:00:00

pages

1002-12

issue

10

eissn

1088-9051

issn

1549-5469

journal_volume

6

pub_type

杂志文章
  • The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.

    abstract::The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.099044.109

    authors: Kvikstad EM,Makova KD

    更新日期:2010-05-01 00:00:00

  • Core promoter T-blocks correlate with gene expression levels in C. elegans.

    abstract::Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.113381.110

    authors: Grishkevich V,Hashimshony T,Yanai I

    更新日期:2011-05-01 00:00:00

  • Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program.

    abstract::Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.183699.114

    authors: Dileep V,Ay F,Sima J,Vera DL,Noble WS,Gilbert DM

    更新日期:2015-08-01 00:00:00

  • Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters.

    abstract::DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.212050.116

    authors: Sarda S,Das A,Vinson C,Hannenhalli S

    更新日期:2017-04-01 00:00:00

  • Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

    abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.109678.110

    authors: Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

    更新日期:2011-04-01 00:00:00

  • Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast.

    abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.164996.113

    authors: McManus CJ,May GE,Spealman P,Shteyman A

    更新日期:2014-03-01 00:00:00

  • YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment.

    abstract::CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.215160.116

    authors: Beagan JA,Duong MT,Titus KR,Zhou L,Cao Z,Ma J,Lachanski CV,Gillis DR,Phillips-Cremins JE

    更新日期:2017-07-01 00:00:00

  • Relationship between histone modifications and transcription factor binding is protein family specific.

    abstract::The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.220079.116

    authors: Xin B,Rohs R

    更新日期:2018-01-11 00:00:00

  • Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.

    abstract::The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.171405.113

    authors: Veloso A,Kirkconnell KS,Magnuson B,Biewen B,Paulsen MT,Wilson TE,Ljungman M

    更新日期:2014-06-01 00:00:00

  • Comparative genomic analysis of the interferon/interleukin-10 receptor gene cluster.

    abstract::Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:

    authors: Reboul J,Gardiner K,Monneron D,Uzé G,Lutfalla G

    更新日期:1999-03-01 00:00:00

  • Multiparameter functional diversity of human C2H2 zinc finger proteins.

    abstract::C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.209643.116

    authors: Schmitges FW,Radovani E,Najafabadi HS,Barazandeh M,Campitelli LF,Yin Y,Jolma A,Zhong G,Guo H,Kanagalingam T,Dai WF,Taipale J,Emili A,Greenblatt JF,Hughes TR

    更新日期:2016-12-01 00:00:00

  • Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis.

    abstract::Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.257816.119

    authors: Ola M,O'Brien CE,Coughlan AY,Ma Q,Donovan PD,Wolfe KH,Butler G

    更新日期:2020-05-01 00:00:00

  • An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

    abstract::Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.146084.112

    authors: Wang Y,Lu J,Yu J,Gibbs RA,Yu F

    更新日期:2013-05-01 00:00:00

  • Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.

    abstract::Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.154286.112

    authors: Li G,Davis BW,Raudsepp T,Pearks Wilkerson AJ,Mason VC,Ferguson-Smith M,O'Brien PC,Waters PD,Murphy WJ

    更新日期:2013-09-01 00:00:00

  • Perspectives: sequence data base searching in the era of large-scale genomic sequencing.

    abstract::Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse ...

    journal_title:Genome research

    pub_type: 杂志文章,评审

    doi:10.1101/gr.6.8.653

    authors: Smith RF

    更新日期:1996-08-01 00:00:00

  • Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.

    abstract::To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3243305

    authors: Chin CS,Chuang JH,Li H

    更新日期:2005-02-01 00:00:00

  • Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.

    abstract::Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.103663.109

    authors: Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

    更新日期:2010-04-01 00:00:00

  • Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining.

    abstract::Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3421505

    authors: Zingler N,Willhoeft U,Brose HP,Schoder V,Jahns T,Hanschmann KM,Morrish TA,Löwer J,Schumann GG

    更新日期:2005-06-01 00:00:00

  • Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.

    abstract::Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3185605

    authors: Hardenbol P,Yu F,Belmont J,Mackenzie J,Bruckner C,Brundage T,Boudreau A,Chow S,Eberle J,Erbilgin A,Falkowski M,Fitzgerald R,Ghose S,Iartchouk O,Jain M,Karlin-Neumann G,Lu X,Miao X,Moore B,Moorhead M,Namsaraev E,

    更新日期:2005-02-01 00:00:00

  • metaSPAdes: a new versatile metagenomic assembler.

    abstract::While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.213959.116

    authors: Nurk S,Meleshko D,Korobeynikov A,Pevzner PA

    更新日期:2017-05-01 00:00:00

  • Extensive variation and low heritability of DNA methylation identified in a twin study.

    abstract::Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.119685.110

    authors: Gervin K,Hammerø M,Akselsen HE,Moe R,Nygård H,Brandt I,Gjessing HK,Harris JR,Undlien DE,Lyle R

    更新日期:2011-11-01 00:00:00

  • A first version of the Caenorhabditis elegans Promoterome.

    abstract::An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.2497604

    authors: Dupuy D,Li QR,Deplancke B,Boxem M,Hao T,Lamesch P,Sequerra R,Bosak S,Doucette-Stamm L,Hope IA,Hill DE,Walhout AJ,Vidal M

    更新日期:2004-10-01 00:00:00

  • Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale.

    abstract::Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these proteins be characterized if we are to develop combative strategies against malaria based on the biology of the parasite....

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.4573206

    authors: Date SV,Stoeckert CJ Jr

    更新日期:2006-04-01 00:00:00

  • Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.

    abstract::Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7105007

    authors: Rasmussen MD,Kellis M

    更新日期:2007-12-01 00:00:00

  • A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling.

    abstract::Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene famil...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.2126104

    authors: Sam-Yellowe TY,Florens L,Johnson JR,Wang T,Drazba JA,Le Roch KG,Zhou Y,Batalov S,Carucci DJ,Winzeler EA,Yates JR 3rd

    更新日期:2004-06-01 00:00:00

  • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.

    abstract::The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial comm...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.142315.112

    authors: Sharon I,Morowitz MJ,Thomas BC,Costello EK,Relman DA,Banfield JF

    更新日期:2013-01-01 00:00:00

  • Global analysis of protein homomerization in Saccharomyces cerevisiae.

    abstract::In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.231860.117

    authors: Kim Y,Jung JP,Pack CG,Huh WK

    更新日期:2019-01-01 00:00:00

  • Genome-scale identification of cellular pathways required for cell surface recognition.

    abstract::Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challen...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.231183.117

    authors: Sharma S,Bartholdson SJ,Couch ACM,Yusa K,Wright GJ

    更新日期:2018-09-01 00:00:00

  • Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

    abstract::Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.142661.112

    authors: Arnold P,Schöler A,Pachkov M,Balwierz PJ,Jørgensen H,Stadler MB,van Nimwegen E,Schübeler D

    更新日期:2013-01-01 00:00:00

  • Telomeric organization of a variable and inducible toxin gene family in the ancient eukaryote Giardia duodenalis.

    abstract::Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7.1.37

    authors: Upcroft P,Chen N,Upcroft JA

    更新日期:1997-01-01 00:00:00