The FSHD region on human chromosome 4q35 contains potential coding regions among pseudogenes and a high density of repeat elements.

Abstract:

:The distal end of chromosome 4q contains the locus involved in facioscapulohumeral muscular dystrophy (FSHD1). Specific genomic deletions within a tandem DNA repeat (D4Z4) are associated with the disease status, but no causal genes have yet been discovered. In a systematic search for genes, a 161-kb stretch of genomic DNA proximal to D4Z4 was sequenced, analyzed for homologies, and subjected to gene prediction programs. A major fraction (45%) of the subtelomeric region is composed of repeat sequences attributable mainly to LINE-1 elements. Apart from the previously identified FRG1 and TUB4q sequences, several additional potential coding regions were identified by analyzing the sequence with exon prediction programs. So far, we have been unable to demonstrate transcripts by RT-PCR or cDNA library hybridization. However, several retrotransposed pseudogenes were identified. The high density of pseudogenes and repeat elements is consistent with the subtelomeric location of this region and explains why previous transcript identification studies have been problematic.

journal_name

Genomics

journal_title

Genomics

authors

van Geel M,Heather LJ,Lyle R,Hewitt JE,Frants RR,de Jong PJ

doi

10.1006/geno.1999.5942

subject

Has Abstract

pub_date

1999-10-01 00:00:00

pages

55-65

issue

1

eissn

0888-7543

issn

1089-8646

pii

S0888-7543(99)95942-6

journal_volume

61

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • Confirmation of linkage of Friedreich ataxia to chromosome 9 and identification of a new closely linked marker.

    abstract::A linkage analysis with chromosome 9 markers was performed in 33 families with Friedreich ataxia (FA). Linkage with D9S15, previously established by S. Chamberlain et al. (1988, Nature London 334:248-249) was confirmed in our sample (z(theta) = 6.82 at theta = 0.02) while INFB (interferon-beta gene) shows looser linka...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(89)90323-6

    authors: Fujita R,Agid Y,Trouillas P,Seck A,Tommasi-Davenas C,Driesel AJ,Olek K,Grzeschik KH,Nakamura Y,Mandel JL,Hanauer A

    更新日期:1989-01-01 00:00:00

  • Localized breakdown in linkage disequilibrium does not always predict sperm crossover hot spots in the human MHC class II region.

    abstract::To investigate the relationship between meiotic crossover hot spots and block-like linkage disequilibrium (LD), we have extended our high-resolution studies of the human MHC class II region to a 90-kb segment upstream of the HLA-DOA gene. LD blocks in this region are not as well defined as in the neighboring 210-kb DN...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2005.03.011

    authors: Kauppi L,Stumpf MP,Jeffreys AJ

    更新日期:2005-07-01 00:00:00

  • Four paralogous protein 4.1 genes map to distinct chromosomes in mouse and human.

    abstract::Four highly conserved members of the skeletal protein 4.1 gene family encode a diverse array of protein isoforms via tissue-specific transcription and developmentally regulated alternative pre-mRNA splicing. In addition to the prototypical red blood cell 4.1R (human gene symbol EPB41,) these include two homologues tha...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5537

    authors: Peters LL,Weier HU,Walensky LD,Snyder SH,Parra M,Mohandas N,Conboy JG

    更新日期:1998-12-01 00:00:00

  • Assignment of xeroderma pigmentosum group C (XPC) gene to chromosome 3p25.

    abstract::The human gene XPC (formerly designated XPCC), which corrects the repair deficiency of xeroderma pigmentosum (XP) group C cells, was mapped to 3p25. A cDNA probe for Southern blot hybridization and diagnostic PCR analyses of hybrid clone panels informative for human chromosomes in general and portions of chromosome 3 ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1256

    authors: Legerski RJ,Liu P,Li L,Peterson CA,Zhao Y,Leach RJ,Naylor SL,Siciliano MJ

    更新日期:1994-05-01 00:00:00

  • Rat gastric H,K-ATPase beta-subunit gene: intron/exon organization, identification of multiple transcription initiation sites, and analysis of the 5'-flanking region.

    abstract::A rat genomic library was screened using a gastric H,K-ATPase beta-subunit cDNA probe, and two clones were identified. Restriction endonuclease mapping and Southern hybridization analyses indicated that each of these clones contains the entire H,K-ATPase beta-subunit gene. The nucleotide sequence was determined for th...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90131-w

    authors: Newman PR,Shull GE

    更新日期:1991-10-01 00:00:00

  • Beware of using small statistical samples when assessing the quality of a DNA library.

    abstract::DNA libraries often contain very large numbers of clones (from 1000 up to 700,000). Since at present it is impossible to analyze all of these clones, usually statistical samples comprising less than 100 clones are tested. The quality of the library is then assessed by linear extrapolation. Occasionally, full coverage ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1476

    authors: Köllner M,Greulich KO

    更新日期:1994-09-01 00:00:00

  • Identification of a psoriasis susceptibility candidate gene by linkage disequilibrium mapping with a localized single nucleotide polymorphism map.

    abstract::Psoriasis is a chronic inflammatory disease of the skin with both genetic and environmental risk factors. Here we describe the creation of a single-nucleotide polymorphism (SNP) map spanning 900-1200 kb of chromosome 3q21, which had been previously recognized as containing a psoriasis susceptibility locus, PSORS5. We ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2002.6720

    authors: Hewett D,Samuelsson L,Polding J,Enlund F,Smart D,Cantone K,See CG,Chadha S,Inerot A,Enerback C,Montgomery D,Christodolou C,Robinson P,Matthews P,Plumpton M,Wahlstrom J,Swanbeck G,Martinsson T,Roses A,Riley J,Purvi

    更新日期:2002-03-01 00:00:00

  • Molecular and cytogenetic characterization of a Chinese hamster/human hybrid cell line containing a der (21)t(Ypter-->cenY::cen21-->21qter) chromosome.

    abstract::Human/rodent somatic cell hybrids have been exceedingly useful in assigning human genes and DNA sequences to specific human chromosomes. As new technologies for analyzing the human chromosome complement of such human/rodent hybrid cells become available, it is of critical importance that these be applied to enhance ch...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1993.1026

    authors: Patterson D,Hart I,Lai LW,Brahe C,Moscetti A,Tassone F,Raimondi E,Jones C

    更新日期:1993-01-01 00:00:00

  • Chromosomal mapping of the human Mu class glutathione S-transferases to 1p13.

    abstract::The chromosomal localization of the human Mu class glutathione S-transferase (GST) genes has been complicated by two factors; the total number of genes is unknown and there is a polymorphism that results from the presence or absence of the GSTM1 gene. Three human Mu class glutathione S-transferase isoenzymes, GSTM1, G...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1993.1429

    authors: Ross VL,Board PG,Webb GC

    更新日期:1993-10-01 00:00:00

  • Chromosome translocations in breast cancer with breakpoints at 8p12.

    abstract::Unbalanced chromosome translocations with breakpoints around 8p12, resulting in loss of distal 8p, are common in carcinomas. We have mapped the 8p12 breakpoints in three breast cancer cell lines, T-47D, MDA-MB-361, and ZR-75-1, using YACs and PACs between D8S540 and D8S255 by fluorescence in situ hybridization. All th...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2000.6178

    authors: Courtay-Cahen C,Morris JS,Edwards PA

    更新日期:2000-05-15 00:00:00

  • Characterization of the human talin (TLN) gene: genomic structure, chromosomal localization, and expression pattern.

    abstract::Talin is a high-molecular-weight cytoskeletal protein, localized at cell-extracellular matrix associations known as focal contacts. In these regions, talin is thought to link integrin receptors to the actin cytoskeleton. Talin plays a key role in the assembly of actin filaments and in spreading and migration of variou...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.6019

    authors: Ben-Yosef T,Francomano CA

    更新日期:1999-12-01 00:00:00

  • CLAN, a novel human CED-4-like gene.

    abstract::Proteins governing cell death form the basis of many normal processes and contribute to the pathogenesis of many diseases when dysregulated. Here we report the cloning of a novel human CED-4-like gene, CLAN, and several of its alternatively spliced isoforms. These caspase-associated recruitment domain (CARD)-containin...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2001.6579

    authors: Damiano JS,Stehlik C,Pio F,Godzik A,Reed JC

    更新日期:2001-07-01 00:00:00

  • An extended genetic linkage map and an "index" map for human chromosome 17.

    abstract::Our previous genetic map for chromosome 17 has been expanded to include 72 loci defined by 90 RFLP markers and four microsatellite markers assayed by the polymerase chain reaction. Forty-one of these loci were ordered with odds greater than 1000:1 against local inversion, and the other 31 were ordered within 95% confi...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1993.1007

    authors: O'Connell P,Plaetke R,Matsunami N,Odelberg S,Jorde L,Chance P,Leppert M,Lalouel JM,White R

    更新日期:1993-01-01 00:00:00

  • Human SLUG gene organization, expression, and chromosome map location on 8q.

    abstract::SLUG is a member of the snail family of zinc finger proteins. It is involved in epithelial to mesenchyme cell transition during neurulation and plays a role in limb bud development. We have isolated and described the human SLUG gene by sequencing a region spanning 4034 bp. The human SLUG gene contains three exons. The...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5367

    authors: Cohen ME,Yin M,Paznekas WA,Schertzer M,Wood S,Jabs EW

    更新日期:1998-08-01 00:00:00

  • Fructose-1,6-bisphosphatase: genetic and physical mapping to human chromosome 9q22.3 and evaluation in non-insulin-dependent diabetes mellitus.

    abstract::PCR primers specific to the human liver fructose-1,6-bisphosphatase (FBP) gene were designed and used to isolate a cosmid clone. Physical mapping of the FBP cosmid by FISH, and genetic mapping of an associated GA repeat polymorphism (PIC = 0.35), located the liver FBP gene to chromosome 9q22.3 with no recombination be...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1230

    authors: Rothschild CB,Freedman BI,Hodge R,Rao PN,Pettenati MJ,Anderson RA,Akots G,Qadri A,Roh B,Fajans SS

    更新日期:1995-09-01 00:00:00

  • Defective repair of radiation-induced DNA damage is complemented by a CHORI-230-65K18 BAC clone on rat chromosome 4.

    abstract::The Long Evans cinnamon (LEC) rat is highly susceptible to X-irradiation due to defective DNA repair and is thus a model for hepatocellular carcinogenesis. We constructed a bacterial artificial chromosome (BAC) contig of rat chromosome 4 completely covering the region associated with radiation susceptibility. We used ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2005.09.020

    authors: Tsuji AB,Sugyo A,Sudo H,Sagara M,Ishikawa A,Ohtsuki M,Kimura T,Ogiu T,Miyagishi M,Taira K,Imai T,Harada YN

    更新日期:2006-02-01 00:00:00

  • Identification of EPSTI1, a novel gene induced by epithelial-stromal interaction in human breast cancer.

    abstract::During growth, invasion, and metastasis, tumor cells interact extensively with the surrounding stroma. To identify genes that are upregulated during this process, we compared mRNA pooled from tumor cells and fibroblasts cultured separately to mRNA from cells in coculture. Using differential display (DD), a transcript ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2002.6755

    authors: Nielsen HL,Rønnov-Jessen L,Villadsen R,Petersen OW

    更新日期:2002-05-01 00:00:00

  • Polymorphisms in matricellular SPP1 and SPARC contribute to susceptibility to papillary thyroid cancer.

    abstract::There is a compelling need to identify novel genetic variants for papillary thyroid cancer (PTC) susceptibility. The Cancer Genome Atlas (TCGA) data showed associations between SPP1 and SPARC mRNA overexpression and aggressive behaviors of PTC, which prompted us to assess potential associations between genetic variant...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2020.09.018

    authors: Su X,Xu BH,Zhou DL,Ye ZL,He HC,Yang XH,Zhang X,Liu Q,Ma JJ,Shao Q,Yang AK,He CY

    更新日期:2020-11-01 00:00:00

  • Identification and characterization of a cDNA and the structural gene encoding the mouse epithelial membrane protein-1.

    abstract::The PMP22/EMP/MP20 gene family includes four closely related proteins, peripheral myelin protein-22 (PMP22), epithelial membrane protein-1 (EMP-1), epithelial membrane protein-2 (EMP-2), and epithelial membrane protein-3 (EMP-3), which share amino acid identities ranging from 33 to 43%. In addition, the lens-specific ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0482

    authors: Lobsiger CS,Magyar JP,Taylor V,Wulf P,Welcher AA,Program AE,Suter U

    更新日期:1996-09-15 00:00:00

  • CancerProView: a graphical image database of cancer-related genes and proteins.

    abstract::We have developed a graphical image database CancerProView (URL: http://cancerproview.dmb.med.keio.ac.jp/php/cpv.html) to assist the search for alterations of the motifs/domains in the cancer-related proteins that are caused by mutations in the corresponding genes. For the CancerProView, we have collected various kind...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2012.05.011

    authors: Mitsuyama S,Shimizu N

    更新日期:2012-08-01 00:00:00

  • Rapid detection of mitochondrial sequence polymorphisms using multiplex solid-phase fluorescent minisequencing.

    abstract::This work describes a novel method, multiplex solid-phase fluorescent minisequencing, for the simultaneous detection of several point mutations and/or small deletions and insertions. The method is applied to the analysis of mitochondrial DNA polymorphisms for the purposes of individual identification. A database of 15...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0247

    authors: Tully G,Sullivan KM,Nixon P,Stones RE,Gill P

    更新日期:1996-05-15 00:00:00

  • Comparative transcriptome analysis of diploid and triploid hybrid groupers (Epinephelus coioides♀ × E. lanceolatus♂) reveals the mechanism of abnormal gonadal development in triploid hybrids.

    abstract::In our previous studies, diploid and triploid hybrids have been detected from the hybridization of Epinephelus coioides♀ × E. lanceolatus♂. The triploid groupers have been found to be delayed in gonadal development, but the mechanism remains poorly understood. In this study, we examined the gonadal development, assaye...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2018.11.010

    authors: Xiao L,Wang D,Guo Y,Tang Z,Liu Q,Li S,Zhang Y,Lin H

    更新日期:2019-05-01 00:00:00

  • A physical and transcriptional map of the preaxial polydactyly locus on chromosome 7q36.

    abstract::Preaxial polydactyly is a congenital hand malformation that includes duplicated thumbs, various forms of triphalangeal thumbs, and duplications of the index finger. A locus for preaxial polydactyly has been mapped to a region of 1.9 cM on chromosome 7q36 between polymorphic markers D7S550 and D7S2423. We constructed a...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5796

    authors: Heus HC,Hing A,van Baren MJ,Joosse M,Breedveld GJ,Wang JC,Burgess A,Donnis-Keller H,Berglund C,Zguricas J,Scherer SW,Rommens JM,Oostra BA,Heutink P

    更新日期:1999-05-01 00:00:00

  • The 2p21 deletion syndrome: characterization of the transcription content.

    abstract::The vast majority of small-deletion syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We have previously identified a homozygous deletion of 179,311 bp on chromosome 2p21 as the cause of a unique syndrome, inherited in a recessive mode, consisting of cystinuria,...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2005.04.001

    authors: Parvari R,Gonen Y,Alshafee I,Buriakovsky S,Regev K,Hershkovitz E

    更新日期:2005-08-01 00:00:00

  • Genomic organization, alternative splicing, and expression patterns of the DSCR1 (Down syndrome candidate region 1) gene.

    abstract::Down syndrome is a major cause of mental retardation and congenital heart defects and is due to the presence of three copies of human chromosome 21 in the affected individual. We have identified a gene, DSCR1 (HGMW-approved symbol), from the region 21q22.1-q22.2, which is highly expressed in human fetal brain and adul...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4866

    authors: Fuentes JJ,Pritchard MA,Estivill X

    更新日期:1997-09-15 00:00:00

  • HIVID: an efficient method to detect HBV integration using low coverage sequencing.

    abstract::We reported HIVID (high-throughput Viral Integration Detection), a novel experimental and computational method to detect the location of Hepatitis B Virus (HBV) integration breakpoints in Hepatocellular Carcinoma (HCC) genome. In this method, the fragments with HBV sequence were enriched by a set of HBV probes and the...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2013.07.002

    authors: Li W,Zeng X,Lee NP,Liu X,Chen S,Guo B,Yi S,Zhuang X,Chen F,Wang G,Poon RT,Fan ST,Mao M,Li Y,Li S,Wang J,Jianwang,Xu X,Jiang H,Zhang X

    更新日期:2013-10-01 00:00:00

  • Mapping of equine cerebellar abiotrophy to ECA2 and identification of a potential causative mutation affecting expression of MUTYH.

    abstract::Equine Cerebellar Abiotrophy (CA) is a neurological disease found in Arabian horses. CA is characterized by post-natal degeneration of the Purkinje cells of the cerebellum. Signs of CA include ataxia, head tremors, and a lack of balance equilibrium. We have discovered a linkage of the CA phenotype to a microsatellite ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2010.11.006

    authors: Brault LS,Cooper CA,Famula TR,Murray JD,Penedo MC

    更新日期:2011-02-01 00:00:00

  • Machine learning method using position-specific mutation based classification outperforms one hot coding for disease severity prediction in haemophilia 'A'.

    abstract::Haemophilia is an X-linked genetic disorder in which A and B types are the most common that occur due to absence or lack of protein factors VIII and IX, respectively. Severity of the disease depends on mutation. Available Machine Learning (ML) methods that predict the mutational severity by using traditional encoding ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2020.09.020

    authors: Singh VK,Maurya NS,Mani A,Yadav RS

    更新日期:2020-11-01 00:00:00

  • The human glutamate dehydrogenase gene family: gene organization and structural characterization.

    abstract::Glutamate dehydrogenase is a mitochondrially located, key metabolic enzyme. In addition to its general metabolic role, GLUD is important in neurotransmission. Significant alterations in GLUD enzymatic activity have been associated with certain neurodegenerative human disorders. Although a single species of human GLUD ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1993.1152

    authors: Michaelidis TM,Tzimagiorgis G,Moschonas NK,Papamatheakis J

    更新日期:1993-04-01 00:00:00

  • Point mutation in the human dystrophin gene: identification through western blot analysis.

    abstract::Using antibodies directed against the amino-terminus of dystrophin, we identified a truncated protein in a Duchenne muscular dystrophy patient. Antibodies directed against the carboxy-terminus failed to identify any cross-reactive material, a result consistent with premature termination of dystrophin translation. The ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90332-9

    authors: Bulman DE,Gangopadhyay SB,Bebchuck KG,Worton RG,Ray PN

    更新日期:1991-06-01 00:00:00