Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression.

Abstract:

BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). RESULTS:To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus, appearing as large DAPI-dense staining blocks, defined by histone H3 lysine-9 trimethylation and association of the proteins heterochromatin protein 1 and structural maintenance of chromosomes flexible hinge domain containing 1. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. CONCLUSIONS:Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states, a property that is likely compromised by WSTF haploinsufficiency in WBS patients.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Culver-Cochran AE,Chadwick BP

doi

10.1186/1471-2164-14-740

subject

Has Abstract

pub_date

2013-10-29 00:00:00

pages

740

issn

1471-2164

pii

1471-2164-14-740

journal_volume

14

pub_type

杂志文章
  • Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST).

    abstract:BACKGROUND:Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) has significantly impaired this proces...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1982-6

    authors: Astolfi A,Urbini M,Indio V,Nannini M,Genovese CG,Santini D,Saponara M,Mandrioli A,Ercolani G,Brandi G,Biasco G,Pantaleo MA

    更新日期:2015-11-03 00:00:00

  • De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.

    abstract:BACKGROUND:The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2124-x

    authors: Lee AK,Kulcsar KA,Elliott O,Khiabanian H,Nagle ER,Jones ME,Amman BR,Sanchez-Lockhart M,Towner JS,Palacios G,Rabadan R

    更新日期:2015-12-07 00:00:00

  • Regulation of microRNAs miR-30a and miR-143 in cerebral vasculature after experimental subarachnoid hemorrhage in rats.

    abstract:BACKGROUND:microRNAs (miRNAs) are important regulators of translation and have been implicated in the pathogenesis of a number of cardiovascular diseases, including stroke, and suggested as possible prognostic biomarkers. Our aim was to identify miRNAs that are differentially regulated in cerebral arteries after subara...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1341-7

    authors: Müller AH,Povlsen GK,Bang-Berthelsen CH,Kruse LS,Nielsen J,Warfvinge K,Edvinsson L

    更新日期:2015-02-22 00:00:00

  • Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.

    abstract:BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-150

    authors: Dharmawardhana P,Brunner AM,Strauss SH

    更新日期:2010-03-04 00:00:00

  • Relating past and present diet to phenotypic and transcriptomic variation in the fruit fly.

    abstract:BACKGROUND:Sub-optimal developmental diets often have adverse effects on long-term fitness and health. One hypothesis is that such effects are caused by mismatches between the developmental and adult environment, and may be mediated by persistent changes in gene expression. However, there are few experimental tests of ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3968-z

    authors: May CM,Zwaan BJ

    更新日期:2017-08-22 00:00:00

  • Accuracy of genomic selection for alfalfa biomass yield in different reference populations.

    abstract:BACKGROUND:Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Pre...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2212-y

    authors: Annicchiarico P,Nazzicari N,Li X,Wei Y,Pecetti L,Brummer EC

    更新日期:2015-12-01 00:00:00

  • The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.

    abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-686

    authors: Natali L,Cossu RM,Barghini E,Giordani T,Buti M,Mascagni F,Morgante M,Gill N,Kane NC,Rieseberg L,Cavallini A

    更新日期:2013-10-06 00:00:00

  • Treatment-independent miRNA signature in blood of Wilms tumor patients.

    abstract:BACKGROUND:Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001. RESULTS:We did not find a significant difference between miRNA signature of both groups...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-379

    authors: Schmitt J,Backes C,Nourkami-Tutdibi N,Leidinger P,Deutscher S,Beier M,Gessler M,Graf N,Lenhof HP,Keller A,Meese E

    更新日期:2012-08-07 00:00:00

  • Autocorrelation analysis reveals widespread spatial biases in microarray experiments.

    abstract:BACKGROUND:DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-ran...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-164

    authors: Koren A,Tirosh I,Barkai N

    更新日期:2007-06-12 00:00:00

  • Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease.

    abstract:BACKGROUND:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1154

    authors: Krishna A,Biryukov M,Trefois C,Antony PM,Hussong R,Lin J,Heinäniemi M,Glusman G,Köglsberger S,Boyd O,van den Berg BH,Linke D,Huang D,Wang K,Hood L,Tholey A,Schneider R,Galas DJ,Balling R,May P

    更新日期:2014-12-20 00:00:00

  • Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.

    abstract:BACKGROUND:Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) hav...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2031-1

    authors: Lopez L,Barreiro R,Fischer M,Koch MA

    更新日期:2015-10-13 00:00:00

  • Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.

    abstract:BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-16

    authors: Greminger MP,Stölting KN,Nater A,Goossens B,Arora N,Bruggmann R,Patrignani A,Nussberger B,Sharma R,Kraus RH,Ambu LN,Singleton I,Chikhi L,van Schaik CP,Krützen M

    更新日期:2014-01-10 00:00:00

  • Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis.

    abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2209-6

    authors: Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya G

    更新日期:2015-12-01 00:00:00

  • Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish.

    abstract:BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4570-8

    authors: Lie KK,Tørresen OK,Solbakken MH,Rønnestad I,Tooming-Klunderud A,Nederbragt AJ,Jentoft S,Sæle Ø

    更新日期:2018-03-06 00:00:00

  • Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis.

    abstract:BACKGROUND:Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3833-0

    authors: Philippe F,Pelloux J,Rayon C

    更新日期:2017-06-08 00:00:00

  • Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation.

    abstract:BACKGROUND:Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-351

    authors: Salinero KK,Keller K,Feil WS,Feil H,Trong S,Di Bartolo G,Lapidus A

    更新日期:2009-08-03 00:00:00

  • Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes.

    abstract:BACKGROUND:Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires cha...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4653-6

    authors: Valdes Franco JA,Wang Y,Huo N,Ponciano G,Colvin HA,McMahan CM,Gu YQ,Belknap WR

    更新日期:2018-04-19 00:00:00

  • The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids.

    abstract:BACKGROUND:The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin m...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-367

    authors: Mulugeta Achame E,Wassenaar E,Hoogerbrugge JW,Sleddens-Linkels E,Ooms M,Sun ZW,van IJcken WF,Grootegoed JA,Baarends WM

    更新日期:2010-06-10 00:00:00

  • Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery.

    abstract:BACKGROUND:The principal toxicity of acute organophosphate (OP) pesticide poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-291

    authors: Lewis JA,Gehman EA,Baer CE,Jackson DA

    更新日期:2013-04-30 00:00:00

  • Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium.

    abstract:BACKGROUND:The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and their regulation have been investigated in detail in Fusarium fujikuroi. In this and other Fusarium...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5430-x

    authors: Ruger-Herreros M,Parra-Rivero O,Pardo-Medina J,Romero-Campero FJ,Limón MC,Avalos J

    更新日期:2019-01-21 00:00:00

  • miRNA and circRNA expression patterns in mouse brain during toxoplasmosis development.

    abstract:BACKGROUND:Increasing evidence has shown that circular RNAs (circRNAs) are involved in neurodegenerative disorders, but their roles in neurological toxoplasmosis are yet to know. This study examined miRNA and circRNA expressions in mouse brain following oral infection with T. gondii Pru strain. RESULTS:Total RNA extra...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6464-9

    authors: Zhou CX,Ai K,Huang CQ,Guo JJ,Cong H,He SY,Zhu XQ

    更新日期:2020-01-14 00:00:00

  • DArT markers: diversity analyses and mapping in Sorghum bicolor.

    abstract:BACKGROUND:The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obt...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-26

    authors: Mace ES,Xia L,Jordan DR,Halloran K,Parh DK,Huttner E,Wenzl P,Kilian A

    更新日期:2008-01-22 00:00:00

  • Analysis of functional variants in mitochondrial DNA of Finnish athletes.

    abstract:BACKGROUND:We have previously reported on paucity of mitochondrial DNA (mtDNA) haplogroups J and K among Finnish endurance athletes. Here we aimed to further explore differences in mtDNA variants between elite endurance and sprint athletes. For this purpose, we determined the rate of functional variants and the mutatio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6171-6

    authors: Kiiskilä J,Moilanen JS,Kytövuori L,Niemi AK,Majamaa K

    更新日期:2019-10-29 00:00:00

  • Genome-wide transcriptional analysis of T cell activation reveals differential gene expression associated with psoriasis.

    abstract:BACKGROUND:Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in psoriasis are still incompletely understood. The objective of the present study was to characterize th...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-825

    authors: Palau N,Julià A,Ferrándiz C,Puig L,Fonseca E,Fernández E,López-Lasanta M,Tortosa R,Marsal S

    更新日期:2013-11-23 00:00:00

  • A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins.

    abstract:BACKGROUND:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S2-S5

    authors: Tran Vdu T,Chassignet P,Sheikh S,Steyaert JM

    更新日期:2012-04-12 00:00:00

  • Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears.

    abstract:BACKGROUND:The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of ge...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07226-1

    authors: Sun M,Zhang M,Singh J,Song B,Tang Z,Liu Y,Wang R,Qin M,Li J,Khan A,Wu J

    更新日期:2020-11-19 00:00:00

  • Co-modulated behavior and effects of differentially expressed miRNA in colorectal cancer.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in colorectal cancer (CRC) progression through silencing gene expression. Numerous dysregulated miRNAs simultaneously participate in the process of colon cancer development. However, the detailed me...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-S5-S12

    authors: Chen WS,Chen TW,Yang TH,Hu LY,Pan HW,Leung CM,Li SC,Ho MR,Shu CW,Liu PF,Yu SY,Tu YT,Lin WC,Wu TT,Tsai KW

    更新日期:2013-01-01 00:00:00

  • Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes.

    abstract:BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4079-6

    authors: Rane RV,Oakeshott JG,Nguyen T,Hoffmann AA,Lee SF

    更新日期:2017-08-31 00:00:00

  • The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage.

    abstract:BACKGROUND:Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. To date, PAL genes have been less extensively studied in gymnosperms than in angiosperms. Ou...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S3-S1

    authors: Bagal UR,Leebens-Mack JH,Lorenz WW,Dean JF

    更新日期:2012-06-11 00:00:00

  • Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

    abstract:BACKGROUND:Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. RESULTS:In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-36

    authors: Zhou F,Olman V,Xu Y

    更新日期:2008-01-24 00:00:00