Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.

Abstract:

BACKGROUND:Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS:Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS:Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Ebert G,Steininger A,Weißmann R,Boldt V,Lind-Thomsen A,Grune J,Badelt S,Heßler M,Peiser M,Hitzler M,Jensen LR,Müller I,Hu H,Arndt PF,Kuss AW,Tebel K,Ullmann R

doi

10.1186/1471-2164-15-537

subject

Has Abstract

pub_date

2014-06-29 00:00:00

pages

537

issn

1471-2164

pii

1471-2164-15-537

journal_volume

15

pub_type

杂志文章
  • Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis.

    abstract:BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-260

    authors: Lafontaine I,Dujon B

    更新日期:2010-04-22 00:00:00

  • The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions.

    abstract:BACKGROUND:A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects th...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-586

    authors: Johnson BR,Atallah J,Plachetzki DC

    更新日期:2013-08-28 00:00:00

  • Database of exact tandem repeats in the Zebrafish genome.

    abstract:BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-347

    authors: Rouchka EC

    更新日期:2010-06-01 00:00:00

  • PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities.

    abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, mos...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5497-4

    authors: Pyfrom SC,Luo H,Payton JE

    更新日期:2019-02-15 00:00:00

  • Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene.

    abstract:BACKGROUND:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced chan...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07164-y

    authors: Kajihara D,Hon CC,Abdullah AN,Wosniak J Jr,Moretti AIS,Poloni JF,Bonatto D,Hashimoto K,Carninci P,Laurindo FRM

    更新日期:2020-11-04 00:00:00

  • Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow.

    abstract:BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5099-6

    authors: Wright ES,Baum DA

    更新日期:2018-10-03 00:00:00

  • Gene expression changes during caste-specific neuronal development in the damp-wood termite Hodotermopsis sjostedti.

    abstract:BACKGROUND:One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological differences as well as behavioral differences can be recognized among castes. However, very little is ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-314

    authors: Ishikawa Y,Okada Y,Ishikawa A,Miyakawa H,Koshikawa S,Miura T

    更新日期:2010-05-20 00:00:00

  • Proteome-wide analysis of Anopheles culicifacies mosquito midgut: new insights into the mechanism of refractoriness.

    abstract:BACKGROUND:Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgut proteins and their potential role in refractoriness for malaria control in Anopheles mosquitoes. T...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4729-3

    authors: Vijay S,Rawal R,Kadian K,Singh J,Adak T,Sharma A

    更新日期:2018-05-08 00:00:00

  • Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.

    abstract:BACKGROUND:Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. METHODS:In this work, ta...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4873-9

    authors: Mei S,Flemington EK,Zhang K

    更新日期:2018-06-28 00:00:00

  • De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

    abstract:BACKGROUND:Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, Toxoplasma gondii, are based on computer model predictions without cDNA sequence ver...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-696

    authors: Hassan MA,Melo MB,Haas B,Jensen KD,Saeij JP

    更新日期:2012-12-12 00:00:00

  • A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.

    abstract:BACKGROUND:Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4640-y

    authors: Olohan L,Gardiner LJ,Lucaci A,Steuernagel B,Wulff B,Kenny J,Hall N,Hall A

    更新日期:2018-04-13 00:00:00

  • A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping.

    abstract:BACKGROUND:Bayesian mixture models in which the effects of SNP are assumed to come from normal distributions with different variances are attractive for simultaneous genomic prediction and QTL mapping. These models are usually implemented with Monte Carlo Markov Chain (MCMC) sampling, which requires long compute times ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3082-7

    authors: Wang T,Chen YP,Bowman PJ,Goddard ME,Hayes BJ

    更新日期:2016-09-21 00:00:00

  • Transcriptional ontogeny of the developing liver.

    abstract:BACKGROUND:During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and pancreas. Early in organogenesis the fetal liver is populated by hematopoietic stem cells, the sourc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-33

    authors: Lee JS,Ward WO,Knapp G,Ren H,Vallanat B,Abbott B,Ho K,Karp SJ,Corton JC

    更新日期:2012-01-19 00:00:00

  • Correction to: De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia.

    abstract::Following the publication of this article [1], the authors reported that the original shading in columns 3 and 4 of Table 3, which indicated the presence or absence of viruses in each library, had been removed during typesetting. ...

    journal_title:BMC genomics

    pub_type: 杂志文章,已发布勘误

    doi:10.1186/s12864-019-6067-5

    authors: Belda E,Nanfack-Minkeu F,Eiglmeier K,Carissimo G,Holm I,Diallo M,Diallo D,Vantaux A,Kim S,Sharakhov IV,Vernick KD

    更新日期:2019-09-05 00:00:00

  • Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.

    abstract:BACKGROUND:Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT:We have studied gene co...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4098-3

    authors: Chatterjee P,Roy D,Bhattacharyya M,Bandyopadhyay S

    更新日期:2017-09-12 00:00:00

  • Flatfish monophyly refereed by the relationship of Psettodes in Carangimorphariae.

    abstract:BACKGROUND:The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4788-5

    authors: Shi W,Chen S,Kong X,Si L,Gong L,Zhang Y,Yu H

    更新日期:2018-05-25 00:00:00

  • Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.

    abstract:BACKGROUND:Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS:To visualize the dynamics...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-813

    authors: Soriano I,Quintales L,Antequera F

    更新日期:2013-11-21 00:00:00

  • Genome-wide profiling of G protein-coupled receptors in cerebellar granule neurons using high-throughput, real-time PCR.

    abstract:BACKGROUND:G protein-coupled receptors (GPCRs) are major players in cell communication, regulate a whole range of physiological functions during development and throughout adult life, are affected in numerous pathological situations, and constitute so far the largest class of drugable targets for human diseases. The co...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-241

    authors: Maurel B,Le Digarcher A,Dantec C,Journot L

    更新日期:2011-05-16 00:00:00

  • Evolutionary balance between LRR domain loss and young NBS-LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner.

    abstract:BACKGROUND:Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6212-1

    authors: Song H,Guo Z,Hu X,Qian L,Miao F,Zhang X,Chen J

    更新日期:2019-11-13 00:00:00

  • A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.

    abstract:BACKGROUND:Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "m...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-S1-S1

    authors: Chen Q,Sun F

    更新日期:2013-01-01 00:00:00

  • Effect of CAR activation on selected metabolic pathways in normal and hyperlipidemic mouse livers.

    abstract:BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-384

    authors: Rezen T,Tamasi V,Lövgren-Sandblom A,Björkhem I,Meyer UA,Rozman D

    更新日期:2009-08-19 00:00:00

  • The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations.

    abstract:BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6004-7

    authors: Dang X,Xie Z,Liu W,Sun Y,Liu X,Zhu Y,Staehelin C

    更新日期:2019-08-12 00:00:00

  • Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution.

    abstract:BACKGROUND:Nuclear receptors are hormone-regulated transcription factors whose signaling controls numerous aspects of development and physiology. Many receptors recognize DNA hormone response elements formed by direct repeats of RGKTCA motifs separated by 1 to 5 bp (DR1-DR5). Although many known such response elements ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-23

    authors: Laperriere D,Wang TT,White JH,Mader S

    更新日期:2007-01-19 00:00:00

  • GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    abstract:BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3731-5

    authors: Yu N,Guo X,Zelikovsky A,Pan Y

    更新日期:2017-05-24 00:00:00

  • A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits.

    abstract:BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-606

    authors: Decker JE,Vasco DA,McKay SD,McClure MC,Rolf MM,Kim J,Northcutt SL,Bauck S,Woodward BW,Schnabel RD,Taylor JF

    更新日期:2012-11-09 00:00:00

  • Speckle reducing bilateral filter for cattle follicle segmentation.

    abstract:BACKGROUND:Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultrasound images affect the post-processing, such as follicle segmentation and finally affect the measur...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-S2-S9

    authors: Tang J,Guo S,Sun Q,Deng Y,Zhou D

    更新日期:2010-11-02 00:00:00

  • Transversions have larger regulatory effects than transitions.

    abstract:BACKGROUND:Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unk...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3785-4

    authors: Guo C,McDowell IC,Nodzenski M,Scholtens DM,Allen AS,Lowe WL,Reddy TE

    更新日期:2017-05-19 00:00:00

  • Conservation of noncoding microsatellites in plants: implication for gene regulation.

    abstract:BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-323

    authors: Zhang L,Zuo K,Zhang F,Cao Y,Wang J,Zhang Y,Sun X,Tang K

    更新日期:2006-12-25 00:00:00

  • Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction.

    abstract:BACKGROUND:About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S6-S21

    authors: Wang Y,Yang T,Ma Y,Halade GV,Zhang J,Lindsey ML,Jin YF

    更新日期:2012-01-01 00:00:00

  • Identification of genetic loci that modulate cell proliferation in the adult rostral migratory stream using the expanded panel of BXD mice.

    abstract:BACKGROUND:Adult neurogenesis, which is the continual production of new neurons in the mature brain, demonstrates the strikingly plastic nature of the nervous system. Adult neural stem cells and their neural precursors, collectively referred to as neural progenitor cells (NPCs), are present in the subgranular zone (SGZ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-206

    authors: Poon A,Goldowitz D

    更新日期:2014-03-19 00:00:00