Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo.


BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook the first detailed study to describe the methylation status of all known LTP-associated genes during LTP induction in the dentate gyrus of live rats. Using a methylated DNA immunoprecipitation (MeDIP)-array, together with previously published matched RNA-seq and public histone modification data, we discover widespread changes in methylation status of LTP-genes. We further show that the expression of many LTP-genes is correlated with their methylation status. We show that these correlated genes are enriched for RNA-processing, active histone marks, and specific transcription factors. These data reveal that the synaptic activity-evoked methylation changes correlates with pre-existing activation of the chromatin landscape. Finally, we show that methylation of Brain-derived neurotrophic factor (Bdnf) CpG-islands correlates with isoform switching from transcripts containing exon IV to exon I. CONCLUSIONS:Together, these data provide the first evidence of widespread regulation of methylation status in LTP-associated genes.


BMC Genomics


BMC genomics


Maag JL,Kaczorowski DC,Panja D,Peters TJ,Bramham CR,Wibrand K,Dinger ME




Has Abstract


2017-03-23 00:00:00












  • Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.

    abstract:BACKGROUND:Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the patho...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Galia W,Leriche F,Cruveiller S,Garnier C,Navratil V,Dubost A,Blanquet-Diot S,Thevenot-Sergentet D

    更新日期:2017-08-03 00:00:00

  • Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.

    abstract:BACKGROUND:The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar h...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ralph SG,Chun HJ,Cooper D,Kirkpatrick R,Kolosova N,Gunter L,Tuskan GA,Douglas CJ,Holt RA,Jones SJ,Marra MA,Bohlmann J

    更新日期:2008-01-29 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


    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

  • Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

    abstract:BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Park KD,Park J,Ko J,Kim BC,Kim HS,Ahn K,Do KT,Choi H,Kim HM,Song S,Lee S,Jho S,Kong HS,Yang YM,Jhun BH,Kim C,Kim TH,Hwang S,Bhak J,Lee HK,Cho BW

    更新日期:2012-09-12 00:00:00

  • Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L.

    abstract:BACKGROUND:Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites - especially the essential oils present in flowers are also different, especially the terpen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Tai Y,Hou X,Liu C,Sun J,Guo C,Su L,Jiang W,Ling C,Wang C,Wang H,Pan G,Si X,Yuan Y

    更新日期:2020-02-18 00:00:00

  • Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus.

    abstract:BACKGROUND:Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Owen J,Hedley BA,Svendsen C,Wren J,Jonker MJ,Hankard PK,Lister LJ,Stürzenbaum SR,Morgan AJ,Spurgeon DJ,Blaxter ML,Kille P

    更新日期:2008-06-03 00:00:00

  • In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides.

    abstract:BACKGROUND:An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sharma G,Parales R,Singer M

    更新日期:2018-10-19 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


    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

  • Assessing structural variation in a personal genome-towards a human reference diploid genome.

    abstract:BACKGROUND:Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: English AC,Salerno WJ,Hampton OA,Gonzaga-Jauregui C,Ambreth S,Ritter DI,Beck CR,Davis CF,Dahdouli M,Ma S,Carroll A,Veeraraghavan N,Bruestle J,Drees B,Hastie A,Lam ET,White S,Mishra P,Wang M,Han Y,Zhang F,Stankie

    更新日期:2015-04-11 00:00:00

  • COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

    abstract:BACKGROUND:A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatment, and prognosis of the disease. There are numerous databases and applications with which to archi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jho S,Kim BC,Ghang H,Kim JH,Park D,Kim HM,Jung SY,Yoo KY,Kim HJ,Lee S,Bhak J

    更新日期:2009-12-03 00:00:00

  • The landscape of mitochondrial small non-coding RNAs in the PGCs of male mice, spermatogonia, gametes and in zygotes.

    abstract:BACKGROUND:Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivotal post-transcriptional regulators, widening the landscape of their diversity and functions. In mamma...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Larriba E,Rial E,Del Mazo J

    更新日期:2018-08-28 00:00:00

  • Unlocking the bovine genome.

    abstract::The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

    journal_title:BMC genomics

    pub_type: 社论


    authors: Tellam RL,Lemay DG,Van Tassell CP,Lewin HA,Worley KC,Elsik CG

    更新日期:2009-04-24 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


    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

  • The transcriptome of a "sleeping" invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum.

    abstract:BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insigh...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Parmakelis A,Kotsakiozi P,Kontos CK,Adamopoulos PG,Scorilas A

    更新日期:2017-06-28 00:00:00

  • The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens.

    abstract:BACKGROUND:Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to Campylobacter could potentially redu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Psifidi A,Fife M,Howell J,Matika O,van Diemen PM,Kuo R,Smith J,Hocking PM,Salmon N,Jones MA,Hume DA,Banos G,Stevens MP,Kaiser P

    更新日期:2016-04-18 00:00:00

  • SCUD: Saccharomyces cerevisiae ubiquitination database.

    abstract:BACKGROUND:Ubiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important. DESCRIPTION:SCUD is a web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's y...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lee WC,Lee M,Jung JW,Kim KP,Kim D

    更新日期:2008-09-24 00:00:00

  • Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis.

    abstract:BACKGROUND:Castor oil is the only commercial source of hydroxy fatty acid that has industrial value. The production of castor oil is hampered by the presence of the toxin ricin in its seed. Lesquerella seed also accumulates hydroxy fatty acid and is free of ricin, and thus it is being developed as a new crop for hydrox...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim HU,Chen GQ

    更新日期:2015-03-24 00:00:00

  • Distribution and diversity of ribosome binding sites in prokaryotic genomes.

    abstract:BACKGROUND:Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction betwe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Omotajo D,Tate T,Cho H,Choudhary M

    更新日期:2015-08-14 00:00:00

  • Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora.

    abstract:BACKGROUND:Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia am...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Peng J,Triplett LR,Sundin GW

    更新日期:2021-01-22 00:00:00

  • Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle.

    abstract:BACKGROUND:As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Saatchi M,Garrick DJ,Tait RG Jr,Mayes MS,Drewnoski M,Schoonmaker J,Diaz C,Beitz DC,Reecy JM

    更新日期:2013-10-25 00:00:00

  • A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.

    abstract:BACKGROUND:Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cel...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lahens NF,Ricciotti E,Smirnova O,Toorens E,Kim EJ,Baruzzo G,Hayer KE,Ganguly T,Schug J,Grant GR

    更新日期:2017-08-10 00:00:00

  • Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus.

    abstract:BACKGROUND:Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the pre...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vieira FA,Gregório SF,Ferraresso S,Thorne MA,Costa R,Milan M,Bargelloni L,Clark MS,Canario AV,Power DM

    更新日期:2011-10-07 00:00:00

  • Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring.

    abstract:BACKGROUND:Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast' variation pattern of poplar at the single-base level during...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu S,Xu M,Wang H,Pan H,Wang G,Huang M

    更新日期:2018-05-29 00:00:00

  • Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.

    abstract:BACKGROUND:The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vázquez-Castellanos JF,García-López R,Pérez-Brocal V,Pignatelli M,Moya A

    更新日期:2014-01-18 00:00:00

  • Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach.

    abstract:BACKGROUND:The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and d...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: He D,Liu ZP,Chen L

    更新日期:2011-12-02 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


    authors: Wright ES,Baum DA

    更新日期:2018-10-03 00:00:00

  • A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

    abstract:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pilkington SM,Crowhurst R,Hilario E,Nardozza S,Fraser L,Peng Y,Gunaseelan K,Simpson R,Tahir J,Deroles SC,Templeton K,Luo Z,Davy M,Cheng C,McNeilage M,Scaglione D,Liu Y,Zhang Q,Datson P,De Silva N,Gardiner SE,Bas

    更新日期:2018-04-16 00:00:00

  • Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance.

    abstract:BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Tadmor-Levi R,Doron-Faigenboim A,Marcos-Hadad E,Petit J,Hulata G,Forlenza M,Wiegertjes GF,David L

    更新日期:2019-12-26 00:00:00

  • The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects.

    abstract:BACKGROUND:The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondr...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Negrisolo E,Babbucci M,Patarnello T

    更新日期:2011-05-10 00:00:00

  • Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes.

    abstract:BACKGROUND:The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sanchez-Alberola N,Campoy S,Barbé J,Erill I

    更新日期:2012-02-03 00:00:00