Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp).

Abstract:

BACKGROUND:In a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was specifically detected in the adult stage. A nucleotide sequence comparison between the 32-nt small RNA and predicted tRNA sequences in the draft nuclear genomic DNA showed that the small RNA was derived from tRNA(Gly)(GCC). To determine the overall features of the tRNA-derived fragments (tRFs) of T. cancriformis, the small RNA sequences in each of the six developmental stages (egg, 1st-4th instar larvae, and adult) were compared with the mitochondrial and nuclear tRNA sequences. RESULTS:We found that the tRFs were derived from mitochondrial and nuclear tRNAs corresponding to 16 and 39 anticodons, respectively. The total read number of nuclear tRFs was approximately 400 times larger than the number of mitochondrial tRFs. Interestingly, the main regions in each parental tRNA from which these tRFs were derived differed, depending on the parental anticodon. Mitochondrial tRF(Ser)(GCU)s were abundantly produced from the 5' half regions of the parental tRNA, whereas mitochondrial tRF(Val)(UAC)s were mainly produced from the 3' end regions. Highly abundant nuclear tRFs, tRF(Gly)(GCC)s, tRF(Gly)(CCC)s, tRF(Glu)(CUC)s, and tRF(Lys)(CUU)s were derived from the 5' half regions of the parental tRNAs. Further analysis of the tRF read counts in the individual developmental stages suggested that the expression of mitochondrial and nuclear tRFs differed during the six stages. Based on these data, we precisely summarized the positions of the tRFs in their parental tRNAs and their expression changes during development. CONCLUSIONS:Our results reveal the entire dynamics of the tRFs from both the nuclear and mitochondrial genomes of T. cancriformis and indicate that the majority of tRFs in the cell are derived from nuclear tRNAs. This study provides the first examples of developmentally expressed mitochondrial tRFs.

journal_name

BMC Genet

journal_title

BMC genetics

authors

Hirose Y,Ikeda KT,Noro E,Hiraoka K,Tomita M,Kanai A

doi

10.1186/s12863-015-0245-5

subject

Has Abstract

pub_date

2015-07-14 00:00:00

pages

83

issn

1471-2156

pii

10.1186/s12863-015-0245-5

journal_volume

16

pub_type

杂志文章
  • Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene.

    abstract:BACKGROUND:Neuropeptide Y is a key neurotransmitter of the central nervous system which plays a vital role in the feed energy homeostasis in mammals. Mutations in the regulatory and coding regions of the bovine NPY gene can potentially affect the neuronal regulation of appetite and feeding behaviour in cattle. The obje...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-9-91

    authors: Bahar B,Sweeney T

    更新日期:2008-12-23 00:00:00

  • Microsatellite linkage analysis, single-nucleotide polymorphisms, and haplotype associations with ECB21 in the COGA data.

    abstract::This study, part of the Genetic Analysis Workshop 14 (GAW14), explored real Collaborative Study on the Genetics of Alcoholism data for linkage and association mapping between genetic polymorphisms (microsatellite and single-nucleotide polymorphisms (SNPs)) and beta (16.5-20 Hz) oscillations of the brain rhythms (ecb21...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-6-S1-S94

    authors: Kraja AT,Borecki IB,Province MA

    更新日期:2005-12-30 00:00:00

  • MicroRNA-146a rs2910164 is associated with severe preeclampsia in Black South African women on HAART.

    abstract:BACKGROUND:South African (SA) Black women have a high prevalence of preeclampsia and HIV, both conditions associated with increased inflammation. miR-146a is an inflammatory-associated miR and a common single nucleotide polymorphism (rs2910164) has been associated with several disease conditions. To date, this SNP has ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0469-z

    authors: Maharaj NR,Ramkaran P,Pillay S,Chuturgoon AA

    更新日期:2017-01-19 00:00:00

  • Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

    abstract:BACKGROUND:DGAT2 is a promising candidate gene for obesity because of its function as a key enzyme in fat metabolism and because of its localization on chromosome 11q13, a linkage region for extreme early onset obesity detected in our sample. We performed a mutation screen in 93 extremely obese children and adolescents...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-17

    authors: Friedel S,Reichwald K,Scherag A,Brumm H,Wermter AK,Fries HR,Koberwitz K,Wabitsch M,Meitinger T,Platzer M,Biebermann H,Hinney A,Hebebrand J

    更新日期:2007-05-03 00:00:00

  • Molecular mechanism of estrogen-mediated neuroprotection in the relief of brain ischemic injury.

    abstract:BACKGROUND:This study aimed to explore the molecular mechanism of estrogen-mediated neuroprotection in the relief of cerebral ischemic injury. The gene expression profiles were downloaded from Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified using limma package in R software. ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0630-y

    authors: He J,Gao Y,Wu G,Lei X,Zhang Y,Pan W,Yu H

    更新日期:2018-07-20 00:00:00

  • Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces.

    abstract:BACKGROUND:Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present st...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-019-0736-x

    authors: Yao F,Zhang X,Ye X,Li J,Long L,Yu C,Li J,Wang Y,Wu Y,Wang J,Jiang Q,Li W,Ma J,Wei Y,Zheng Y,Chen G

    更新日期:2019-03-26 00:00:00

  • Association study of stuttering candidate genes GNPTAB, GNPTG and NAGPA with dyslexia in Chinese population.

    abstract:BACKGROUND:Dyslexia is a polygenic speech and language disorder characterized by an unexpected difficulty in reading in children and adults despite normal intelligence and schooling. Increasing evidence reveals that different speech and language disorders could share common genetic factors. As previous study reported a...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0172-5

    authors: Chen H,Xu J,Zhou Y,Gao Y,Wang G,Xia J,Huen MS,Siok WT,Jiang Y,Tan LH,Sun Y

    更新日期:2015-02-03 00:00:00

  • Effectiveness of 10 polymorphic microsatellite markers for parentage and pedigree analysis in plateau pika (Ochotona curzoniae).

    abstract:BACKGROUND:The plateau pika (Ochotona curzoniae) is an underground-dwelling mammal, native to the Tibetan plateau of China. A set of 10 polymorphic microsatellite loci has been developed earlier. Its reliability for parentage assignment has been tested in a plateau pika population. Two family groups with a known pedigr...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-101

    authors: Li K,Geng J,Qu J,Zhang Y,Hu S

    更新日期:2010-11-10 00:00:00

  • Age-stratified heritability estimation in the Framingham Heart Study families.

    abstract::The Framingham Heart Study provides a unique source of longitudinal family data related to CVD risk factors. Age-stratified heritability estimates were obtained over three age groups (31-49 years, 50-60 years, and 61-79 years), reflecting the longitudinal nature of the data, for four quantitative traits. Age-adjusted ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-4-S1-S32

    authors: Brown WM,Beck SR,Lange EM,Davis CC,Kay CM,Langefeld CD,Rich SS,Framingham Heart Study.

    更新日期:2003-12-31 00:00:00

  • Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs.

    abstract:BACKGROUND:Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least on...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-92

    authors: Tortereau F,Sanchez MP,Fève K,Gilbert H,Iannuccelli N,Billon Y,Milan D,Bidanel JP,Riquet J

    更新日期:2011-10-27 00:00:00

  • The use of the SLC16A1 gene as a potential marker to predict race performance in Arabian horses.

    abstract:BACKGROUND:Arabian horses are commonly believed to be one of the oldest and the most popular horse breeds in the world, characterized by favourable stamina traits and exercise phenotypes. During intensive training, the rates of lactate production and utilization are critical to avoid muscle fatigue and a decrease in ex...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-019-0774-4

    authors: Ropka-Molik K,Stefaniuk-Szmukier M,Szmatoła T,Piórkowska K,Bugno-Poniewierska M

    更新日期:2019-09-11 00:00:00

  • The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars.

    abstract:BACKGROUND:Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the ec...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-35

    authors: Ramos AM,Duijvesteijn N,Knol EF,Merks JW,Bovenhuis H,Crooijmans RP,Groenen MA,Harlizius B

    更新日期:2011-04-20 00:00:00

  • Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers.

    abstract:BACKGROUND:Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum. RESULTS:In the present study, 15 new EST-SSR markers were developed from publicly available ESTs...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0261-5

    authors: Teshome A,Bryngelsson T,Dagne K,Geleta M

    更新日期:2015-08-19 00:00:00

  • Comparisons of methods for linkage analysis and haplotype reconstruction using extended pedigree data.

    abstract::We compare and contrast the performance of SIMPLE, a Monte Carlo based software, with that of several other methods for linkage and haplotype analyses, focusing on the simulated data from the New York City population. First, a whole-genome scan study based on the microsatellite markers was performed using GENEHUNTER. ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-6-S1-S76

    authors: Lin S,Ding J,Dong C,Liu Z,Ma ZJ,Wan S,Xu Y

    更新日期:2005-12-30 00:00:00

  • MTH1 and RGT1 demonstrate combined haploinsufficiency in regulation of the hexose transporter genes in Saccharomyces cerevisiae.

    abstract:BACKGROUND:The SNF3 gene in the yeast Saccharomyces cerevisiae encodes a low glucose sensor that regulates expression of an important subset of the hexose transporter (HXT) superfamily. Null mutations of snf3 result in a defect in growth on low glucose concentrations due to the inability to relieve repression of a subs...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-13-107

    authors: Dietzel KL,Ramakrishnan V,Murphy EE,Bisson LF

    更新日期:2012-12-12 00:00:00

  • Molecular organization and chromosomal localization of 5S rDNA in Amazonian Engystomops (Anura, Leiuperidae).

    abstract:BACKGROUND:For anurans, knowledge of 5S rDNA is scarce. For Engystomops species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species Engystomops freibergi and Engystomops peter...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-13-17

    authors: Rodrigues DS,Rivera M,Lourenço LB

    更新日期:2012-03-20 00:00:00

  • Replacement of the essential Dictyostelium Arp2 gene by its Entamoeba homologue using parasexual genetics.

    abstract:BACKGROUND:Cell motility is an essential feature of the pathogenesis and morbidity of amoebiasis caused by Entamoeba histolytica. As motility depends on cytoskeletal organisation and regulation, a study of the molecular components involved is key to a better understanding of amoebic pathogenesis. However, little is kno...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-28

    authors: Zaki M,King J,Fütterer K,Insall RH

    更新日期:2007-06-06 00:00:00

  • Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype.

    abstract:BACKGROUND:RNA sequencing (RNA-seq) technology has identified multiple differentially expressed (DE) genes associated to complex disease, however, these genes only explain a modest part of variance. Omnigenic model assumes that disease may be driven by genes with indirect relevance to disease and be propagated by funct...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-019-0739-7

    authors: Shao F,Wang Y,Zhao Y,Yang S

    更新日期:2019-03-19 00:00:00

  • An investigation of the effects of lipid-lowering medications: genome-wide linkage analysis of lipids in the HyperGEN study.

    abstract:BACKGROUND:Use of anti-hyperlipidemic medications compromises genetic analysis because of altered lipid profiles. We propose an empirical method to adjust lipid levels for medication effects so that the adjusted lipid values substitute the unmedicated lipid values in the genetic analysis. RESULTS:Published clinical tr...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-60

    authors: Wu J,Province MA,Coon H,Hunt SC,Eckfeldt JH,Arnett DK,Heiss G,Lewis CE,Ellison RC,Rao DC,Rice T,Kraja AT

    更新日期:2007-09-10 00:00:00

  • Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing.

    abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bu...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0671-2

    authors: Wang Z,Zhu T,Ma W,Wang N,Qu G,Zhang S,Wang J

    更新日期:2018-09-20 00:00:00

  • Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon.

    abstract:BACKGROUND:The disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00870-2

    authors: Yang WJ,Yan AZ,Xu YJ,Guo XY,Fu XG,Li D,Liao J,Zhang D,Lan FH

    更新日期:2020-06-18 00:00:00

  • Polymorphisms of two loci at the oxytocin receptor gene in populations of Africa, Asia and South Europe.

    abstract:BACKGROUND:The oxytocin (OT) system is known to be implicated in the regulation of complex social behavior, particularly empathy and parenting. The goal of this study was to estimate the gender and population differences in polymorphisms of two oxytocin receptor gene SNPs, rs53576 and rs2254298, in four populations. R...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0323-8

    authors: Butovskaya PR,Lazebny OE,Sukhodolskaya EM,Vasiliev VA,Dronova DA,Fedenok JN,Rosa A,Peletskaya EN,Ryskov AP,Butovskaya ML

    更新日期:2016-01-06 00:00:00

  • Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle.

    abstract:BACKGROUND:Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We per...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-0837-6

    authors: An B,Xu L,Xia J,Wang X,Miao J,Chang T,Song M,Ni J,Xu L,Zhang L,Li J,Gao H

    更新日期:2020-03-14 00:00:00

  • Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle.

    abstract:BACKGROUND:Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poor...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-15-15

    authors: Ogawa S,Matsuda H,Taniguchi Y,Watanabe T,Nishimura S,Sugimoto Y,Iwaisaki H

    更新日期:2014-02-03 00:00:00

  • Clustering by genetic ancestry using genome-wide SNP data.

    abstract:BACKGROUND:Population stratification can cause spurious associations in a genome-wide association study (GWAS), and occurs when differences in allele frequencies of single nucleotide polymorphisms (SNPs) are due to ancestral differences between cases and controls rather than the trait of interest. Principal components ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-108

    authors: Solovieff N,Hartley SW,Baldwin CT,Perls TT,Steinberg MH,Sebastiani P

    更新日期:2010-12-09 00:00:00

  • The TCF7L2 rs7903146 polymorphism, dietary intakes and type 2 diabetes risk in an Algerian population.

    abstract:BACKGROUND:The transcription factor 7-like 2 (TCF7L2) gene is the most significant genetic risk factor for type 2 diabetes (T2D). Association analyses were performed on participants (n = 751, aged between 30 and 64) in the ISOR population-based study in the city of Oran. Dietary intakes were estimated using a weekly fo...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-014-0134-3

    authors: Ouhaibi-Djellouli H,Mediene-Benchekor S,Lardjam-Hetraf SA,Hamani-Medjaoui I,Meroufel DN,Boulenouar H,Hermant X,Saidi-Mehtar N,Amouyel P,Houti L,Goumidi L,Meirhaeghe A

    更新日期:2014-12-10 00:00:00

  • Genetic diversity of Bm86 sequences in Rhipicephalus (Boophilus) microplus ticks from Mexico: analysis of haplotype distribution patterns.

    abstract:BACKGROUND:Ticks are a problem for cattle production mainly in tropical and subtropical regions, because they generate great economic losses. Acaricides and vaccines have been used to try to keep tick populations under control. This has been proven difficult given the resistance to acaricides and vaccines observed in t...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-019-0754-8

    authors: Martínez-Arzate SG,Sánchez-Bermúdez JC,Sotelo-Gómez S,Diaz-Albiter HM,Hegazy-Hassan W,Tenorio-Borroto E,Barbabosa-Pliego A,Vázquez-Chagoyán JC

    更新日期:2019-07-12 00:00:00

  • Genome-wide linkage analysis of congenital heart defects using MOD score analysis identifies two novel loci.

    abstract:BACKGROUND:Congenital heart defects (CHD) is the most common cause of death from a congenital structure abnormality in newborns and is often associated with fetal loss. There are many types of CHD. Human genetic studies have identified genes that are responsible for the inheritance of a particular type of CHD and for s...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-14-44

    authors: Flaquer A,Baumbach C,Piñero E,García Algas F,de la Fuente Sanchez MA,Rosell J,Toquero J,Alonso-Pulpon L,Garcia-Pavia P,Strauch K,Heine-Suñer D

    更新日期:2013-05-24 00:00:00

  • A second generation genetic map for rainbow trout (Oncorhynchus mykiss).

    abstract:BACKGROUND:Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-9-74

    authors: Rexroad CE 3rd,Palti Y,Gahr SA,Vallejo RL

    更新日期:2008-11-19 00:00:00

  • A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition.

    abstract:BACKGROUND:Non-pathological cognitive ageing is a distressing condition affecting an increasing number of people in our 'ageing society'. Oxidative stress is hypothesised to have a major role in cellular ageing, including brain ageing. RESULTS:Associations between cognitive ageing and 325 single nucleotide polymorphis...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-43

    authors: Harris SE,Fox H,Wright AF,Hayward C,Starr JM,Whalley LJ,Deary IJ

    更新日期:2007-07-02 00:00:00