Abstract:
BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of industrial biotechnology. RESULTS:In this study, we measured changes in transcriptome at three time points during the exponential growth phase of K. marxianus by using strand-specific RNA-seq. We found that approximately 60% of the transcriptome consists of ncRNAs transcribed from antisense and intergenic regions of the genome that were transcribed at lower levels than mRNA. In the transcriptome, a substantial number of long antisense ncRNAs (lancRNAs) are differentially expressed and enriched in carbohydrate and energy metabolism pathways. Furthermore, this enrichment is evolutionarily conserved, at least in yeast. Particularly, the mode of regulation of mRNA/lancRNA pairs is associated with mRNA transcription levels; the correlation between the pairs is positive at high mRNA transcriptional levels and negative at low levels. In addition, significant induction of mRNA and coverage of more than half of the mRNA sequence by a lancRNA strengthens the positive correlation between mRNA/lancRNA pairs. CONCLUSIONS:Transcriptome sequencing of K. marxianus in the exponential growth phase reveals pervasive transcription of ncRNAs with evolutionarily conserved functions. Studies of the mode of regulation of mRNA/lancRNA pairs suggest that induction of lancRNA may be associated with switch-like behavior of mRNA/lancRNA pairs and efficient regulation of the carbohydrate and energy metabolism pathways in the exponential growth phase of K. marxianus being used in industrial applications.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BKdoi
10.1186/s12864-016-2474-zsubject
Has Abstractpub_date
2016-02-29 00:00:00pages
154issn
1471-2164pii
10.1186/s12864-016-2474-zjournal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that ca...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-428
更新日期:2010-07-12 00:00:00
abstract:BACKGROUND:Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-74
更新日期:2011-01-27 00:00:00
abstract:BACKGROUND:Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyze...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-362
更新日期:2014-05-12 00:00:00
abstract:BACKGROUND:We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS:The assembly process consisted of multipl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-180
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2139-3
更新日期:2015-11-14 00:00:00
abstract:BACKGROUND:Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-346
更新日期:2012-07-28 00:00:00
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
更新日期:2013-11-23 00:00:00
abstract:BACKGROUND:Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type thr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3921-1
更新日期:2017-07-12 00:00:00
abstract:BACKGROUND:An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i) the bromodomain, which can recognize certain acetylation marks and (ii) the chromodomain, which can recognize certain meth...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-6
更新日期:2006-01-16 00:00:00
abstract:BACKGROUND:The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-230
更新日期:2012-06-09 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-291
更新日期:2011-06-04 00:00:00
abstract:BACKGROUND:Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyano...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2846-4
更新日期:2016-08-02 00:00:00
abstract:BACKGROUND:Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotrans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-142
更新日期:2013-03-04 00:00:00
abstract:BACKGROUND:Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS:The analyses show that neighbou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-42
更新日期:2009-01-22 00:00:00
abstract:BACKGROUND:High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2797-9
更新日期:2016-08-18 00:00:00
abstract:BACKGROUND:Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-225
更新日期:2013-04-04 00:00:00
abstract:BACKGROUND:Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copie...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1860-2
更新日期:2015-09-03 00:00:00
abstract:BACKGROUND:Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. RESULTS:We have d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S7
更新日期:2015-01-01 00:00:00
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
doi:10.1186/1471-2164-12-490
更新日期:2011-10-07 00:00:00
abstract:BACKGROUND:Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. RESULTS:Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06846-x
更新日期:2020-06-24 00:00:00
abstract:BACKGROUND:The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers. Effective navigation approaches...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S7-S24
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4606-0
更新日期:2018-04-06 00:00:00
abstract:BACKGROUND:Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-352
更新日期:2009-08-04 00:00:00
abstract:BACKGROUND:Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-318
更新日期:2014-04-28 00:00:00
abstract:BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-632
更新日期:2010-11-15 00:00:00
abstract:BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/s12864-016-2481-0
更新日期:2016-02-25 00:00:00
abstract:BACKGROUND:Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-103
更新日期:2008-02-27 00:00:00
abstract:BACKGROUND:Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-396
更新日期:2011-08-05 00:00:00
abstract:BACKGROUND:Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4861-0
更新日期:2018-06-20 00:00:00
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
更新日期:2019-01-21 00:00:00