Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling.

Abstract:

:RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for unique insights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternative splicing events and the presence of non-coding RNAs. It has been realised non-coding RNAs are more then just artefacts of erroneous transcription and play vital regulatory roles at the genomic, transcriptional and translational level. Transcription of the DNA sense strand produces antisense transcripts. This is known as antisense transcription and often results in the production of non-coding RNAs that are complementary to their associated sense transcripts. Antisense tran-scription has been identified in bacteria, fungi, protozoa, plants, invertebrates and mammals. It seems that antisense tran-scriptional 'hot spots' are located around nucleosome-free regions such as those associated with promoters, indicating that it is likely that antisense transcripts carry out important regulatory functions. This underlines the importance of identifying the presence and understanding the function of these antisense non-coding RNAs. The information concerning strand ori-gin is often lost during conventional RNA-Seq; capturing this information would substantially increase the worth of any RNA-Seq experiment. By manipulating the input cDNA during the template preparation stage it is possible to retain this vital information. This forms the basis of strand-specific RNA-Seq. With an ability to unlock immense portions of new in-formation surrounding the transcriptome, this cutting edge technology may hold the key to developing a greater under-standing of the transcriptome.

journal_name

Curr Genomics

journal_title

Current genomics

authors

Mills JD,Kawahara Y,Janitz M

doi

10.2174/1389202911314030003

subject

Has Abstract

pub_date

2013-05-01 00:00:00

pages

173-81

issue

3

eissn

1389-2029

issn

1875-5488

pii

CG-14-173

journal_volume

14

pub_type

杂志文章
  • Antigenic Differences Between Normal and Malignant Cells as a Basis for Treatment of Intracerebral Neoplasms Using a DNA-Based Vaccine.

    abstract::Antigenic differences between normal and malignant cells of the cancer patient form the rationale for clinical immunotherapeutic strategies. Because the antigenic phenotype of neoplastic cells varies widely among different cells within the same malignant cell-population, immunization with a vaccine that stimulates imm...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920206778426951

    authors: Lichtor T,Glick RP,O-Sullivan I,Cohen EP

    更新日期:2006-06-01 00:00:00

  • Transcriptional Regulation of Telomeric Expression Sites and Antigenic Variation in Trypanosomes.

    abstract:Introduction:Trypanosoma brucei uses antigenic variation to evade the host antibody clearance by periodically changing its Variant Surface Glycoprotein (VSGs) coat. T. brucei encode over 2,500 VSG genes and pseudogenes, however they transcribe only one VSG gene at time from one of the 20 telomeric Expression Sites (ESs...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202918666170911161831

    authors: Cestari I,Stuart K

    更新日期:2018-02-01 00:00:00

  • MicroRNAs in Lung Cancer Oncogenesis and Tumor Suppression: How it Can Improve the Clinical Practice?

    abstract:Background:Lung cancer (LC) development is a process that depends on genetic mutations. The DNA methylation, an important epigenetic modification, is associated with the expression of non-coding RNAs, such as microRNAs. MicroRNAs are particularly essential for cell physiology, since they play a critical role in tumor s...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202921999200630144712

    authors: Pozza DH,De Mello RA,Araujo RLC,Velcheti V

    更新日期:2020-08-01 00:00:00

  • EGFR Intron Recombination in Human Gliomas: Inappropriate Diversion of V(D)J Recombination?

    abstract::The epidermal growth factor receptor (EGFR) is a membrane-bound, 170 kDa, protein tyrosine kinase that plays an important role in tumorigenesis. The EGFR gene, which is composed of over 168 kb of sequence, including a 123-kb first intron, is frequently amplified and rearranged in malignant gliomas leading to the expre...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207780833838

    authors: Fenstermaker RA,Ciesielski MJ

    更新日期:2007-05-01 00:00:00

  • Estrogen Regulation of MicroRNA Expression.

    abstract::Women outlive men, but life expectancy is not influenced by hormone replacement (estrogen + progestin) therapy. Estrogens appear to protect brain, cardiovascular tissues, and bone from aging. Estrogens regulate genes directly through binding to estrogen receptors alpha and beta (ERalpha and ERbeta) that are ligand-act...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209788185289

    authors: Klinge CM

    更新日期:2009-05-01 00:00:00

  • Retromer Dysfunction and Neurodegenerative Disease.

    abstract::In recent years, genomic, animal and cell biology studies have implicated deficiencies in retromer-mediated trafficking of proteins in an increasing number of neurodegenerative diseases including Alzheimer's Disease (AD), Parkinson's Disease (PD) and Frontotemporal Lobar Degener-ation (FTLD). The retromer complex, whi...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202919666171024122809

    authors: Reitz C

    更新日期:2018-05-01 00:00:00

  • Clinical and Rehabilitative Management of Retinitis Pigmentosa: Up-to-Date.

    abstract::The term retinitis pigmentosa (RP) indicates a heterogeneous group of genetic rare ocular diseases in which either rods or cones are prevalently damaged. RP represents the most common hereditary cause of blindness in people from 20 to 60 years old. In general, the different RP forms consist of progressive photo-recept...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211795860125

    authors: Parmeggiani F,Sato G,De Nadai K,Romano MR,Binotto A,Costagliola C

    更新日期:2011-06-01 00:00:00

  • The Relation Between Promoter Chromatin Status, Xyr1 and Cellulase Ex-pression in Trichoderma reesei.

    abstract::The ascomycete Trichoderma reesei is used for the production of plant cell wall-degrading enzymes in industrial scale. The interplay of the transactivator Xyr1 and the repressor Cre1 mainly regulates the expression of these enzymes. During induc-ing conditions, such as in the presence of sophorose, the transcription o...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666151116211812

    authors: Mello-de-Sousa TM,Rassinger A,Derntl C,Poças-Fonseca MJ,Mach RL,Mach-Aigner AR

    更新日期:2016-04-01 00:00:00

  • Plant spliceosomal introns: not only cut and paste.

    abstract::Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carr...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208784533629

    authors: Morello L,Breviario D

    更新日期:2008-06-01 00:00:00

  • Genetic variants in diseases of the extrapyramidal system.

    abstract::Knowledge on the genetics of movement disorders has advanced significantly in recent years. It is now recognized that disorders of the basal ganglia have genetic basis and it is suggested that molecular genetic data will provide clues to the pathophysiology of normal and abnormal motor control. Progress in molecular g...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202914666131210213327

    authors: Oczkowska A,Kozubski W,Lianeri M,Dorszewska J

    更新日期:2014-02-01 00:00:00

  • miR-15b and miR-21 as Circulating Biomarkers for Diagnosis of Glioma.

    abstract::Malignant gliomas are lethal primary intracranial tumors. To date, little information on the role of deregulated genes in gliomas have been identified. As the involvement of miRNAs in the carcinogenesis is well known, we carried out a pilot study to identify, as potential biomarkers, differentially expressed microRNAs...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202916666150707155610

    authors: Ivo D'Urso P,Fernando D'Urso O,Damiano Gianfreda C,Mezzolla V,Storelli C,Marsigliante S

    更新日期:2015-10-01 00:00:00

  • Array-based approaches for the identification of epigenetic silenced tumor suppressor genes.

    abstract::Carcinogenesis involves the inactivation or inhibition of genes that function as tumor suppressors. Deletions, mutations, or epigenetic silencing of tumor suppressor genes can lead to altered growth, differentiation, and apoptosis. DNA methylation and histone modifications are important epigenetic mechanisms of gene r...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208783884892

    authors: Takai N,Narahara H

    更新日期:2008-03-01 00:00:00

  • Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice.

    abstract::In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) ar...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202918666170228134530

    authors: Tripathi A,Chacon O,Singla-Pareek SL,Sopory SK,Sanan-Mishra N

    更新日期:2018-01-01 00:00:00

  • CENPA a genomic marker for centromere activity and human diseases.

    abstract::Inheritance of genetic material requires that chromosomes segregate faithfully during cell division. Failure in this process can drive to aneuploidy phenomenon. Kinetochores are unique centromere macromolecular protein structures that attach chromosomes to the spindle for a proper movement and segregation. A unique ty...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209788920985

    authors: Valdivia MM,Hamdouch K,Ortiz M,Astola A

    更新日期:2009-08-01 00:00:00

  • Vegetable Oil: Nutritional and Industrial Perspective.

    abstract::Oils of plant origin have been predominantly used for food-based applications. Plant oils not only represent a non-polluting renewable resource but also provide a wide diversity in fatty acids (FAs) composition with diverse applications. Besides being edible, they are now increasingly being used in industrial applicat...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160202220107

    authors: Kumar A,Sharma A,Upadhyaya KC

    更新日期:2016-06-01 00:00:00

  • Repurposing Pathogenic Variants of DMD Gene and its Isoforms for DMD Exon Skipping Intervention.

    abstract:Background:Duchenne Muscular Dystrophy (DMD) is a progressive, fatal neuromuscular disorder caused by mutations in the DMD gene. Emerging antisense oligomer based exon skipping therapy provides hope for the restoration of the reading frame. Objectives:Population-based DMD mutation database may enable exon skipping to ...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202920666191107142754

    authors: Tyagi R,Kumar S,Dalal A,Mohammed F,Mohanty M,Kaur P,Anand A

    更新日期:2019-11-01 00:00:00

  • Integrated analysis of transcriptomic and proteomic data.

    abstract::Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent st...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202911314020003

    authors: Haider S,Pal R

    更新日期:2013-04-01 00:00:00

  • Preterm Birth and the Risk of Neurodevelopmental Disorders - Is There a Role for Epigenetic Dysregulation?

    abstract::Preterm Birth (PTB) accounts for approximately 11% of all births worldwide each year and is a profound physiological stressor in early life. The burden of neuropsychiatric and developmental impairment is high, with severity and prevalence correlated with gestational age at delivery. PTB is a major risk factor for the ...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202919666171229144807

    authors: Fitzgerald E,Boardman JP,Drake AJ

    更新日期:2018-11-01 00:00:00

  • MDM4 (MDMX) and its Transcript Variants.

    abstract::MDM family proteins are crucial regulators of the oncosuppressor p53. Alterations of their gene status, mainly amplification events, have been frequently observed in human tumors.MDM4 is one of the two members of the MDM family. The human gene is located on chromosome 1 at q32-33 and codes for a protein of 490aa. In a...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209787581280

    authors: Mancini F,Di Conza G,Moretti F

    更新日期:2009-03-01 00:00:00

  • Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.

    abstract::The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding re...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207780368178

    authors: Nikolaev LG,Akopov SB,Chernov IP,Sverdlov ED

    更新日期:2007-04-01 00:00:00

  • Genetic alterations in poorly differentiated and undifferentiated thyroid carcinomas.

    abstract::Thyroid gland presents a wide spectrum of tumours derived from follicular cells that range from well differentiated, papillary and follicular carcinoma (PTC and FTC, respectively), usually carrying a good prognosis, to the clinically aggressive, poorly differentiated (PDTC) and undifferentiated thyroid carcinoma (UTC)...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211798120853

    authors: Soares P,Lima J,Preto A,Castro P,Vinagre J,Celestino R,Couto JP,Prazeres H,Eloy C,Máximo V,Sobrinho-Simões M

    更新日期:2011-12-01 00:00:00

  • Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends.

    abstract::Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of th...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211794520187

    authors: Bolle C,Schneider A,Leister D

    更新日期:2011-03-01 00:00:00

  • Analytical Models For Genetics of Human Traits Influenced By Sex.

    abstract::Analytical models usually assume an additive sex effect by treating it as a covariate to identify genetic associations with sex-influenced traits. Their underlying assumptions are violated by ignoring interactions of sex with genetic factors and heterogeneous genetic effects by sex. Methods to deal with the problems a...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160420142601

    authors: Lee C

    更新日期:2015-10-01 00:00:00

  • A Genome-wide Association Analysis in Four Populations Reveals Strong Genetic Heterogeneity For Birth Weight.

    abstract::Low or high birth weight is one of the main causes for neonatal morbidity and mortality. They are also associated with adulthood chronic illness. Birth weight is a complex trait which is affected by baby's genes, maternal environments as well as the complex interactions between them. To understand the genetic basis of...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160726152033

    authors: Luo T,Liu X,Cui Y

    更新日期:2016-10-01 00:00:00

  • Haploinsufficiency of DNA Damage Response Genes and their Potential Influence in Human Genomic Disorders.

    abstract::Genomic disorders are a clinically diverse group of conditions caused by gain, loss or re-orientation of a genomic region containing dosage-sensitive genes. One class of genomic disorder is caused by hemizygous deletions resulting in haploinsufficiency of a single or, more usually, several genes. For example, the hete...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208784340795

    authors: O'Driscoll M

    更新日期:2008-05-01 00:00:00

  • Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach.

    abstract::Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence t...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202921999200422122253

    authors: Shukla AK,Singh AK

    更新日期:2020-04-01 00:00:00

  • Genomic instability and carcinogenesis: an update.

    abstract::Cancers arise as a result of stepwise accumulation of mutations which may occur at the nucleotide level and/or the gross chromosomal level. Many cancers particularly those of the colon display a form of genomic instability which may facilitate and speed up tumor initiation and development. In few instances, a "mutator...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208786847926

    authors: Abdel-Rahman WM

    更新日期:2008-12-01 00:00:00

  • Immune related genes underpin the evolution of adaptive immunity in jawless vertebrates.

    abstract::The study of immune related genes in lampreys and hagfish provides a unique perspective on the evolutionary genetic underpinnings of adaptive immunity and the evolution of vertebrate genomes. Separated from their jawed cousins at the stem of the vertebrate lineage, these jawless vertebrates have many of the gene famil...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920212799860670

    authors: McCurley N,Hirano M,Das S,Cooper MD

    更新日期:2012-04-01 00:00:00

  • High-Throughput Omics Technologies: Potential Tools for the Investigation of Influences of EMF on Biological Systems.

    abstract::The mode of action of a huge amount of agents on biological systems is still unknown. One example where more questions than answers exist is covered by the term electromagnetic fields (EMF). Use of wireless communication, e.g. mobile phones, has been escalated in the last few years. Due to this fact, a lot of discussi...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209787847050

    authors: Blankenburg M,Haberland L,Elvers HD,Tannert C,Jandrig B

    更新日期:2009-04-01 00:00:00

  • Molecular Population Genetics and Evolution of the Chagas' Disease Vector Triatoma infestans (Hemiptera: Reduviidae).

    abstract::Triatoma infestans (Klug) is the main vector of Chagas' disease in the Southern Cone of Latin America between the latitudes 10° S and 46° S. The long-term effectiveness of the control campaigns is greatly dependent upon the vector population structure. Mitochondrial DNA (mtDNA) genes have been used in a number of T. i...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/13892029113149990006

    authors: García BA,de Rosas AR,Blariza MJ,Grosso CG,Fernández CJ,Stroppa MM

    更新日期:2013-08-01 00:00:00