Review of massively parallel DNA sequencing technologies

Moorthie, Sowmiya; Mattocks, Christopher; Wright, Caroline F.

doi:10.1007/s11568-011-9156-3

Cited by 72 publications

(39 citation statements)

References 82 publications

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“…This article will focus on the analysis of chimeric transcription using paired-end RNA-seq. For technical descriptions of contemporary sequencing platforms and methodologies the reader is referred to recent reviews (36)(37)(38)(39)(40)(41)(42)(43).…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Utility of next‐generation RNA‐sequencing in identifying chimeric transcription involving human endogenous retroviruses

Sokol

Jessen

Pedersen

2016

APMIS

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Sokol M, Jessen KM, Pedersen FS. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. APMIS 2016; 124: 127-139. Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the c-and b-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied nextgeneration paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights the high suitability of contemporary sequencing methods in future analyses of human biology in relation to evolutionary acquired retroviruses in the human genome.

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Section: Next-generation Sequencingmentioning

confidence: 99%

Utility of next‐generation RNA‐sequencing in identifying chimeric transcription involving human endogenous retroviruses

Sokol

Jessen

Pedersen

2016

APMIS

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Section: Applications Of Ngsmentioning

confidence: 99%

“…For instance, NGS has been used in the field of complete genome resequencing to understand polymorphisms in addition to mutation discovery in human genomes [134,135]. Regarding reduced representation sequencing, NGS has helped to discover large-scale polymorphisms [136][137][138], and resequencing of targeted genomes has been used to detect targeted polymorphisms and mutations [135,139]. This technique has been used to find inherited as well as obtained structural variations via paired end sequencing [140,141] and in the discovery of commensal and infectious flora through metagenomic sequencing [142,143].…”

Section: Applications Of Ngsmentioning

confidence: 99%

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

et al. 2015

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Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

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“…In this regard, it is fortuitous and timely that future crop genetic improvement will be aided by several developments in plant breeding that are underpinned by the massive increase in DNA sequence information flowing into databases from new methods of reading DNA that were developed in the mid 2000's (Moorthie et al. 2011). A stark example of this revolution in sequencing speed is seen in the progress of rice genomics where, after about three years work, the first draft genomic sequence of rice was published in 2002 (Goff et al.…”

mentioning

confidence: 99%

“…In addition to the important targets of yield, nutritional quality and resilience to abiotic stresses, breeding for resistance to pests and diseases will become even more critical as the availability of plant protection products is further diminished by regulation and/or the lack of new active ingredients coming to market (Chapman 2014) and by consumer preferences for fewer inputs. In this regard, it is fortuitous and timely that future crop genetic improvement will be aided by several developments in plant breeding that are underpinned by the massive increase in DNA sequence information flowing into databases from new methods of reading DNA that were developed in the mid 2000 ' s (Moorthie et al 2011). A stark example of this revolution in sequencing speed is seen in the progress of rice genomics where, after about three years work, the first draft genomic sequence of rice was published in 2002 (Goff et al 2002;Yu et al 2002).…”

mentioning

confidence: 99%