An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver

Xie, Linglin; Weichel, Brent; Ohm, Joyce E.; Zhang, Ke

doi:10.1186/1752-0509-5-s3-s4

Cited by 34 publications

(20 citation statements)

References 38 publications

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“…Several groups have already reanalyzed these data for a variety of purposes [33]–[35]. In our study, we reanalyzed the available RNA-Seq data from human tissues to assess the expression of OR genes in a broad range of tissues.…”

Section: Resultsmentioning

confidence: 99%

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

et al. 2013

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Olfactory receptors (ORs) provide the molecular basis for the detection of volatile odorant molecules by olfactory sensory neurons. The OR supergene family encodes G-protein coupled proteins that belong to the seven-transmembrane-domain receptor family. It was initially postulated that ORs are exclusively expressed in the olfactory epithelium. However, recent studies have demonstrated ectopic expression of some ORs in a variety of other tissues. In the present study, we conducted a comprehensive expression analysis of ORs using an extended panel of human tissues. This analysis made use of recent dramatic technical developments of the so-called Next Generation Sequencing (NGS) technique, which encouraged us to use open access data for the first comprehensive RNA-Seq expression analysis of ectopically expressed ORs in multiple human tissues. We analyzed mRNA-Seq data obtained by Illumina sequencing of 16 human tissues available from Illumina Body Map project 2.0 and from an additional study of OR expression in testis. At least some ORs were expressed in all the tissues analyzed. In several tissues, we could detect broadly expressed ORs such as OR2W3 and OR51E1. We also identified ORs that showed exclusive expression in one investigated tissue, such as OR4N4 in testis. For some ORs, the coding exon was found to be part of a transcript of upstream genes. In total, 111 of 400 OR genes were expressed with an FPKM (fragments per kilobase of exon per million fragments mapped) higher than 0.1 in at least one tissue. For several ORs, mRNA expression was verified by RT-PCR. Our results support the idea that ORs are broadly expressed in a variety of tissues and provide the basis for further functional studies.

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Section: Resultsmentioning

confidence: 99%

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

et al. 2013

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“…Second, the study detects a direct correlation between TNNT1 promoter methylation and expression, in contrast with the popular view that promoter hypomethylation favours transcription. When taken together with previous data on the lack of correlation between DNA methylation and transcription in somatic cells [8], the conclusions of the study by Guay et al demonstrate that our understanding of the functional epigenome is still incomplete. Clearly, 'omics' demand more, not less, basic research before they can contribute to lessen the burden of human diseases.…”

mentioning

confidence: 71%

Atherosclerosis

Zaina¹,

Lund²

2013

Current Opinion in Lipidology

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“…Practical application of RNA-seq data in nephrology. Xie et al 34 analyzed the DNA methylation and RNA-seq for the human kidney. They clarified that DNA methylation reflects tissue specificity and that gene methylation and its transcriptional levels were comprehensively correlated.…”

Section: Rna-seqmentioning

confidence: 99%

Revolution of nephrology research by deep sequencing: ChIP-seq and RNA-seq

Mimura

Kanki

Kodama

et al. 2014

Kidney International

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The recent and rapid advent of next-generation sequencing (NGS) has made this technology broadly available not only to researchers in various molecular and cellular biology fields but also to those in kidney disease. In this paper, we describe the usage of ChIP-seq (chromatin immunoprecipitation with sequencing) and RNA-seq for sample preparation and interpretation of raw data in the investigation of biological phenomenon in renal diseases. ChIP-seq identifies genome-wide transcriptional DNA-binding sites as well as histone modifications, which are known to regulate gene expression, in the intragenic as well as in the intergenic regions. With regard to RNA-seq, this process analyzes not only the expression level of mRNA but also splicing variants, non-coding RNA, and microRNA on a genome-wide scale. The combination of ChIP-seq and RNA-seq allows the clarification of novel transcriptional mechanisms, which have important roles in various kinds of diseases, including chronic kidney disease. The rapid development of these techniques requires an update on the latest information and methods of NGS. In this review, we highlight the merits and characteristics of ChIP-seq and RNA-seq and discuss the use of the genome-wide analysis in kidney disease.

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An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver

Cited by 34 publications

References 38 publications

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

Atherosclerosis

Revolution of nephrology research by deep sequencing: ChIP-seq and RNA-seq

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