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      • Record: found
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      Expression profiling of white sponge nevus by RNA sequencing revealed pathological pathways

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          Abstract

          Background

          White sponge nevus (WSN) is a rare periodontal hereditary disease. To date, almost all WSN studies have focused on case reports or mutation reports. Thus, the mechanism behind WSN is still unclear. We investigated the pathogenesis of WSN using expression profiling.

          Methods

          Sequence analysis of samples from a WSN Chinese family revealed a mutation (332 T > C) in the KRT13 gene that resulted in the amino acid change Leu111Pro. The pathological pathway behind the WSN expression profile was investigated by RNA sequencing (RNA-seq).

          Results

          Construction of a heatmap revealed 24 activated genes and 57 reduced genes in the WSN patients. The ribosome structure was damaged in the WSN patients. Moreover, the translation rate was limited in the WSN patients, whereas ubiquitin-mediated proteolysis was enhanced.

          Conclusions

          Our results suggest that the abnormal degradation of the KRT13 protein in WSN patients may be associated with keratin 7 (KRT7) and an abnormal ubiquitination process.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s13023-015-0285-y) contains supplementary material, which is available to authorized users.

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          Most cited references30

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          The transcriptional landscape of the yeast genome defined by RNA sequencing.

          U Nagalakshmi, Z. Wang, K. Waern … (2008)
          The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
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            The impact of next-generation sequencing technology on genetics.

            Elaine R. Mardis (2008)
            If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.
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              Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

              Zhigang Xue, Kevin Huang, Chaochao Cai … (2013)
              Mammalian pre-implantation development is a complex process involving dramatic changes in the transcriptional architecture. We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing. Based on single-nucleotide variants in human blastomere messenger RNAs and paternal-specific single-nucleotide polymorphisms, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25 to 53%). By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely to be key in driving mammalian pre-implantation development. Together, the results provide a valuable resource to dissect gene regulatory mechanisms underlying progressive development of early mammalian embryos.
              Article 0 comments Cited 415 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Wenping Cai: wenpingcai@126.com
                Beizhan Jiang: jiangbeizhan@tongji.edu.cn
                Tienan Feng: tienan_feng@126.com
                Jinfeng Xue: xuejinfeng@sklmg.edu.cn
                Jianhua Yang: jianhuay@bcm.edu
                Zhenghu Chen: chenzhenghu111@163.com
                Junjun Liu: ljj19931202@163.com
                Rongbin Wei: ljj19931202@163.com
                Shouliang Zhao: slzhao@tongji.edu.cn
                Xiaoping Wang: wxp990@hotmail.com
                Shangfeng Liu: shangfengliufudan@163.com
                Journal
                Journal ID (nlm-ta): Orphanet J Rare Dis
                Journal ID (iso-abbrev): Orphanet J Rare Dis
                Title: Orphanet Journal of Rare Diseases
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1750-1172
                Publication date (Electronic): 11 June 2015
                Publication date PMC-release: 11 June 2015
                Publication date Collection: 2015
                Volume: 10
                Electronic Location Identifier: 72
                Affiliations
                [ ]Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, 200040 P. R. China
                [ ]Laboratory of Oral Biomedical Science and Translational Medicine, School of Stomatology, Tongji University, Shanghai, 200072 P. R. China
                [ ]School of Life sciences and Technology, Tongji University, Shanghai, 200065 P. R. China
                [ ]State Key Laboratory of Medical Genetics, Central South University, Changsha, 410078 P. R. China
                [ ]Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 P. R. China
                Article
                Publisher ID: 285
                DOI: 10.1186/s13023-015-0285-y
                PMC ID: 4474461
                PubMed ID: 26062705
                SO-VID: 0b938851-374e-445a-813f-6160b29b016f
                Copyright © © Cai et al. 2015
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 28 November 2014
                Date accepted : 14 May 2015
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © The Author(s) 2015

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: white sponge nevus,keratin7,keratin13,ubiquitin c (ubc),rna sequencing (rna-seq)
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: white sponge nevus, keratin7, keratin13, ubiquitin c (ubc), rna sequencing (rna-seq)

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