Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle

Patel, Amrutlal K.; Bhatt, Vaibhav D.; Tripathi, Ajai K.; Sajnani, Manisha R.; Jakhesara, Subhash J.; Koringa, Prakash G.; Joshi, Chaitanya G.

doi:10.1016/j.ygeno.2012.10.001

Cited by 8 publications

(7 citation statements)

References 31 publications

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“…An alternative splice variant lacking the sequence PPPNPGYPGGPQPPMPPYAQ (fragment 15–34) has been found in the Alzheimer cortex (NCBI accession AK294127), but its relevance is still unknown. Moreover, alternative splicing of GRINA has been reported in horn cancer, a very common type of squamous cell carcinoma, in Zebu cattle [19].…”

Section: The Gene Coding For Grinamentioning

confidence: 99%

Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport

Jiménez-González

Ogalla-García

García-Quintanilla

et al. 2019

IJMS

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The Glutamate Receptor Ionotropic NMDA-Associated Protein 1 (GRINA) belongs to the Lifeguard family and is involved in calcium homeostasis, which governs key processes, such as cell survival or the release of neurotransmitters. GRINA is mainly associated with membranes of the endoplasmic reticulum, Golgi, endosome, and the cell surface, but its presence in the nucleus has not been explained yet. Here we dissect, with the help of different software tools, the potential roles of GRINA in the cell and how they may be altered in diseases, such as schizophrenia or celiac disease. We describe for the first time that the cytoplasmic N-terminal half of GRINA (which spans a Proline-rich domain) contains a potential DNA-binding sequence, in addition to cleavage target sites and probable PY-nuclear localization sequences, that may enable it to be released from the rest of the protein and enter the nucleus under suitable conditions, where it could participate in the transcription, alternative splicing, and mRNA export of a subset of genes likely involved in lipid and sterol synthesis, ribosome biogenesis, or cell cycle progression. To support these findings, we include additional evidence based on an exhaustive review of the literature and our preliminary data of the protein–protein interaction network of GRINA.

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Section: The Gene Coding For Grinamentioning

confidence: 99%

Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport

Jiménez-González

Ogalla-García

García-Quintanilla

et al. 2019

IJMS

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“…Although not completely replacing other technologies, such as microarray (Kogenaru et al 2012), arrays in general are less sensitive than RNA-seq and have limited ability to detect alternative spliced mRNA isoforms (Wang et al 2009;McGettigan, 2013). Detection of transcript variants by RNA-seq still has its challenges (Marioni et al 2008), but RNA-seq data maintain a higher level of resolution when compared with microarrays (Loraine et al 2013;Patel et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Assessment of myometrial transcriptome changes associated with spontaneous human labour by high‐throughput RNA‐seq

Chan

Berg

Moore

et al. 2014

Experimental Physiology

120

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New Findings r What is the central question of this study?In this study, we sought to survey the total transcript repertoire of human myometrium, comparing samples taken from patients at term who were not in labour with samples taken at term in spontaneous labour. These sequenced transcriptomes show the repertoire of possible proteins and their variants in myometrial smooth muscle, as well as transcriptional changes associated with term spontaneous labour. r What is the main finding and its importance?We describe, for the first time, the transcriptome of the human myometrial samples taken from patients prior to and after the onset of spontaneous labour. We document a significant number of novel transcripts of both protein-coding mRNA and microRNA. This information will be useful for the development of novel therapeutics and the formulation of new hypotheses to be tested by physiological experimentation.The transition of the human uterus from a quiescent to a contractile state takes place over a number of weeks. On such biological time scales, cellular phenotype is modified by changes in the transcriptome, which in turn is under the control of the underlying endocrine, paracrine, and biophysical processes resulting from the ongoing pregnancy. In this study, we characterize the transition of the human myometrial transcriptome at term from not in labour (NIL) to in labour (LAB) using high throughput RNA sequencing (RNA-seq). RNA was isolated from the myometrium of uterine biopsies from patients at term who were not in labour (n = 5) and at term in spontaneous labour (n = 5) without augmentation. A total of 143.6 million separate reads were sequenced, achieving, on average, ß13 times coverage of the expressed human transcriptome per sample. Principal component analysis indicated that the NIL and LAB transcriptomes could be distinguished as two distinct clusters. A comparison of the NIL and LAB groups, using three different statistical approaches (baySeq, edgeR, and DESeq), demonstrated an overlap of 764 differentially expressed genes. A comparison with currently available microarray data revealed only a partial overlap in differentially expressed genes. We conclude that the described RNA-seq data sets represent the first fully annotated catalogue of expressed mRNAs in human myometrium. When considered together, the full expression repertoire and the differentially

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“…Since horn cancer has been analysed previously for detection of novel splice variants (Patel et al 2013), we sought to identify any differences or similarities between results, if any. Surprisingly, none of the previously identified and validated eight splice isoforms were detected in the present study.…”

Section: Discussionmentioning

confidence: 99%

“…Until recently, profound cost, limited coverage and sensitivity of the sequencing and microarray studies were hindering the global study of AS events in the cell; however, with advancement in the next-generation sequencing technologies now it is possible to do the same. Although, HC has been studied recently for detection of AS events, the information generated was on limited scale, with small size of dataset and analysis lacking RNA-Seq-specific pipeline (Patel et al 2013). In the present study, we employed high-throughput pyro sequencing combined with Cufflinks workflow optimized for RNA-Seq to elucidate complexity of the AS in HC transcriptome.…”

Section: Introductionmentioning

confidence: 99%

Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq

et al. 2016

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Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions. Based on pathway clustering and in silico verification, 102 novel splice isoforms were selected and further analysed with respect to change in protein sequence using Blastp. Finally, fourteen novel splicing events supported both by Cufflinks and UCSC genome browser were selected and confirmed expression by RT-qPCR. Future studies targeted at in-depth characterization of these potential candidate splice isoforms might be helpful in the development of relevant biomarkers for early diagnosis of HC. The results reported in this study refine the available information on transcriptome repertoire of bovine species and boost the research in the line of development of relevant biomarkers for early diagnosis of HC.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0577-5) contains supplementary material, which is available to authorized users.

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Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle

Cited by 8 publications

References 31 publications

Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport

Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport

Assessment of myometrial transcriptome changes associated with spontaneous human labour by high‐throughput RNA‐seq

Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq

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