Validation of Alternative Transcript Splicing in Chicken Lines that Differ in Genetic Resistance to Marek’s Disease

Kaya, Muhammet; Preeyanon, Likit; Dodgson, Jerry B.; Cheng, Hans H.

doi:10.1080/10495398.2016.1178139

Cited by 9 publications

(6 citation statements)

References 28 publications

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“…HAfT18, 19, 21 and 22). Our strategy of using primer-based PCR to improve computational transcript models is similar to other researchers that have reported refinements in the human transcriptome [ 48 ], for various disease state transcriptomes like pulmonary fibrosis [ 49 ] and in the transcriptomes of other species including equine [ 50 ], avian [ 51 ] and murine [ 52 ] species.…”

Section: Discussionmentioning

confidence: 75%

HAfTs are novel lncRNA transcripts from aflatoxin exposure

et al. 2018

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The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5’- and 3’-RACE. BLAST alignments showed, with two exceptions, HAfT transcripts were lncRNAs, >200nt without apparent long open reading frames. Six rat HAfT transcripts were classified as ‘novel’ without RefSeq annotation. Sequence alignment and genomic synteny showed each rat lncRNA had a homologous locus in the mouse genome and over half had homologous loci in the human genome, including at least two loci (and possibly three others) that were previously unannotated. While HAfT functions are not yet clear, coregulatory roles may be possible from their adjacent orientation to known coding genes with altered expression that include 8 HAfT-gene pairs. For example, a unique rat HAfT, homologous to Pvt1, was adjacent to known genes controlling cell proliferation. Additionally, PCR and RACE Sanger sequencing showed many alternative splice variants and refinements of exon sequences compared to Cufflinks assembled transcripts and gene prediction algorithms. Presence of multiple splice variants and short tandem repeats found in some HAfTs may be consequential for secondary structure, transcriptional regulation, and function. In summary, we report novel, differentially expressed lncRNAs after exposure to the genotoxicant, AFB1, prior to neoplastic lesions. Complete cloning and sequencing of such transcripts could pave the way for a new set of sensitive and early prediction markers for chemical hepatocarcinogens.

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Section: Discussionmentioning

confidence: 75%

HAfTs are novel lncRNA transcripts from aflatoxin exposure

et al. 2018

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“…Several studies also illustrated the mechanism of susceptive or resistance from the epigenomic level [ 56 , 57 , 58 ]. Alternative splicing transcripts were also detected in MD pathogenies [ 27 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

“…Jarosinski and Schat [ 28 ] found that there were multiple splice variants of meq, RLORF5a, and RLORF4 to exons II and III of vIL-8, and these alternatively spliced transcripts were the time-dependent expression. Kaya et al [ 29 ] validated alternatively spliced transcripts of seven genes in line 6 (MD resistant) and seven (MD susceptible) using RNA-Seq data, including ITGB2, SGPL1, COMMD5, MOCS2, CCBL2, ATAD1, and CHTF18.…”

Section: Introductionmentioning

confidence: 99%

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Wang

Zheng

Yuan

et al. 2021

Genes

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Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.

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“…Non-MHC genes' role is seen in line 6 (resistant) and line 7 (susceptible) chickens which are both homozygous for MHC B 2 allele but differ in MD susceptibility [129]. Other areas of the genome are related to resistance to MD and evaluation of which loci are involved is underway [130][131][132][133][134][135][136][137].…”

Section: Geneticsmentioning

confidence: 99%

Evaluation of Factors That Influence Dose Variability of Marek's Disease Vaccines

et al. 2019

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for the wealth of knowledge, friendship, and for the patience and kindness shown to me since the very beginning. To my wonderful committee, Drs. Oscar Fletcher, James Guy, and Hsiao-Ching Liu, for helping me improve and shaping me into a better scientist. Many thanks to all of the students I have shared my time with at the laboratory, especially Dr. Allison Boone and Arithat Limsatanun, with whom it has been a pleasure to work. Thanks to Dr. Tobias Käser and Amanda Amaral for their help with the microscope camera. I would like to thank my friends for believing in me, especially Rocio, Esther, Giselle, Michelle, Jasmine, Jaylin and Javi. Every one of our conversations is threaded into this accomplishment, making it yours. Thanks also to my work family, first for their understanding, but most importantly for the comradery and countless laughs that served as motivation during these years. Most importantly, thanks to my family, for always being there and for showering me with unconditional love. v TABLE OF CONTENTS LIST OF TABLES .

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Validation of Alternative Transcript Splicing in Chicken Lines that Differ in Genetic Resistance to Marek’s Disease

Cited by 9 publications

References 28 publications

HAfTs are novel lncRNA transcripts from aflatoxin exposure

HAfTs are novel lncRNA transcripts from aflatoxin exposure

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Evaluation of Factors That Influence Dose Variability of Marek's Disease Vaccines

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