Multi-tissue observation of the long non-coding RNA effects on sexually biased gene expression in cattle

다국어 초록 (Multilingual Abstract)

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly.
Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation.
Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues.
Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

참고문헌 (Reference)

1 Liao Y, "featureCounts : an efficient general purpose program for assigning sequence reads to genomic features" 30 : 923-930, 2014

2 X. Yang, "Tissue-specific expression and regulation of sexually dimorphic genes in mice" Cold Spring Harbor Laboratory 16 (16): 995-1004, 2006

3 Derrien T, "The GENCODE v7 catalog of human long noncoding RNAs : analysis of their gene structure, evolution, and expression" 22 : 1775-1789, 2012

4 Da Wei Huang, "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources" Society for Mining, Metallurgy and Exploration Inc. 4 (4): 44-57, 2009

5 Yuichiro Nishida, "Sexually dimorphic gene expression in the hypothalamus, pituitary gland, and cortex" Elsevier BV 85 (85): 679-687, 2005

6 James L Chitwood, "RNA-seq analysis of single bovine blastocysts" Society for Mining, Metallurgy and Exploration Inc. 14 (14): 350-, 2013

7 Sanchez-Cardenas C, "Pituitary growth hormone network responses are sexually dimorphic and regulated by gonadal steroids in adulthood" 107 : 21878-21883, 2010

8 Immonen E, "Mating changes sexually dimorphic gene expression in the seed beetle Callosobruchus maculatus" 9 : 677-699, 2017

9 Kévin Muret, "Long noncoding RNA repertoire in chicken liver and adipose tissue" Society for Mining, Metallurgy and Exploration Inc. 49 (49): 6-, 2017

10 Zhang Y, "Life without A tail : new formats of long noncoding RNAs" 54 : 338-349, 2014

11 Daehwan Kim, "HISAT: a fast spliced aligner with low memory requirements" Society for Mining, Metallurgy and Exploration Inc. 12 (12): 357-360, 2015

12 Robert J. Handa, "Gonadal Steroid Hormone Receptors and Sex Differences in the Hypothalamo-Pituitary-Adrenal Axis" Elsevier BV 28 (28): 464-476, 1994

13 R K Splan, "Genetic parameters for sex-specific traits in beef cattle." American Society of Health System Pharmacists 76 (76): 2272-, 1998

14 Rhodes ME, "Functional sex differences('sexual diergism')of central nervous system cholinergic systems, vasopressin, and hypothalamic–pituitary–adrenal axis activity in mammals : a selective review" 30 : 135-152, 1999

15 Nelder JAaB RJ, "Encyclopedia of Statistical Sciences" 2006

16 Gómez E, "Embryonic sex induces differential expression of proteins in bovine uterine fluid" 12 : 1199-1210, 2013

17 Junichi Iwakiri, "Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome" Society for Mining, Metallurgy and Exploration Inc. 12 (12): 15-, 2017

18 Seo M, "Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq" 17 : 81-, 2016

19 Jennifer L Gill, "Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle" Society for Mining, Metallurgy and Exploration Inc. 41 (41): 36-, 2009

20 Aimin Li, "ALDB: A Domestic-Animal Long Noncoding RNA Database" Public Library of Science (PLoS) 10 (10): e0124003-, 2015

21 Okeyo Mwai, "- Invited Review - African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World" 아세아·태평양축산학회 28 (28): 911-921, 2015