Tissue-Specific Expression Pattern in Ancherythroculter nigrocauda, a Sexually Size Dimorphic Fish

Certain members of the Actinopterygii class are known to exhibit sexual dimorphism (SD) that results in major phenotypic differences between male and female fishes of a species. One of the most common differences between the two sexes is in body weight, a factor with a high economic value in aquaculture. In this study, we used RNA sequencing (RNA-seq) to study the liver and brain transcriptomes of Ancherythroculter nigrocauda, a fish exhibiting SD. Females attain about fourfold body weight of males at sexual maturity. Sample clustering showed that both sexes were grouped well with their sex phenotypes. In addition, 2,395 and 457 differentially expressed genes (DEGs) were identified in the liver and brain tissues, respectively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses predicted the association of PPAR signaling, cytochrome P450, and steroid hormone biosynthesis to the differences in sexual size. In addition, weighted gene co-expression network analyses (WGCNA) were conducted, and the green module was identified to be significantly correlated with sexual size dimorphism (SSD). Altogether, these results improve our understanding of the molecular mechanism underlying SSD in A. nigrocauda.

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Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

10.21203/rs.3.rs-209376/v1 ◽

2021 ◽

Author(s):

Yu Ding ◽

Ding-Hai Yang ◽

Ma-Yin Wang ◽

Dai-Cheng Hao ◽

Wei-Shi Li ◽

...

Keyword(s):

Differential Expression ◽

Economic Value ◽

Flower Color ◽

Rna Seq ◽

Transcription Level ◽

Color Formation ◽

Pathway Enrichment ◽

Differential Expression Genes ◽

Important Position ◽

Transcriptome Level

Abstract Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

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Human USP18 is regulated by miRNAs via the 3’UTR, a sequence duplicated in lincRNA genes residing in chr22q11.21

10.1101/2020.10.07.328385 ◽

2020 ◽

Author(s):

Erminia Rubino ◽

Melania Cruciani ◽

Nicolas Tchitchek ◽

Anna Le Tortorec ◽

Antoine D. Rolland ◽

...

Keyword(s):

Cell Types ◽

Type I ◽

Rna Seq ◽

Specific Expression ◽

Tissue Specific ◽

Specific Expression Pattern ◽

Post Transcriptional Regulation ◽

Different Cell Types ◽

Fine Tune ◽

Feedback Regulator

ABSTRACTUbiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of interferon-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here we explored post-transcriptional regulation of USP18 by microRNAs (miRNAs) and identified four miRNAs (miR-24-3p, miR-191-5p, miR-423-5p and miR-532-3p) that efficiently target USP18 through binding to the 3’UTR. Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In human, we found several copies of the 3’UTR that are embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and exhibiting a tissue-specific expression pattern. Interestingly, one of these lincRNAs (here named linc-UR-B1) is uniquely and highly expressed in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.SIGNIFICANT STATEMENTUSP18 is a non-redundant negative feedback regulator of type I IFN signaling and a key determinant of cell responsiveness to IFN. How baseline USP18 is set in different human cell types is ill defined. We identified three microRNAs that restrain USP18 level notably in primary monocytes through binding the 3’UTR. We found several copies of the USP18 3’UTR embedded in long intergenic non-coding (linc) RNAs which reside in a complex region of human chromosome 22. These lincRNAs are expressed in a tissue-specific manner. We describe one lincRNA expressed only in testis, and most notably in germ cells. Correlative analyses suggest that microRNAs and lincRNAs may form a network controlling baseline USP18 and IFN responsiveness.

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RNA-Seq Provides New Insights into the Molecular Events Involved in “Ball-Skin versus Bladder Effect” on Fruit Cracking in Litchi

International Journal of Molecular Sciences ◽

10.3390/ijms22010454 ◽

2021 ◽

Vol 22 (1) ◽

pp. 454

Author(s):

Jun Wang ◽

Xiao Fang Wu ◽

Yong Tang ◽

Jian Guo Li ◽

Ming Lei Zhao

Keyword(s):

Transcription Factors ◽

Plant Hormones ◽

Fruit Development ◽

Economic Value ◽

Lipid Synthesis ◽

Expression Level ◽

Agricultural Product ◽

Rna Seq ◽

Fruit Cracking ◽

Molecular Events

Fruit cracking is a disorder of fruit development in response to internal or external cues, which causes a loss in the economic value of fruit. Therefore, exploring the mechanism underlying fruit cracking is of great significance to increase the economic yield of fruit trees. However, the molecular mechanism underlying fruit cracking is still poorly understood. Litchi, as an important tropical and subtropical fruit crop, contributes significantly to the gross agricultural product in Southeast Asia. One important agricultural concern in the litchi industry is that some famous varieties with high economic value such as ‘Nuomici’ are susceptible to fruit cracking. Here, the cracking-susceptible cultivar ‘Nuomici’ and cracking-resistant cultivar ‘Huaizhi’ were selected, and the samples including pericarp and aril during fruit development and cracking were collected for RNA-Seq analysis. Based on weighted gene co-expression network analysis (WGCNA) and the “ball-skin versus bladder effect” theory (fruit cracking occurs upon the aril expanding pressure exceeds the pericarp strength), it was found that seven co-expression modules genes (1733 candidate genes) were closely associated with fruit cracking in ‘Nuomici’. Importantly, we propose that the low expression level of genes related to plant hormones (Auxin, Gibberellins, Ethylene), transcription factors, calcium transport and signaling, and lipid synthesis might decrease the mechanical strength of pericarp in ‘Nuomici’, while high expression level of genes associated with plant hormones (Auxin and abscisic acid), transcription factors, starch/sucrose metabolism, and sugar/water transport might increase the aril expanding pressure, thereby resulting in fruit cracking in ‘Nuomici’. In conclusion, our results provide comprehensive molecular events involved in the “ball-skin versus bladder effect” on fruit cracking in litchi.

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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Identification and expression analysis of Dazl homologue in Cynops cyanurus

Zygote ◽

10.1017/s0967199421000538 ◽

2021 ◽

pp. 1-6

Author(s):

Yinjiao Zhao ◽

Ya Du ◽

Qinglan Ge ◽

Fang Yan ◽

Shu Wei

Keyword(s):

Phylogenetic Analysis ◽

Comparative Studies ◽

Rna Binding ◽

Rna Binding Protein ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Specific Expression ◽

Recognition Motif ◽

Deleted In Azoospermia ◽

Specific Expression Pattern

Summary The Dazl (deleted in azoospermia-like) gene encodes an RNA-binding protein containing an RNA recognition motif (RRM) and a DAZ motif. Dazl is essential for gametogenesis in vertebrates. In this study, we report the cloning of Dazl cDNA from Cynops cyanurus. Ccdazl mRNA showed a germline-specific expression pattern as expected. Ccdazl expression gradually decreased during oogenesis, suggesting that it may be involved in oocyte development. Phylogenetic analysis revealed that the Ccdazl protein shares conserved motifs/domains with Dazl proteins from other species. Cloning of Ccdazl provides a new tool to carry out comparative studies of germ cell development in amphibians.

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Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽

10.3390/plants10071465 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1465

Author(s):

Ramon de Koning ◽

Raphaël Kiekens ◽

Mary Esther Muyoka Toili ◽

Geert Angenon

Keyword(s):

Common Bean ◽

Seed Development ◽

Expression Analysis ◽

De Novo ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Raffinose Family Oligosaccharides ◽

Specific Expression ◽

Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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Replicate sequencing libraries are important for quantification of allelic imbalance

Nature Communications ◽

10.1038/s41467-021-23544-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Asia Mendelevich ◽

Svetlana Vinogradova ◽

Saumya Gupta ◽

Andrey A. Mironov ◽

Shamil R. Sunyaev ◽

...

Keyword(s):

Allelic Imbalance ◽

False Positive Rate ◽

Error Rates ◽

Differential Analysis ◽

Rna Seq ◽

Specific Expression ◽

Technical Noise ◽

Specific Analysis ◽

Positive Rate ◽

Allele Specific

AbstractA sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.

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Neuroendocrine prostate cancer has distinctive, non-prostatic HOX code that is represented by the loss of HOXB13 expression

Scientific Reports ◽

10.1038/s41598-021-82472-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Siyuan Cheng ◽

Shu Yang ◽

Yingli Shi ◽

Runhua Shi ◽

Yunshin Yeh ◽

...

Keyword(s):

Prostate Cancer ◽

Hox Genes ◽

Human Cancer ◽

Specific Expression ◽

Hox Gene ◽

Human Cancer Cell Lines ◽

All Trans Retinoic Acid ◽

Neuroendocrine Prostate Cancer ◽

Hox Code ◽

Specific Expression Pattern

AbstractHOX gene-encoded homeobox proteins control body patterning during embryonic development; the specific expression pattern of HOX genes may correspond to tissue identity. In this study, using RNAseq data of 1019 human cancer cell lines that originated from 24 different anatomic sites, we established HOX codes for various types of tissues. We applied these HOX codes to the transcriptomic profiles of prostate cancer (PCa) samples and found that the majority of prostate adenocarcinoma (AdPCa) samples sustained a prostate-specific HOX code whereas the majority of neuroendocrine prostate cancer (NEPCa) samples did not, which reflects the anaplastic nature of NEPCa. Also, our analysis showed that the NEPCa samples did not correlate well with the HOX codes of any other tissue types, indicating that NEPCa tumors lose their prostate identities but do not gain new tissue identities. Additionally, using immunohistochemical staining, we evaluated the prostatic expression of HOXB13, the most prominently changed HOX gene in NEPCa. We found that HOXB13 was expressed in both benign prostatic tissues and AdPCa but its expression was reduced or lost in NEPCa. Furthermore, we treated PCa cells with all trans retinoic acid (ATRA) and found that the reduced HOXB13 expression can be reverted. This suggests that ATRA is a potential therapeutic agent for the treatment of NEPCa tumors by reversing them to a more treatable AdPCa.

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The Effect of Cyanine Dye NK-4 on Photoreceptor Degeneration in a Rat Model of Early-Stage Retinitis Pigmentosa

Pharmaceuticals ◽

10.3390/ph14070694 ◽

2021 ◽

Vol 14 (7) ◽

pp. 694

Author(s):

Shihui Liu ◽

Toshihiko Matsuo ◽

Mary Miyaji ◽

Osamu Hosoya

Keyword(s):

Retinitis Pigmentosa ◽

Rat Model ◽

Metal Ion ◽

Toxic Substance ◽

Cyanine Dye ◽

Pathway Enrichment Analysis ◽

Rna Seq ◽

Pathway Enrichment ◽

Metal Ion Homeostasis ◽

Rcs Rats

The present study aimed to evaluate the effects of NK-4 on the apoptosis of photoreceptors in a rat model of retinitis pigmentosa and explore the mechanism underlying anti-apoptosis activity. The Royal College of Surgeons (RCS) rats received an intravitreous injection of NK-4 solution in the left eye and vehicle control in the right eye. Apoptosis was detected by TUNEL method in frozen sections of the eyes. The retinal tissues of the rats were dissected for RNA-seq analysis. Functional and pathway enrichment analyses of differentially expressed genes (DEGs) were performed by using Metascape and DAVID software. The expression levels of DEGs were confirmed by real-time quantitative PCR (RT-qPCR). The number of apoptotic cells decreased in the outer nuclear layer (ONL) and the thickness of the ONL was significantly thicker in the retina of NK-4-injected eyes, compared with control eyes. Five DEGs were identified by RNA-seq analysis, and Hmox1, Mt1, Atf5, Slc7a11, and Bdh2 were confirmed to be up-regulated by RT-qPCR. Functional and pathway enrichment analysis of the up-regulated genes showed that anti-apoptosis effects of NK-4 in the retina of RCS rats may be related to the pathways of metal ion homeostasis, negative regulation of neuron death, response to toxic substance, and pigment metabolic process. We found a potential mechanism of NK-4, providing a new viewpoint for the development of more therapeutic uses of NK-4 in the future.

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