scholarly journals Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 884
Author(s):  
Dominique J. Wiener ◽  
Kátia R. Groch ◽  
Magdalena A.T. Brunner ◽  
Tosso Leeb ◽  
Vidhya Jagannathan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Profiling ◽  
Structure And Function ◽  
Hair Follicles ◽  
Cellular Growth ◽  
Genes Encoding ◽  
Interfollicular Epidermis ◽  
Differential Gene ◽  
And Function

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.

scholarly journals Why Pashmina Goat Produces Long Hair-fiber and Barbari doesn’t: A Differential Gene Expression Study

2021 ◽  
Author(s):  
Rashid Saif ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Assembly ◽  
Hair Shaft ◽  
Hair Follicles ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Dermal Papilla Cells ◽  
Differential Gene ◽  
Hair Fiber

The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak region. Pashmina is famous for its long hair-fiber (Cashmere) production while Barbari is not-selected for this trait. So, the mRNA expression profiling in the skin samples of both breeds would be an attractive and judicious approach for detecting putative genes involved in this valued trait. Here, we performed differential gene expression analysis on publicly available RNA-Seq data from both breeds. Out of 44,617,994 filtered reads of Pashmina and 55,995,999 of Barbari which are 76.48% and 73.69% mapped to the ARS1 reference transcriptome assembly respectively. A pairwise comparison of both breeds resulted in 47,159 normalized expressed transcripts while 8,414 transcripts are differentially expressed above the significant threshold. Among these, 4,788 are upregulated in Pashmina while 3,626 transcripts are upregulated in Barbari. Fifty-nine transcripts harbor 57 genes including 32 LOC genes and 24 are annotated genes which were selected on the basis of TMM counts > 500. Genes with ectopic expressions other than uncharacterized and LOC symbol genes are Keratins (KRT) and Keratin Associated Proteins (KRTAPs), CystatinA&6, TCHH, SPRR4, PPIA, SLC25A4, S100A11, DMKN, LOR, ANXA2, PRR9 and SFN. All of these genes are likely to be involved in keratinocyte differentiation, sulfur matrix proteins, dermal papilla cells, hair follicles proliferation, hair curvature, wool fiber diameter, hair transition, hair shaft differentiation and its keratinization. These differentially expressed reported genes are critically valuable for enhancing the quality and quantity of the pashmina fiber and overall breed improvement. This study will also provide important information on hair follicle differentiation for further enrichment analyses and introducing this valued trait to other goat breeds as well.

scholarly journals Evaluating Methods for Differential Gene Expression And Alternative Splicing Using Internal Synthetic Controls

2020 ◽  
Author(s):  
Sudeep Mehrotra ◽  
Revital Bronstein ◽  
Daniel Navarro-Gomez ◽  
Ayellet V. Segrè ◽  
Eric A. Pierce
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Internal Control ◽  
Accurate Determination ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Specificity And Sensitivity ◽  
Differential Gene ◽  
Synthetic Controls

AbstractHigh-throughput transcriptome sequencing has become a powerful tool in the study of human diseases. Identification of causal mechanisms may entail analysis of differential gene expression (DGE), differential transcript/isoform expression (DTE) and identification, classification and quantification of alternative splicing (AS) and/or detection of novel AS events. For such a global transcriptome profiling execution of multi-level data analysis methodologies is required. Each level presents its own unique challenges and the questions about their performance remains. In this work we present results from systematic and consistent assessing and comparing a number of widely used methods for detecting DGE, DTE and AS using internal control “spike-in” sequences (Sequins) in RNA-seq data. We demonstrated that inclusion of internal controls in RNA-seq experiments allows accurate determination of lower bounds detection levels, and better assessment of DGE, DTE and AS accuracy and sensitivity. Tools for RNA-seq read alignment and detection of DGE performed reasonably. More efforts are needed to improve specificity and sensitivity of DTE and AS detection. Low expression of isoforms accompanied with sequencing depth does impact sensitivity and specificity of DTE and AS tools.

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