PDF(Pubmed)
Abstract：
BACKGROUND: The hair follicle development process is regulated by sophisticated genes and signaling networks, and the hair grows from the hair follicle. The Tianzhu white yak population exhibits differences in hair length, especially on the forehead and shoulder region. However, the genetic mechanism is still unclear. Isoform sequencing (Iso-seq) technology with advantages in long reads sequencing. Hence, we combined the Iso-seq and RNA-seq methods to investigate the transcript complexity and difference between long-haired yak (LHY) and normal-haired yak (NHY).
RESULTS: The hair length measurement result showed a significant difference between LHY and NHY on the forehead and the shoulder (P-value < 0.001). The skin samples from the forehead and the shoulder of LHY and NHY were pooled for isoform sequencing (Iso-seq). We obtained numerous long transcripts, including novel isoforms, long non-coding RNA, alternative splicing events, and alternative polyadenylation events. Combined with RNA-seq data, we performed differential isoforms (DEIs) analysis between LHY and NHY. We found that some hair follicle and skin development-related DEIs, like BMP4, KRT2, IGF2R, and COL1A2 in the forehead skin; BMP1, KRT1, FGF5, COL2A1, and IGFBP5 in the shoulder skin. Enrichment analysis revealed that DEIs in both two comparable groups significantly participated in skin and hair follicle development-related pathways, like ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling pathways. The results indicated that the hair follicle development of Tianzhu white yak may influence the hair length difference. Besides, the protein-protein interaction (PPI) network of DEIs showed COL2A1 and COL3A1 exhibited a high degree of centrality, and these two genes were suggested as potential candidates for the hair length growth of Tianzhu white yak.
CONCLUSIONS: The results provided a comprehensive analysis of the transcriptome complexity and identified differential transcripts that enhance our understanding of the molecular mechanisms underlying the variation in hair length growth in Tianzhu white yak.
RESULTS: The hair length measurement result showed a significant difference between LHY and NHY on the forehead and the shoulder (P-value < 0.001). The skin samples from the forehead and the shoulder of LHY and NHY were pooled for isoform sequencing (Iso-seq). We obtained numerous long transcripts, including novel isoforms, long non-coding RNA, alternative splicing events, and alternative polyadenylation events. Combined with RNA-seq data, we performed differential isoforms (DEIs) analysis between LHY and NHY. We found that some hair follicle and skin development-related DEIs, like BMP4, KRT2, IGF2R, and COL1A2 in the forehead skin; BMP1, KRT1, FGF5, COL2A1, and IGFBP5 in the shoulder skin. Enrichment analysis revealed that DEIs in both two comparable groups significantly participated in skin and hair follicle development-related pathways, like ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling pathways. The results indicated that the hair follicle development of Tianzhu white yak may influence the hair length difference. Besides, the protein-protein interaction (PPI) network of DEIs showed COL2A1 and COL3A1 exhibited a high degree of centrality, and these two genes were suggested as potential candidates for the hair length growth of Tianzhu white yak.
CONCLUSIONS: The results provided a comprehensive analysis of the transcriptome complexity and identified differential transcripts that enhance our understanding of the molecular mechanisms underlying the variation in hair length growth in Tianzhu white yak.
摘要：
背景：毛囊发育过程受复杂基因和信号网络的调控，头发从毛囊中长出来.天祝白牦牛种群的毛发长度存在差异,尤其是额头和肩膀区域。然而,遗传机制尚不清楚。同种型测序(Iso-seq)技术在长读数测序中具有优势。因此，我们结合Iso-seq和RNA-seq方法来研究长毛牦牛（LHY）和正常毛牦牛（NHY）之间的转录复杂性和差异。
结果：头发长度测量结果显示，前额和肩部的LHY和NHY之间存在显着差异（P值<0.001）。合并来自LHY和NHY的前额和肩部的皮肤样品用于同种型测序(Iso-seq)。我们获得了许多长成绩单，包括新的同工型，长链非编码RNA，选择性剪接事件，和选择性聚腺苷酸化事件。结合RNA-seq数据，我们在LHY和NHY之间进行了差异同工型(DEIs)分析。我们发现一些毛囊和皮肤发育相关的DEIs，像BMP4，KRT2，IGF2R，和COL1A2在前额皮肤;BMP1，KRT1，FGF5，COL2A1和IGFBP5在肩部皮肤。富集分析显示，两个可比组中的DEI均显着参与皮肤和毛囊发育相关途径，就像ECM-受体相互作用一样，病灶粘连,和PI3K-Akt信号通路。结果表明，天祝白牦牛毛囊发育可能影响毛长差异。此外,DEIs的蛋白-蛋白相互作用(PPI)网络显示COL2A1和COL3A1表现出高度的中心性,这两个基因被认为是天祝白牦牛毛发长度生长的潜在候选基因。
结论：结果提供了对转录组复杂性的全面分析，并鉴定了差异转录本，增强了我们对天祝白牦牛毛发长度生长变化的分子机制的理解。
结果：头发长度测量结果显示，前额和肩部的LHY和NHY之间存在显着差异（P值<0.001）。合并来自LHY和NHY的前额和肩部的皮肤样品用于同种型测序(Iso-seq)。我们获得了许多长成绩单，包括新的同工型，长链非编码RNA，选择性剪接事件，和选择性聚腺苷酸化事件。结合RNA-seq数据，我们在LHY和NHY之间进行了差异同工型(DEIs)分析。我们发现一些毛囊和皮肤发育相关的DEIs，像BMP4，KRT2，IGF2R，和COL1A2在前额皮肤;BMP1，KRT1，FGF5，COL2A1和IGFBP5在肩部皮肤。富集分析显示，两个可比组中的DEI均显着参与皮肤和毛囊发育相关途径，就像ECM-受体相互作用一样，病灶粘连,和PI3K-Akt信号通路。结果表明，天祝白牦牛毛囊发育可能影响毛长差异。此外,DEIs的蛋白-蛋白相互作用(PPI)网络显示COL2A1和COL3A1表现出高度的中心性,这两个基因被认为是天祝白牦牛毛发长度生长的潜在候选基因。
结论：结果提供了对转录组复杂性的全面分析，并鉴定了差异转录本，增强了我们对天祝白牦牛毛发长度生长变化的分子机制的理解。
