- However, their function and expression profile in the HFs cycle of yak are yet unknown. - Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. - group, 280 DELs were obtained in the Jan.- vs-Mar. - group, and 340 DELs were obtained in the Mar.-vs-Oct. - To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties.. - Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. - The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.. - The morphological changes in hair growth take place following different phases of the HF cycle [3]. - In the anagen phase, an entire hair shaft from follicles is produced, this phase determines the length of the hair shaft. - Moreover, some hor- mones and molecules, such as melatonin, estrogen, fibroblast growth factor 5 (FGF5), vascular endothelial growth factor (VEGF), and so on, have been identified influencing the development of the HFs cycle [6–9].. - In addition, lncRNAs have been found to par- ticipate in the regulation of the HFs cycle in cashmere goats, sheep and Angora rabbit, besides regulating skin pigmentation in goats and cattle [17 – 20]. - The growth pattern of HFs in yak and cash- mere goat provided a good animal model for the sequence conservation study of lncRNAs in the same trait.. - 0.125) were selected for sample collection in different phases of the HFs cycle that included the following five time points: Jan., Mar., Jun., Aug., and Oct.. - Based on the count data of lncRNA expression, sample similarities of the three groups (Jan., Mar., and Oct.) was analyzed via principal component analysis (PCA). - Function enrichment analysis of the nearby genes of differential lncRNAs. - To further screen the key lncRNAs in the HFs cycle of yak, DELs paired with differently expressed genes (DEGs) were screened by comparing analysis the lncRNA data with our previous mRNA data [43]. - The lncRNA dataset of the cashmere goat was used as “blastdb database”, and the DELs of the yak were used as “query database”. - The lncRNA dataset of the cashmere goat was downloaded from a previous study [19]. - Identification and differential expression analysis of lncRNAs in the yak skin. - Furthermore, the data showed that approximately 40% of the novel lncRNAs were antisense lncRNAs and 60% were sense lncRNAs (Fig. - 1c), besides approximately 90% of the novel lncRNAs with two to three exons (Fig.. - was selected in the ana- gen phase with Jan. - comparison groups had a higher number of DELs, while the number of DELs was relatively minor in the Mar.-vs-Jun. - In the differential expression analysis of the 3 groups (Jan., Mar. - 280 DELs were ob- tained in the Jan.-vs-Mar., 340 and 198 DELs were ob- tained in the Mar.-vs-Oct. - Also, 22 of these DELs were shared in the 3 comparison groups (Fig. - 1h showed that the sample-to- sample distances are closer in the same group. - a Screening of the candidate lncRNAs in skin transcriptome. - and Mar.-vs-Oct., the lncRNAs shared with the three groups indicated differently expressed in every comparison group. - h PCA and the analysis of sample-to-sample distance were used to check the sample similarities of the three groups (Jan., Mar. - In the Mar.-vs-Oct. - in the present study.. - The pathways among distinct phases coincidentally corresponding with the biological process of hair cycling seemed to orchestrate a dynamic genesis of the HFs cycle at the molecular level. - 2 GO and KEGG enrichment analysis of the nearest genes of differently expressed lncRNAs. - a GO analysis of the nearest genes of. - b KEGG enrichment analysis of the nearest genes of differently expressed lncRNAs. - The size of the bubble indicates gene number, and the color indicates P value. - LncRNAs were selected based on the expres- sion levels and potential function of the paired protein- coding gene in hair development. - Figure 3a shows the RT-qPCR result and the comparison of the sequencing data and RT-qPCR data.. - Comparation of the expression pattern of the sequencing data and RT-qPCR data (below). - b Cluster analysis of the aligned 24 DELs and their paired 23 differently expressed mRNAs in yak. - lncRNAs of these 110 DELs with the lncRNA data of the cashmere goat in the HFs cycle (532 lncRNA se- quences) [19]. - Then, the expression profiles of aligned DELs in the yak with their respective alignments in the cashmere goat dataset were comparatively ana- lyzed. - Excluding the repetitive lncRNA sequences, a total of 287 alignments including 125 lncRNA se- quences in the cashmere goat dataset were aligned by 24 DELs of the yak dataset (Additional files 6 and 7). - Among the 125 lncRNA sequences, 41 were found to be differentially expressed in the cashmere goat during the HFs cycle [19]. - Comparative analysis found that the expression profiles of most of the differently expressed align- ments (approximately 80%) in the cashmere goat in anagen and telogen were similar to those of the aligned DELs in the yak in anagen (Oct.) and the transition from catagen (Jan.) to telogen (Mar.) (Additional file 8). - The expression pattern of the sequence conserved DELs between the yak and cashmere goat data had a little difference, which probably related to the difference from species and sampling time, considering only two phases of the HFs cycle in the cashmere goat. - Figure 3b shows the 24 DELs and their paired 23 DEGs of the yak with a heat map. - In addition, com- parative analysis of the 93 DEGs in the yak with the DEGs between the anagen and telogen of cashmere goat data [19] found that 10 DEGs were differentially expressed both in the yak and cashmere goat during the HFs cycle and the expression tendency in the cyc- lic process was consistent (Fig. - In the above section, the sequence conservation of the 110 DELs in yak was investigated by compared with cashmere goat lncRNA data during HFs cycle using NCBI BLAST-2.9.0+. - Then, a detailed analysis of the se- quence conservation properties of these aligned lncRNAs were performed. - In the result of NCBI BLAST- 2.9.0+, total of 287 alignments including 332 hits were obtained in goat lncRNA data, which were aligned by 24 DELs of the yak database (Additional file 6) [19]. - Length of the matching regions (identities) of the hits was dis- tributed between 36 and 3765 bp, and the matching per- centage was more than 80% (Additional file 6). - Interestingly, the analysis of every aligned lncRNA found that most of the queried lncRNAs of the yak had numerous align- ments with cashmere goat lncRNA dataset while the matching regions on one lncRNA in the yak were con- strained (Additional files 6 and 7). - Then, a local multiple se- quence alignment was manually performed in the matching region of TCONS_00008989 with other aligned 11 different sequences in cashmere goat. - 4 Analysis of conservation properties of the lncRNA alignments between yak and cashmere goat. - a Length distribution of the matching sequence of all the hits by NCBI BLAST-2.9.0+. - b Sequence logo of the highly conserved sequences between TCONS_00008989 and its aligned 10 cashmere goat lncRNAs using WebLogo3. - c Dot plot of TCONS_00020227 and the detailed ranges of the repeats on TCONS_00020227 were analyzed using dottup website and Clone Manager software, respectively. - f Typical alignments example of the two key matching regions, about and in the chromosome of Ovis canadensis canadensis and Bos mutus (yak). - This result showed that the matching regions repeatedly existed in TCONS_00020227 and further indicated the importance of the matching sequences. - Besides, the data also indicated the effectivity of the BLAST+ result.. - regions 2881–3029 and 3191–3365 of TCONS_0001611 searched using NCBI BLAST-2.9.0+ between yak and cashmere goat lncRNA data emerged in nearly all of the mapped sequences in the first page using Nucleotide BLAST (Fig. - Figure 4f shows an example of the searched results. - This finding was consistent with the reported conservation properties of lncRNAs in terms of the conserved second- ary structure [13]. - LncRNAs, as key regulatory molecules have been found to play an important role in the HFs cycle. - In the HFs cycle, anagen is the longest stage occupying more than half of the whole cycle (1 year) [50]. - Division of the HFs cycle in yak has been rarely reported to data. - After a preliminary analysis of the DELs data between the comparison groups, Oct. - was selected as the optimum time in the anagen with Jan. - The samples in the HFs cycle of yak were collected referring to the phase division of a cashmere goat data and based on the phenotypic changes in yak [50]. - Previous studies reported that the phase division of the HFs cycle in Shai- bei cashmere goat in North China was as follows: the anagen was from Apr. - to Oct., the catagen was from Nov. - had more changes in the anagen phase compared with Jun. - After confirming the optimum three phases of the HFs cycle in the yak, the functional analysis of the DELs in the three distinct phases were performed.. - LncRNAs could affect the gene expression in the immediate genomic vicinity (in cis) [12, 14]. - The result showed that in the transition from the anagen to catagen (Oct.-vs-Jan. - In the transition from the catagen to the telogen (Jan.-vs-Mar. - Interestingly, the functions associated with protein ubiquitination was enriched several times in the transition from the telogen to the anagen. - VEGF was involved in the regulation of the HFs cycle by inducing the angiogen- esis of dermal papilla [9]. - The HIF-1 signaling path- way was enriched in the Mar.-vs-Oct. - From a holistic perspective, the pathways that emerged in the distinct phases seemed to orches- trate a dynamic genesis of the HFs cycle at a molecu- lar level that corresponded with the biological process of HFs development.. - In the present study, yak and cashmere goat all belong to the Bovidae family of ruminants. - The NCBI BLAST-2.9.0+ result showed that 24 lncRNAs among 110 DELs of the yak. - A large number of the queried alignments in yak were aligned to multiple lncRNA sequences in cashmere goat dataset, while the matching regions in the queried lncRNAs of yak were constrained. - In the present study, three lncRNAs were selected for further de- tailed analysis. - for example, the lncRNA TCONS_00016111 found in the BLAST analysis in the present study. - Meanwhile, these data also indicated the efficiency of the aligned con- servation elements using NCBI BLAST-2.9.0. - The functions of the identified DELs were indirectly pre- dicted via the enrichment analysis of the function of their nearest mRNAs. - In addition, several sequence-conserved lncRNAs between yak and cashmere goat in the HFs cycle were searched using NCBI BLAST-2.9.0+, and the se- quence conservation properties were analyzed. - The con- served sequence elements might play an important role in the regulation of the HFs cycle. - The finding of the present study might provide valuable insight into the study of lncRNAs functionality and mechanism in the HFs cycle.. - The funding bodies played no role in the design of the study and collection, analysis, and inter- pretation of data and in writing the manuscript.. - Growth of secondary hair follicles of the cashmere goat in vitro and their response to prolactin and melatonin. - lincRNAs act in the circuitry controlling pluripotency and differentiation. - Systematic Analysis of Non-coding RNAs Involved in the Angora Rabbit (Oryctolagus cuniculus) Hair Follicle Cycle by RNA Sequencing. - The seasonal development dynamics of the yak hair cycle transcriptome. - Systematic analysis of long noncoding RNAs in the senescence-accelerated mouse prone 8 brain using RNA sequencing. - Comparative expression dynamics of Intergenic long noncoding RNAs in the genus drosophila. - Whales originated from aquatic artiodactyls in the Eocene epoch of India
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