Transcriptomic Analysis of circRNAs and mRNAs Reveals a Complex Regulatory Network That Participate in Follicular Development in Chickens

Shen, Manman; Li, Tingting; Chen, Fuxiang; Wu, Pengfeng; Wāng, Ying; Chen, Lan; Xie, Kaizhou; Wang, Jinyu; Zhang, Genxi

doi:10.3389/fgene.2020.00503

Cited by 17 publications

(6 citation statements)

References 94 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Following this, each sample with three duplicates, was tested on a LightCycler R 96 Real-Time PCR system (Roche, Basel, Switzerland) using TB GreenPremix Ex Taq II (Takara, Dalian, Liaoning, China). The qRT-PCR conditions were: 95 • C for 30 s and then 40 cycles at 95 • C for 10 s, 60 • C for 30 s, followed by 72 • C for 10 s. β-actin was used as the reference gene (Shen et al, 2020;Zhang et al, 2020). The validated primers used for RT-qPCR are listed in the Supplementary Table 1.…”

Section: Qrt-pcrmentioning

confidence: 99%

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Shang

Wang²,

Ma³

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

BackgroundInner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells.ResultIn this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA–miRNA–mRNA, and formed a total of 102 pairs of circRNA–miRNA and 126 pairs of miRNA–mRNA interactions. The binding relationship of circRNA3236–chi-miR-27b-3p and circRNA3236–chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship.ConclusionTo summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA–miRNA–mRNA was constructed and preliminarily verified using DE circRNAs.

show abstract

Section: Qrt-pcrmentioning

confidence: 99%

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Shang

Wang²,

Ma³

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Generally, ovarian follicles can be categorized by size or/and according to color (white or yellow), into at least four types, including small white resting follicles (less than 2 mm diameter), slow growing white follicles (GWF, from 2 mm up to 6 mm diameter), small yellow follicles (SYF, 6 up to 8 mm) of recruitment into the follicular hierarchy (at the stage of follicle selection), and large yellow follicles (LWF) at the differentiated preovulatory stage, being 9 to 12 mm in diameter and five to six hierarchical follicles of increased sizes (from F6 to F1) in hen ovary [ 4 , 5 ]. In the different phases of follicular development, many divergent biological processes affect oocyte growth, and proliferation and differentiation of granulosa and theca cells within the various-sized follicles [ 4 , 6 , 7 ]. Moreover, a plethora of ovarian paracrine and autocrine factors was involved in regulation of the follicle development and its function as well as the positive or negative controls through the endocrinal hormones from the hypothalamus and pituitary, including gonadotropin releasing hormone (GNRH), gonadotropin inhibitory hormone (GNIH), and follicle stimulating hormone (FSH) [ 1 , 2 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

et al. 2021

View full text Add to dashboard Cite

Background Ovarian follicle development plays an important role in determination of poultry egg production. The follicles at the various developmental stages possess their own distinct molecular genetic characteristics and have different biological roles in chicken ovary development and function. In the each stage, several genes of follicle-specific expression and biological pathways are involved in the vary-sized follicular development and physiological events. Identification of the pivotal genes and signaling pathways that control the follicular development is helpful for understanding their exact regulatory functions and molecular mechanisms underlying egg-laying traits of laying hens. Results The comparative mRNA transcriptomic analysis of ovarian follicles at three key developmental stages including slow growing white follicles (GWF), small yellow follicles (SYF) of recruitment into the hierarchy, and differentiated large yellow follicles (LYF), was accomplished in the layers with lower and higher egg production. Totally, 137, 447, and 229 of up-regulated differentially expressed genes (DEGs), and 99, 97, and 157 of down-regulated DEGs in the GWF, SYF and LYF follicles, including VIPR1, VIPR2, ADRB2, and HSD17B1 were identified, respectively. Moreover, NDUFAB1 and GABRA1 genes, two most promising candidates potentially associated with egg-laying performance were screened out from the 13 co-expressed DEGs in the GWF, SYF and LYF samples. We further investigated the biological effects of NDUFAB1 and GABRA1 on ovarian follicular development and found that NDUFAB1 promotes follicle development by stimulating granulosa cell (GC) proliferation and decreasing cell apoptosis, increases the expression of CCND1 and BCL-2 but attenuates the expression of caspase-3, and facilitates steroidogenesis by enhancing the expression of STAR and CYP11A1. In contrast, GABRA1 inhibits GC proliferation and stimulates cell apoptosis, decreases the expression of CCND1, BCL-2, STAR, and CYP11A1 but elevates the expression of caspase-3. Furthermore, the three crucial signaling pathways such as PPAR signaling pathway, cAMP signaling pathway and neuroactive ligand-receptor interaction were significantly enriched, which may play essential roles in ovarian follicle growth, differentiation, follicle selection, and maturation. Conclusions The current study provided new molecular data for insight into the regulatory mechanism underlying ovarian follicle development associated with egg production in chicken.

show abstract

“…In the chicken ovary, expression of the ESR1 gene is higher than that of the ESR2 gene. ESR1 is reported to be associated with ovarian functions, especially during follicular development [83,84], and to be one of the candidate genes for traits related to egg production in chicken and quail [85,86]. This gene has also been be associated with reproductive traits in pigs and sheep [87,88].…”

Section: Genes Related To Growth and Reproductive Traitsmentioning

confidence: 99%

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes

et al. 2021

View full text Add to dashboard Cite

Background Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. Results Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). Conclusions Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

show abstract

Transcriptomic Analysis of circRNAs and mRNAs Reveals a Complex Regulatory Network That Participate in Follicular Development in Chickens

Cited by 17 publications

References 94 publications

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes

Contact Info

Product

Resources

About