Time-Course Transcriptional and Chromatin Accessibility Profiling Reveals Genes Associated With Asymmetrical Gonadal Development in Chicken Embryos

Abstract

In birds, male gonads form on both sides whereas most females develop asymmetric gonads. Multiple early lines of evidence suggested that the right gonad fails to develop into a functional ovary, mainly due to differential expression of PITX2 in the gonadal epithelium. Despite some advances in recent years, the molecular mechanisms underlying asymmetric gonadal development remain unclear. Here, using bulk analysis of whole gonads, we established a relatively detailed profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. We revealed that many candidate genes were significantly enriched in morphogenesis, meiosis and subcellular structure formation, which may be responsible for asymmetric gonadal development. Further chromatin accessibility analysis suggested that the transcriptional activities of the candidate genes might be regulated by nearby open chromatin regions, which may act as transcription factor (TF) binding sites and potential cis-regulatory elements. We found that LHX9 was a promising TF that bound to the left-biased peaks of many cell cycle-related genes. In summary, this study provides distinctive insights into the potential molecular basis underlying the asymmetric development of chicken gonads.

Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers

“…The integration of RNA-seq and ATAC-seq data holds the potential to enhance the characterization of chromatin accessibility and gene expression patterns critical for the progression of pectoral muscle development in broiler chickens. Here, we did observe a certain correlation between the expression of DEGs and the accessibility of DARs, which is consistent with the results from other studies [ 72 , 73 ]. By combining the results of DEGs with DARs, we identified the upregulation of TMEM164 in the CC group at D21.…”

ATAC-seq and RNA-seq analysis unravel the mechanism of sex differentiation and infertility in sex reversal chicken

“…On E10 (HH36), the left gonads of the White Leghorn chicken embryos were dissected from the mesonephros and halved. The remaining bodies were collected to identify sex using CHD1 primers with a direct PCR kit (TransGen Biotech, Beijing, China) (Additional file 4 : Table S9) [ 86 ]. In addition, the gonads of all the genetic females from the treated group (reversal) and eight biological replicate samples of genetic males and females from the control group were prepared for the following steps.…”

“…Samtools was used to convert the SAM files to the BAM format, and PCR duplicates were cleared by the Picard MarkDuplicates option to generate filtered BAM files [ 91 ]. Then, the peaks were identified by MACS2 using the filtered BAM files with the parameters described in a previous article [ 86 , 92 ]. All alignment files were scaled to Reads Per Kilobase per Million mapped reads (RPKM)-normalized read coverage files by deepTools [ 93 ].…”

Transcriptomic and epigenomic insights into pectoral muscle fiber formation at the late embryonic development in pure chicken lines

“…Combining this technique with RNA-seq greatly enhances our understanding of gene regulation. Researches using both omics technologies to investigate mechanisms such as sex differentiation ( Li et al, 2022b ; Zhang et al, 2023a ) and the fate specification of feathers/scales ( Lai et al, 2018 ) has been conducted, while studies on muscle development during the embryonic period remain scarce.…”