RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

Abstract

BackgroundBirds have a ZZ male: ZW female sex chromosome system and while the Z-linked DMRT1 gene is necessary for testis development, the exact mechanism of sex determination in birds remains unsolved. This is partly due to the poor annotation of the W chromosome, which is speculated to carry a female determinant. Few genes have been mapped to the W and little is known of their expression.ResultsWe used RNA-seq to produce a comprehensive profile of gene expression in chicken blastoderms and embryonic gonads prior to sexual differentiation. We found robust sexually dimorphic gene expression in both tissues pre-dating gonadogenesis, including sex-linked and autosomal genes. This supports the hypothesis that sexual differentiation at the molecular level is at least partly cell autonomous in birds. Different sets of genes were sexually dimorphic in the two tissues, indicating that molecular sexual differentiation is tissue specific. Further analyses allowed the assembly of full-length transcripts for 26 W chromosome genes, providing a view of the W transcriptome in embryonic tissues. This is the first extensive analysis of W-linked genes and their expression profiles in early avian embryos.ConclusionSexual differentiation at the molecular level is established in chicken early in embryogenesis, before gonadal sex differentiation. We find that the W chromosome is more transcriptionally active than previously thought, expand the number of known genes to 26 and present complete coding sequences for these W genes. This includes two novel W-linked sequences and three small RNAs reassigned to the W from the Un_Random chromosome.

Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation

“…Similar sex bias of miR-122-5p was previously observed in the zebra finch heart based on a comparison of one male and one female individual (Luo et al 2012). In addition, remapping confirmed W linkage of the mir-7b locus (Ayers et al 2013), which belongs to a family with both Z-linked and autosomal members. Given that the chicken W Chromosome is thought to host only 28 protein-coding genes (Bellott et al 2017), miRNAs thus make up a sizable fraction of the total W-linked gene repertoire.…”

Corset: enabling differential gene expression analysis for

“…We tested the performance of Corset against other clustering and counting methods using three RNA-seq datasets: chicken male and female embryonic tissue [24], human primary lung fibroblasts, with and without a small interfering RNA (siRNA) knock down of HOXA1 [25], and yeast grown under batch and chemostat conditions [26]. We selected three model organisms in order to compare our de novo differential gene expression (DGE) results against a genome-based analysis (referred to herein as the truth dataset).…”

“…In the chicken dataset we tested for DGE between males and females. The homology between chicken genes, which is around 90% on the sex chromosomes [24], offered a challenging test for clustering algorithms. The human dataset was selected because human is one of the best annotated species and the yeast was used to assess whether clustering is beneficial for organisms with minimal splicing.…”

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

“…For example, the linkage map in combination with transcriptomes of the flatfish successfully facilitates the assembly and sequence assignment of chromosomes, providing the basis for understanding the evolution of sex chromosomes and the sex determination mechanism (Chen et al, 2014). Determination of full-length transcripts of W-chromosome genes and their expression profiles in early avian embryos provide a complete annotation of the W chromosome (Ayers et al, 2013). Genes in sex determination pathway of Caenorhabditis elegans are found to be poorly conserved in the cyst nematode Globodera pallid, verifying a different sex determination mechanism in G. pallid (Cotton et al, 2013).…”