DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation

Abstract

Although it is apparent that chromosome complement mediates sexually dimorphic expression patterns of some proteins that lead to functional differences, there has been insufficient evidence following the manipulation of the male-specific region of the Y chromosome (MSY) gene expression during neural development. In this study, we profiled the expression of 23 MSY genes and 15 of their X-linked homologues during neural cell differentiation of NTERA-2 human embryonal carcinoma cell line (NT2) cells in three different developmental stages using qRT-PCR, Western blotting, and immunofluorescence. The expression level of 12 Y-linked genes significantly increased over neural differentiation, including RBMY1, EIF1AY, DDX3Y, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. We showed that siRNA-mediated knockdown of DDX3Y, a DEAD box RNA helicase enzyme, in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 917 reproducibly identified proteins detected, 71 proteins were differentially expressed following DDX3Y siRNA treatment compared with mock treated cells. Functional grouping indicated that these proteins were involved in cell cycle, RNA splicing, and apoptosis, among other biological functions. Our results suggest that MSY genes may play an important role in neural differentiation and demonstrate that DDX3Y could play a multifunctional role in neural cell development, probably in a sexually dimorphic manner.

Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia

“…Because Y chromosome data was now available, specific consideration was given to Y-linked differentially expressed genes. The only large (2.3-fold increase) expression change detected in a Y-linked gene was in Usp9y , which is expressed in the human brain and implicated in sex-related brain differences, neuronal differentiation, 60–62 and autism, 63 however expression (sequence counts) was low in both sample pools.…”

“…The X chromosome homolog Usp9x , however, was highly expressed but not differentially expressed between the treatment and control pools. Usp9y (ubiquitin specific peptidase 9, Y-linked) is one of several Y-linked genes implicated in brain sexual dimorphism during human development 103–105 and its expression is increased during neural differentiation, 106 making it an interesting candidate for further study in schizophrenia pathogenicity.…”

When the Lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome

“…Many of these escape genes retain Y homology, although Y copies have been pseudogenized or have acquired distinct functions or expression patterns (e.g. [57,58]). Acquisition of XCI has been proposed to be a response to Y-gene degradation, suggesting some escapees are at an intermediate stage in this process [59].…”

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

“…These low-abundance proteins are likely to exhibit their transcriptional expression at both tissue and subcellular specific manner (PE2 proteins) and may be involved in gene regulation in poorly understood regions of the genome [53]. Because of the large dynamic range of proteins in biological samples, low-abundance isoforms and proteoforms that may be associated with disease, can be extremely difficult to measure [54]. Proteomic analysis has shown that post-translational modifications can be different in alternative splicing variants and that amino-acid polymorphisms can generate additional variants.…”

“…The potential solutions for such problems may be: (i) the development of advanced software for spectral search methods, which can result in greater sensitivity and more accuracy in the search for the MPs [54, 55, 62], (ii) a combined solubilization method for the initial sample treatment step [63]; among the reagents, sodium deoxycholate and RapiGest showed good solubility and enzyme compatibility as well as easy removal in later steps prior to the MS analysis; (iii) the use of high-resolution mass spectrometry; and (iv) the use of RNA Seq analysis to better guide tissue selection and timing and to identify tissues or cells not commonly used for MS analyses [64–66] ( Table 1 ). In particular for PE2 proteins, C-HPP investigators can approach to perform target proteomics in order to identify PE2 class MPs by utilizing genomics dataset (e.g., RNA-seq) obtained from some specific tissues or cell lines [30].…”