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Compensatory upregulation of X-inactivation escape genes in Xq deletion

ABSTRACT: We report on genetic and functional data from an asymptomatic female with a large deletion on the X-chromosome. Blood RNA samples from individual II.3 and an age and sex-matched control were analyzed by RNA-Seq in Illumina platform. Total RNA was purified using poly-T oligo-attached magnetic beads with rRNA removal. The resulting directional RNA-Seq NEB libraries were sequenced in paired-end format. Image analysis and per-cycle base calling were performed with Illumina Real-Time Analysis software (RTA1.9). Conversion to FastQ read format was obtained by CASAVA-1.8 and sequenced reads were quality-checked with FastQC. Sequence adaptors were removed with cutadapt v1.2.1, and reads were aligned to the human reference genome (GRCh37/hg19) with STAR. BAM files were visualized by using the Integrative Genomics Viewer. The quantification of reads were obtained by HTSeq v0.6.1. Transcriptome-wide analysis in individual II.3 uncovered 1,026 differentially blood-expressed genes, as compared with the matched control sample. From the 598 RefSeq genes mapping within the X-chromosome deletion, 241 genes were expressed on blood. From these, 117 transcripts have more than ten counts in at least in one of the samples (individual II.3 or control). Only three genes within the deletion (GPR112, SLC6A8 and, FUNDC2) showed statically significant adjusted p-values and |log2(FoldChange)|.Our data suggest that a protective gene-by-gene mechanism occurs at the transcriptional level in the active X chromosome to counterbalance detrimental effects of large Xq deletions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE141766 | GEO | 2020/03/09

REPOSITORIES: GEO

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Project description:In this study, we extend array CGH technology by making the accurate detection of segmental aneusomies possible from a single lymphoblast and fibroblast following Phi29 DNA polymerase amplification Array CGH experiments were performed on two segmental aneusomic cell lines derived from patients. As a proof of principle, an interstitial 4q-deletion (46, XX, del(4)(q13.1q22.3)) fibroblast cell line and an unbalanced reciprocal translocation involving chromosomes 14 and X (46, XX, der (X) t(X;14)(q21.3;q23.1)) EBV cell line were used. Array CGH experiments were performed using gDNA from the two cell lines to define the exact size of each rearrangement. For the 4q-deletion cell line, the size of the deleted region was 34 Mb corresponding to 39 clones spotted on the array (from RP11-340A13 to RP11-44P19). For the EBV cell line, the size of the 14q-duplication was 47 Mb corresponding to 63 clones (from RP11-62H20 to CTC-820M16) and the Xq-deletion was 58 Mb corresponding to 70 clones (from RP3-380C13 to RP11-218L14). For each cell line, three single cells were amplified. Following DNA amplification, all cells showed the expected DNA yields (n=6; ï?³ = 2.36 Âµg ï?± 0.12). Sex-mismatch array CGH experiments were conducted on amplified DNA samples obtained from the 4q-deletion cell line. Using the chromosome specific threshold obtained from our 18 experiments, sex chromosome and autosome ploidy levels were accurately identified with no false negative and no false positive results. Averaging the 39 clones within the chromosome 4q-deleted region enabled the accurate detection of the deletions. For each of the three amplified single-cell DNA of the unbalanced reciprocal translocation involving chromosomes 14 and X, male and female gDNA were used as references. Sex chromosome and autosome ploidy levels were accurately identified. Averaging intensity ratios of the 63 clones within the chromosome 14 duplicated region enabled the accurate detection of the duplications in the three replicate experiments. When, respectively, male or female gDNA were used as a reference, the average log2 mean ratio of the Xq-deleted region was â??0.04 or â??0.93, close to the theoretical expected value of 0 or minus 1. Interestingly, the log2 mean ratios of chromosomes 1 to 22 were highly similar when the same single cell amplified DNA was used for the two experiments using respectively female and male DNA as a reference. Hence, array CGH intensity ratio profiles were very reproducible.

Project description:Background: In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. To date there has not been a comprehensive and directly comparative analysis of TS vs. KS regarding the changes on the molecular level Methods: We analyzed gene expression patterns with RNA-Seq and DNA methylation patterns with the CpGiant assay in lymphocytes, and chromatin conformation with in situ Hi-C in lymphoblastoid cell lines, from TS and KS patients together with their same gender controls. Results: In TS, differentially expressed escape genes were downregulated but differentially expressed inactive genes were upregulated. In KS, differentially expressed escape genes were upregulated while inactive genes appeared unchanged. Interestingly, 81 differentially expressed genes (DEGs) were associated with both TS and KS, and uniformly displayed expression changes into opposite directions. DEGs on the X chromosome and the autosomes were coexpressed in both TS and KS, indicating that there are molecular ripple effects of the changes in X chromosome dosage that extend to autosomes. Four potentially candidate genes (RPS4X, SEPT6, NKRF and CX0rf57) for KS were identified on Xq. Broad hypomethylation of the X chromosome is observed in TS whereas hypermethylation of chromosome X is present in KS. Only promoters of inactive genes were differentially methylated in both TS and KS while escape genes remained unchanged. The intrachromosomal contact map of the X chromosome in TS was partitioned into two superdomains and exhibited the structure of an active X chromosome. Conclusions: Components of the molecular basis of TS and KS were identified on the levels of the transcriptome and the epigenome, with candidate central genes on Xp for TS and on Xq for KS. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that are transmitting the gene dosage changes to the transcriptome.

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Compensatory upregulation of X-inactivation escape genes in Xq deletion

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