Dataset Information

Anti-SMIM45-107aa Pull-down and mass spectrometry study

ABSTRACT: We acknowledge the commentary by Leushkin et al. on our work, which scrutinizes the status of the de novo genes and the coding potential of a specific case gene (ENSG00000205704) in our proof-of-concept study. While we recognize the evolving nature of defining de novo genes with ribosome profiling data, we respectfully disagree with their assertions for the definition of ages, de novo status, translation and functions of these genes. Notably, the field’s consensus definition of de novo gene is based on the age of the open reading frames (ORFs), rather than that of the locus. Moreover, ribosome profiles alone, although indicative for translation, should not be used as a groundtruth for stable translation and in vivo functions, especially when generated from samples with limited range of temporospatial conditions and analyzed with parameters better suited for highly-expressed, conserved genes, as described in Leushkin et al. Here we present additional data and analyses, especially the verification of the status of these de novo genes and the compelling evidence for in vivo translation of the case gene, to address their concerns. The data presented in our initial report, coupled with this study, robustly support our original conclusions.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain

SUBMITTER: Chunfu Xiao

LAB HEAD: Chuan-Yun Li

PROVIDER: PXD053929 | Pride | 2024-08-12

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	A20240330xiaoq_lichuanyun90min_DDA_ingel_634.ms1	Other
	A20240330xiaoq_lichuanyun90min_DDA_ingel_634.ms2	Other
	A20240330xiaoq_lichuanyun90min_DDA_ingel_634.raw	Raw
	A20240330xiaoq_lichuanyun90min_DDA_ingel_634_HCDFT.mgf	Mgf
	A20240330xiaoq_lichuanyun90min_DDA_ingel_IgG.ms1	Other

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Project description:Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two mothers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one child with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease. We analyzed one patient-parent-mother's parents quintet (case 1) and a patient-siblings-parent quintet (case 2) with Illumina beadchip arrays and one patient-parent trio (case 3) to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients. Here, we analyzed one patient-parent-mother's parents quintet to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients.

Project description:Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a female carrier to her child. The chromothripsis in the carriers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two carriers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one patient with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy carriers strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease. We analyzed one patient-parent-mother's parents quintet (case 1) and a patient-siblings-parent quintet (case 2) with Illumina beadchip arrays and one patient-parent trio (case 3) to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients. For case 2, the mother and patient's SNP array data was previously submitted [GSE37906]. aCGH data for case 3 is submitted seperately.

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Anti-SMIM45-107aa Pull-down and mass spectrometry study

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