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Modulation of global expression by aneuploids and CNV of dosage sensitive regulatory genes

ABSTRACT: Modulation of global expression by aneuploids and CNV of dosage sensitive regulatory genes

PROVIDER: PRJNA746500 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15130841_1.fastq.gz	Fastqsanger.gz
	SRR15130841_2.fastq.gz	Fastqsanger.gz
	SRR15130842_1.fastq.gz	Fastqsanger.gz
	SRR15130842_2.fastq.gz	Fastqsanger.gz
	SRR15130843_1.fastq.gz	Fastqsanger.gz

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Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

Project description:Genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis on RNA-sequencing data of varied dosage of various chromosomal regions in maize (Zea mays) revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). Dysregulation of microRNA (miRNA) dosage has been reported to have profound deleterious effects in many species. miRNAs are preferentially retained as duplicates following whole-genome duplication in grass species and are postulated to be dosage-sensitive. However, little is known regarding the role of miRNAs under genomic imbalance. We examined the impact of increased and/or decreased dosage of 1 interstitial and 19 distal chromosomal regions in concert with a whole-genome ploidy series of haploid, diploid, triploid, and tetraploid via small RNA-sequencing of diploid and haploid maize mature leaf tissue to investigate the impact of aneuploidy and polyploidy on expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. Significant correlations between expression levels of miRNAs and their targets were identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance. The findings provide novel insights into understanding of gene balance from the aspect of the function of miRNAs.

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation

Project description:Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [CUT&Run]

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq]

Project description:Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq]

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [RNA-Seq]

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Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes.

Project description:Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory genes were screened for an inverse dosage effect. Furthermore, we demonstrated that dosage changes of inverse regulator Inr-a/pcf11 can produce a genome-wide inverse dosage effect. All these findings suggest that the mechanism of genomic imbalance is related to the changes in the stoichiometric relationships of macromolecular complex members that affect the overall function. These studies may deepen the understanding of gene expression regulatory mechanisms.

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Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [CUT&Run]

Project description:ATP-dependent chromatin remodelers establish and arrange nucleosome distribution, modifying accessibility of DNA. Brg1 is exclusive ATPase subunit of mSWI/SNF complex. To understand the dosage dependent function of mSWI/SNF complex. We take an advantage of dTag system to precisely control abundancy of BRG1. We found overall Brg1-binding is sensitive to its abundance nevertheless OCT4-target or H3K27ac region, suggesting Brg1 genome-wide distribution rather than being actively recruited. We also reveal open chromatin dependency on BRG1. The chromatin accessibility of super enhancer shows buffered response on depletion of BRG1, whereas weak enhancer is sensitive. Finally, transcriptomic analysis identified that transcription shows buffered dependencies on BRG1 loss. Overall, our results highlight kinetics differences of BRG1-binding to transcriptome underline BRG1 dosage-sensitive mechanism.

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Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq]

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