Developmental<i>Xist</i>induction is mediated by enhanced splicing

Stork, Cheryl; Li, Zhelin; Lin, Lin; Zheng, Sika

doi:10.1093/nar/gky1198

Cited by 7 publications

(7 citation statements)

References 49 publications

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“…XIST is selectively expressed from and physically coats the future inactive X chromosome in XX female cells ( 38 ). Experiments in murine embryonic stem cells showed that developmental Xist induction is mediated by enhanced splicing ( 39 ). XIST displayed significant DAS in 23 tissues, comprising two SE, one A3SS, and one MXE event (fig.…”

Section: Resultsmentioning

confidence: 99%

The impact of biological sex on alternative splicing

Karlebach

Veiga

Mays

et al. 2018

Preprint

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Over 95% of human genes undergo alternative splicing (AS) in a developmental, tissue-specific, or signal transduction-dependent manner. A number of factors including binding of cis-acting sequences by RNA-binding proteins (RBPs) are known to affect AS, but the combinatorial mechanisms leading to the distribution of spliced isoforms remain largely unstudied. Here, in 9011 samples from 532 individuals across 53 tissues from the Genotype-Tissue Expression (GTEx) resource, we identified 4,135 genes with sex-biased expression and 5,925 sex-biased AS events. We find that factors including escape from X-chromosomal inactivation, presence of Alu elements, and oestrogen receptor binding sites affect sex-biased AS. We utilize hierarchical Bayesian modelling to characterize the interactions of exon skipping, gene expression, and RBPs, and demonstrate two categories of sex-biased AS that differ with respect to splice site scores, gene expression, RBP levels, and skipping/inclusion ratio. Alternative splicing (AS), a process by which splice sites are used differentially to create protein diversity, plays an important role in development, 1 disease, 2 and aging. 3 Although some splicing isoforms are produced in the same proportions in all or most cell types, AS is often regulated by developmental or differential cues or in response to external stimuli. 4 Several mechanisms have been demonstrated to regulate AS, although their combinatorial interactions remain poorly understood. Binding of RNA-binding proteins (RBPs) to intronic or exonic cis-acting regulatory sequences may promote or suppress local AS events. 5 Additionally, chromatin-level mechanisms also play a role in AS regulation. Nucleosome density is higher within exons than in introns, suggesting the existence of RNA polymerase II (RNA Pol II)-mediated cross-talk between chromatin structure and exon-intron architecture. 6 Alternative exons with suboptimal splicing signals may require more time to be recognized by the splicing machinery, and faster transcriptional elongation by RNA Pol II may influence exon skipping. 7

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Section: Resultsmentioning

confidence: 99%

The impact of biological sex on alternative splicing

Karlebach

Veiga

Mays

et al. 2018

Preprint

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“…An important question now is how the proteins that interact with repeat E relate to one another. Neither endogenous polypyrimidine tract-binding protein 1 (PTBP1) nor FLAG-matrin 3 (MATR3), both of which interact in vivo (Smola et al, 2016; Stork et al, 2019) (Pandya-Jones et al, 2020), were seen enriched around H3K27me3-marked Xis in fibroblasts (Supplemental Fig. 6).…”

Section: Resultsmentioning

confidence: 99%

A polyglutamine domain is required forde novoCIZ1 assembly formation at the inactive X chromosome

Sofi

Williamson

Turvey

et al. 2020

Preprint

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SummaryCIP1-interacting zinc finger protein 1 (CIZ1) forms large assemblies at the inactive X chromosome (Xi) in female fibroblasts in an Xist lncRNA-dependent manner. Here we address the requirements for assembly formation, and show that CIZ1 interacts directly with Xist via two independent domains in its N- and C-terminus. Interaction with Xist repeat E, assembly at Xi in cells, and the complexity of self-assemblies formed in vitro, are all modulated by alternatively-spliced exons that include two glutamine-rich prion-like domains (PLD1 and PLD2), both conditionally excluded from the N-terminal domain. Exclusion of PLD1 alone is sufficient to abrogate de novo establishment of new CIZ1 assemblies and Xi territories enriched for H3K27me3 in CIZ1-null fibroblasts. Together the data suggest that PLD1-driven CIZ1 assemblies form at Xi, are nucleated by interaction with Xist and amplified by multivalent interaction with RNA, so implicating a polyglutamine tract in the maintenance of epigenetic state.

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“…Although the expression of the XBP1 gene differed among various conditions, the expression levels of uXBP1 and sXBP1 may be measured more reliably than those of other housekeeping genes by using tXBP1, which has been designed as a component common to both uXBP1 and sXBP1. In 2018, Stork and colleagues also reported the use of designed qPCR primer pairs to measure total, spliced, and unspliced Xist transcripts, and normalized the spliced and unspliced Xist to total Xist [31]. In addition, several studies have shown that quantification using the total gene transcript is more accurate for quantifying housekeeping genes [32, 33].…”

Section: Discussionmentioning

confidence: 99%

Real-time PCR quantification of spliced X-box binding protein 1 (XBP1) using a universal primer method

et al. 2019

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X-box binding protein 1 (XBP1) mRNA processing plays a crucial role in the unfolded protein response (UPR), which is activated in response to endoplasmic reticulum (ER) stress. Upon accumulation of the UPR-converted XBP1 mRNA splicing from an unspliced (u) XBP1 (inactive) isoform to the spliced (s) XBP1 (active) isoform, inositol-requiring enzyme 1 α (IRE1α) removes a 26-nucleotide intron from uXBP1 mRNA. Recent studies have reported the assessment of ER stress by examining the ratio of sXBP1 to uXBP1 mRNA (s/uXBP1 ratio) via densitometric analysis of PCR bands relative to increased levels of sXBP1 to uXBP1 using a housekeeping gene for normalization. However, this measurement is visualized by gel electrophoresis, making it very difficult to quantify differences between the two XBP1 bands and complicating data interpretation. Moreover, most commonly used housekeeping genes display an unacceptably high variable expression pattern of the s/uXBP1 ratio under different experimental conditions, such as various phases of development and different cell types, limiting their use as internal controls. For a more quantitative determination of XBP1 splicing activity, we measured the expression levels of total XBP1 (tXBP1: common region of s/uXBP1) and sXBP1 via real-time PCR using specific primer sets. We also designed universal real-time PCR primer sets capable of amplifying a portion of each u/s/tXBP1 mRNA that is highly conserved in eukaryotes, including humans, monkeys, cows, pigs, and mice. Therefore, we provide a more convenient and easily approachable quantitative real-time PCR method that can be used in various research fields to assess ER stress.

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DevelopmentalXistinduction is mediated by enhanced splicing

Cited by 7 publications

References 49 publications

The impact of biological sex on alternative splicing

The impact of biological sex on alternative splicing

A polyglutamine domain is required forde novoCIZ1 assembly formation at the inactive X chromosome

Real-time PCR quantification of spliced X-box binding protein 1 (XBP1) using a universal primer method

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