The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in <i>Drosophila</i>

Wang, Meng; Branco, Alan T.; Lemos, Bernardo

doi:10.1534/genetics.117.300637

Cited by 17 publications

(18 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ontology analysis of the 250 IR events that were more upregulated in E11 females indicated enrichment for the biological processes of regulation of transcription (44), cell cycle (15), protein phosphorylation (14), protein transport (5) and mRNA splicing ( Cd2bp2, Khdrbs2, Rbm5, U2af1l4, Zfp326 ), and enrichment for the molecular process of nucleic acid binding (31) and protein kinase activity (15). Recently, it has been reported that the Y chromosome modulates splicing and sex-biased IR rates in Drosophila [54]. Here, we observed that male and female gonads before the Sry peak (at E11) show a large difference in IR, highlighting the significance of sex-biased IR in tuning sex differences.…”

Section: Discussionsupporting

confidence: 54%

Differential isoform expression and alternative splicing in sex determination in mice

et al. 2019

View full text Add to dashboard Cite

BackgroundAlternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanying GSD in mice.ResultsUsing deep RNA-sequencing, we performed a transcriptional analysis of XX and XY gonads during sex determination on embryonic days 11 (E11) and 12 (E12). Analysis of differentially expressed genes (DEG) identified hundreds of genes related to GSD and early sex differentiation that may represent good candidates for sex reversal. Expression at time point E11 in males was significantly enriched in RNA splicing and mRNA processing Gene Ontology terms. Differentially expressed isoform analysis identified hundreds of specific isoforms related to GSD, many of which showed no differences in the DEG analysis. Hundreds of AS events were identified as modified at E11 and E12. Female E11 gonads featured sex-biased upregulation of intron retention (in genes related to regulation of transcription, protein phosphorylation, protein transport and mRNA splicing) and exon skipping (in genes related to chromatin repression) suggesting AS as a post-transcription mechanism that controls sex determination of the bipotential fetal gonad.ConclusionOur data suggests an important role of splicing regulatory mechanisms for sex determination in mice.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5572-x) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionsupporting

confidence: 54%

Differential isoform expression and alternative splicing in sex determination in mice

et al. 2019

View full text Add to dashboard Cite

show abstract

“…This effect could be direct, leading to inappropriate expression of Y-chromosome-embedded genetic elements that block larval development. Alternatively, this effect could be indirect; de-repression of the Y chromosome could indirectly impact several other chromatin processes genome-wide e.g., due to inappropriate titration of transcription or heterochromatin factors, which could exacerbate an already hypomorphic function of the D. simulans Nnk allele ( Branco et al, 1869 ; Francisco and Lemos, 2014 ; Wang et al, 2018 ; Piergentili, 2010 ; Brown et al, 2020 ). Finally, different functional optimality of male-specific or female-specific Nnk functions could also drive its rapid evolution ( VanKuren and Long, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila

Kasinathan

Colmenares

McConnell

et al. 2020

eLife

View full text Add to dashboard Cite

Contrary to dogma, evolutionarily young and dynamic genes can encode essential functions. We find that evolutionarily dynamic ZAD-ZNF genes, which encode the most abundant class of insect transcription factors, are more likely to encode essential functions in Drosophila melanogaster than ancient, conserved ZAD-ZNF genes. We focus on the Nicknack ZAD-ZNF gene, which is evolutionarily young, poorly retained in Drosophila species, and evolves under strong positive selection. Yet we find that it is necessary for larval development in D. melanogaster. We show that Nicknack encodes a heterochromatin-localizing protein like its paralog Oddjob, also an evolutionarily dynamic yet essential ZAD-ZNF gene. We find that the divergent D. simulans Nicknack protein can still localize to D. melanogaster heterochromatin and rescue viability of female but not male Nicknack-null D. melanogaster. Our findings suggest that innovation for rapidly changing heterochromatin functions might generally explain the essentiality of many evolutionarily dynamic ZAD-ZNF genes in insects.

show abstract

“…Nevertheless, many RNA-seq-based analyses operate on the assumption that PTC transcripts are biologically significant or relevant [88]. Congruously, studies focusing on mature mRNA isoforms in other organisms suggest that non-productive transcripts mediate an additional layer of posttranscriptional regulation, through downstream RNA processing changes such as mRNA turnover, export, and microRNA silencing [54,89,90]. Alternative splicing in apicomplexans may also play a role in these processes.…”

Section: Discussionmentioning

confidence: 99%

Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites

Lee

Judd

Jex

et al. 2020

Preprint

View full text Add to dashboard Cite

Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AT content of Plasmodium RNA, but also the limitations of short read sequencing in deciphering complex splicing events. In this study, we utilised the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies (ONT) to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or near full-length transcripts with comparable quantification to Illumina sequencing. By comparing this data with available gene models, we find widespread alternative splicing, particular intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This work highlights a strategy in using long read sequencing to understand splicing events at the whole transcript level, and has implications in future interpretation of RNA-seq studies.

show abstract

The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in Drosophila

Cited by 17 publications

References 78 publications

Differential isoform expression and alternative splicing in sex determination in mice

Differential isoform expression and alternative splicing in sex determination in mice

Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila

Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites

Contact Info

Product

Resources

About