Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis

Ray, Mukulika; Conard, Ashley Mae; Urban, Jennifer A.; Mahableshwarkar, Pranav; Aguilera, Joseph; Huang, Annie; Vaidyanathan, Smriti; Larschan, Erica

doi:10.7554/elife.87865

Cited by 5 publications

(3 citation statements)

References 67 publications

(113 reference statements)

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“…The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, followed by paired-end RNA-sequencing in Illumina Novaseq 6000. The sequencing data was run through a SUPPA-based time2splice pipeline 14 to identify CLAMP-dependent sex-specific splicing events. Data is to be submitted to the GEO repository.…”

Section: Methodsmentioning

confidence: 99%

“…We test this hypothesis by defining the role of GA-binding TF CLAMP (chromatin-linked adapter for MSL Proteins) in targeting sex-specific splicing to the correct genomic locations on chromatin in Drosophila. CLAMP has several properties that suggest that it could target sex-specific alternative splicing events to chromatin: 1) CLAMP binds to specific GA-enriched DNA motifs via its mapped DNA binding domain, and its binding sites differ in males and females 10–13 ; 2) CLAMP is a pioneer TF that regulates sex-specific splicing in embryos at genes where it does not regulate transcription 14 ; 3) CLAMP is enriched at the intronic region of CLAMP-dependent sex-specifically spliced genes 11,14 ; 4) CLAMP is associated with RBPs that are spliceosome components 9 .…”

Section: Main Textmentioning

confidence: 99%

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Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates

Ray,

Zaborowsky,

Mahableshwarkar

et al. 2024

Preprint

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Despite decades of research, mechanisms by which co-transcriptional alternative splicing events are targeted to the correct genomic locations to drive cell fate decisions remain unknown. By combining structural and molecular approaches, we define a new mechanism by which an essential transcription factor (TF) targets co-transcriptional splicing through physical and functional interaction with RNA and RNA binding proteins (RBPs). We show that an essential TF co-transcriptionally regulates sex-specific alternative splicing by directly interacting with a subset of target RNAs on chromatin and modulating the dynamics of hnRNPA2 homolog nuclear splicing condensates.

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Section: Methodsmentioning

confidence: 99%

Section: Main Textmentioning

confidence: 99%

Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates

Ray,

Zaborowsky,

Mahableshwarkar

et al. 2024

Preprint

Self Cite

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“…Alternative splicing (AS) can identify the skipping exon (SE), mutually exclusive exon (MX), alternative 5′ splice site (A5), alternative 3′ splice site (A3), retained intron (RI), alternative first exon (AF), and alternative last exon (AL), which greatly enriches the diversity of mRNAs and proteins [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. It has been reported that an isoform with intron 1 was retained in Cox-1 regulated human intestinal epithelial osmoregulation in a cyclooxygenase-mediated manner [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing

Zhang,

Xue,

Yang

et al. 2024

Genes

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The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel the transcriptome responses to different salinity conditions in L. marina. Through ONT sequencing under 3‰, 30‰ and 60‰ salinity environments, we obtained 131.78 G clean data and 26,647 non-redundant long-read transcripts, including 6464 novel transcripts. The DEGs obtained from the current ONT lrRNA-seq were highly correlated with those identified in our previously reported Illumina short-read RNA sequencing data. When we compared the 30‰ to the 3‰ salinity condition, we found that GO terms such as oxidoreductase activity, cation transmembrane transport and ion transmembrane transport were shared between the ONT lrRNA-seq and Illumina data. Similarly, GO terms including extracellular space, structural constituents of cuticle, substrate-specific channel activity, ion transport and substrate-specific transmembrane transporter activity were shared between the ONT and Illumina data under 60‰ compared to 30‰ salinity. In addition, we found that 79 genes significantly increased, while 119 genes significantly decreased, as the salinity increased. Furthermore, through the GO enrichment analysis of 214 genes containing DAS, in 30‰ compared to 3‰ salinity, we found that GO terms such as cellular component assembly and coenzyme biosynthetic process were enriched. Additionally, we observed that GO terms such as cellular component assembly and coenzyme biosynthetic process were also enriched in 60‰ compared to 30‰ salinity. Moreover, we found that 86, 125, and 81 genes that contained DAS were also DEGs, in comparisons between 30‰ and 3‰, 60‰ and 30‰, and 60‰ and 3‰ salinity, respectively. In addition, we demonstrated the landscape of alternative polyadenylation in marine nematode under different salinity conditions This report provides several novel insights for the further study of the mechanisms by which euryhalinity formed and evolved, and it might also contribute to the investigation of salinity dynamics induced by global climate change.

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Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

Nanni,

Titus-McQuillan,

Bankole

et al. 2024

Nucleic Acids Research

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Advances in affordable transcriptome sequencing combined with better exon and gene prediction has motivated many to compare transcription across the tree of life. We develop a mathematical framework to calculate complexity and compare transcript models. Structural features, i.e. intron retention (IR), donor/acceptor site variation, alternative exon cassettes, alternative 5′/3′ UTRs, are compared and the distance between transcript models is calculated with nucleotide level precision. All metrics are implemented in a PyPi package, TranD and output can be used to summarize splicing patterns for a transcriptome (1GTF) and between transcriptomes (2GTF). TranD output enables quantitative comparisons between: annotations augmented by empirical RNA-seq data and the original transcript models; transcript model prediction tools for longread RNA-seq (e.g. FLAIR versus Isoseq3); alternate annotations for a species (e.g. RefSeq vs Ensembl); and between closely related species. In C. elegans, Z. mays, D. melanogaster, D. simulans and H. sapiens, alternative exons were observed more frequently in combination with an alternative donor/acceptor than alone. Transcript models in RefSeq and Ensembl are linked and both have unique transcript models with empirical support. D. melanogaster and D. simulans, share many transcript models and long-read RNAseq data suggests that both species are under-annotated. We recommend combined references.

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Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis

Cited by 5 publications

References 67 publications

Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates

Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates

Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing

Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

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