Biology subjects

Eberhard, Q. E.

Publications and source records attributed to Eberhard, Q. E..

4 recordsLinked to original sources

bioRxiv2026

Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR

Long noncoding RNAs (lncRNAs) play roles in gene regulation across kingdoms of life. However, lncRNAs with related functions often lack linear sequence similarity, making it difficult to leverage studies of one lncRNA to inform the understanding of others. We describe a k-mer-based hidden Markov model, hmSEEKR, that enables the scanning of transcriptomes for regions of non-linear sequence similarity to a query domain, without prior knowledge of where within the transcriptome the similarities may be located. When individual lncRNA domains were used as search features, hmSEEKR successfully identified regions in other RNAs that harbor non-linear sequence similarity and bind similar sets of proteins. Applying hmSEEKR to transcriptome-wide searches, we found that certain domains within the lncRNAs XIST, NEAT1, and MALAT1 exhibited widespread regional similarity to both lncRNA and protein-coding genes, while others were more unique, exhibiting similarity to [~]100 genes or fewer. Combinatorial searches uncovered RNAs containing sequential matches to core functional domains of XIST and NEAT1, and eCLIP-inferred protein-interaction networks within these RNAs more closely resembled those of XIST and NEAT1, respectively, than would be expected by chance, suggesting the searches recovered RNAs with similar biological properties. Finally, within annotated sets of cis-activating and cis-repressive lncRNAs, we observed opposing enrichments for similarity to domains associated with transcription-promoting complexes and heterogeneous nuclear ribonucleoprotein (hnRNP) binding, respectively, suggesting the enriched sequences may contribute to regulatory functions. hmSEEKR can be applied with minimal training data and enables the a priori discovery of RNA domains that share nonlinear similarity, offering a sequence-informed approach to discover functional elements within noncoding transcriptomes.

bioinformatics↗

bioRxiv2025

Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing

The lncRNA Xist represents a paradigm to understand the mechanisms of RNA-mediated gene silencing in mammals, which remain largely unresolved. To induce silencing, Xist recruits the RNA-binding protein SPEN through its 5'-proximal Repeat A domain. Yet, how Repeat A recruits SPEN and how SPEN coordinates silencing remain unclear. We report that sequences in Repeat A critical for SPEN recruitment directly bind SR-rich splicing factors. SRSF1, one such factor, is required for optimal SPEN recruitment and its RS-domain recruits SPEN when tethered to Xist. SPEN and SR-protein-binding motifs promote Repeat As association with many proteins, including the m6A machinery and elongating RNA polymerase II. SPEN also represses autosomal genes where its recruitment coincides with SR-protein binding. Our results reveal an unexpectedly essential role for splicing factors in coordinating silencing by Xist and suggest that the sensing of SR-protein-rich assemblies is a general mechanism through which SPEN targets genes for repression.

genetics↗

bioRxiv2023

Ectopically expressed Airn lncRNA deposits Polycomb with a potency that rivals Xist

We report that when expressed at similar levels from an isogenic locus, the Airn lncRNA induces Polycomb deposition with a potency that rivals Xist. However, when subject to the same degree of promoter activation, Xist is more abundant and more potent than Airn. Our data definitively demonstrate that the Airn lncRNA is functional and suggest that Xist achieved extreme potency in part by evolving mechanisms to promote its own abundance.

molecular biology↗

bioRxiv2022

SAFB associates with nascent RNAs to promote gene expression in mouse embryonic stem cells

Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type ESCs and in ESCs in which SAFB and SAFB2 were knocked out. SAFB predominantly associated with introns of protein-coding genes through purine-rich motifs. The transcript most enriched in SAFB association was the lncRNA Malat1, which also contains a purine-rich region in its 5' end. Knockout of SAFB/2 led to down- and upregulation of approximately 1,000 genes associated with multiple biological processes, including genes that are regulated by Polycomb and genes involved in apoptosis, cell division, and cell migration. The spliced and nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes their expression. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of spliced and nascent transcripts. Proteomics analysis revealed a significant enrichment of nuclear speckle-associated and RS-domain containing proteins among SAFB interactors. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.

molecular biology↗