Sambina Islam Aninta

Sambina Islam Aninta

@sambean12.bsky.social

KMILOT Scholar @ UBC | PhD in Biomedical Engineering @ de Boer lab

33 followers120 following6 posts

Sambina Islam Aninta
@sambean12.bsky.social

MPRAs are the gold-standard tool for measuring how DNA sequences drive gene expression and prioritizing variant effects. In this preprint we asked: does it matter WHERE you place a variant in an MPRA? Spoiler: yes, and it might lead you to miss disease-causing variants. 1/6 doi.org/10.64898/202...

biorxiv.orgPosition-dependent variant effects reveal importance of context in genomic regulationGene expression is governed by the DNA sequence, which is read out through complex interactions between transcription factors (TFs), co-activators, and chromatin. Massively Parallel Reporter Assays (MPRAs) provide a high-throughput framework for functionally characterizing how regulatory DNA sequences impact the expression of a model gene. MPRAs have also proven to be useful for measuring the effects of genetic variation, where each allele is typically tested in the center of ~200 bp of genomic context cloned into the MPRA, but the impact of variant position and local context remains largely unexplored. In this study, we systematically investigate how shifting the position of a variant within an MPRA probe influences its regulatory activity using models that predict expression in MPRAs from DNA sequence. We find that while the direction of variant effects is usually preserved across positions, the magnitude of expression changes can vary substantially depending on where the variant is placed within the construct. This positional bias appears to be largely explained by the strong position-dependent activity of TFs whose binding the variants perturb. In a subset of cases, interactions consistent with cooperativity between TFs also contribute to position-specific effects. ~1% of variants appear to disrupt RNA polymerase III (Pol III) promoters within Alu elements, resulting in position-specificity because both A and B boxes are required for function and exclusion of either motif due to window shifts disrupts the variants' effects. However, we saw little evidence to support the hypothesis that the positional dependence of variant effects resulted from the redundancy of motifs. Overall, our study demonstrates the complexity of cis-regulatory grammar and how it can confound the interpretation of regulatory variants. ### Competing Interest Statement R.T. has filed intellectual property related to MPRA and MPRA models. The other authors declare no competing interests.
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Sambina Islam Aninta
@sambean12.bsky.social

Overall, the library design choices made when building an MPRA can directly affect which variant effects are measured and how large they appear. Functionally important variants may be underestimated or missed depending on where they are placed in the construct. 6/6

Sambina Islam Aninta
@sambean12.bsky.social

MPRAs are the gold-standard tool for measuring how DNA sequences drive gene expression and prioritizing variant effects. In this preprint we asked: does it matter WHERE you place a variant in an MPRA? Spoiler: yes, and it might lead you to miss disease-causing variants. 1/6 doi.org/10.64898/202...

biorxiv.orgPosition-dependent variant effects reveal importance of context in genomic regulationGene expression is governed by the DNA sequence, which is read out through complex interactions between transcription factors (TFs), co-activators, and chromatin. Massively Parallel Reporter Assays (MPRAs) provide a high-throughput framework for functionally characterizing how regulatory DNA sequences impact the expression of a model gene. MPRAs have also proven to be useful for measuring the effects of genetic variation, where each allele is typically tested in the center of ~200 bp of genomic context cloned into the MPRA, but the impact of variant position and local context remains largely unexplored. In this study, we systematically investigate how shifting the position of a variant within an MPRA probe influences its regulatory activity using models that predict expression in MPRAs from DNA sequence. We find that while the direction of variant effects is usually preserved across positions, the magnitude of expression changes can vary substantially depending on where the variant is placed within the construct. This positional bias appears to be largely explained by the strong position-dependent activity of TFs whose binding the variants perturb. In a subset of cases, interactions consistent with cooperativity between TFs also contribute to position-specific effects. ~1% of variants appear to disrupt RNA polymerase III (Pol III) promoters within Alu elements, resulting in position-specificity because both A and B boxes are required for function and exclusion of either motif due to window shifts disrupts the variants' effects. However, we saw little evidence to support the hypothesis that the positional dependence of variant effects resulted from the redundancy of motifs. Overall, our study demonstrates the complexity of cis-regulatory grammar and how it can confound the interpretation of regulatory variants. ### Competing Interest Statement R.T. has filed intellectual property related to MPRA and MPRA models. The other authors declare no competing interests.
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Sambina Islam Aninta
@sambean12.bsky.social

The main driver of this positional bias is position-dependent TF activity. TFs don't contribute equally to expression from all locations in a sequence, so variants that perturb TF binding inherit this dependence. Closer to the TSS tends to show larger effects, but this is TF-specific. 3/6

Sambina Islam Aninta
@sambean12.bsky.social

MPRAs are the gold-standard tool for measuring how DNA sequences drive gene expression and prioritizing variant effects. In this preprint we asked: does it matter WHERE you place a variant in an MPRA? Spoiler: yes, and it might lead you to miss disease-causing variants. 1/6 doi.org/10.64898/202...

biorxiv.orgPosition-dependent variant effects reveal importance of context in genomic regulationGene expression is governed by the DNA sequence, which is read out through complex interactions between transcription factors (TFs), co-activators, and chromatin. Massively Parallel Reporter Assays (MPRAs) provide a high-throughput framework for functionally characterizing how regulatory DNA sequences impact the expression of a model gene. MPRAs have also proven to be useful for measuring the effects of genetic variation, where each allele is typically tested in the center of ~200 bp of genomic context cloned into the MPRA, but the impact of variant position and local context remains largely unexplored. In this study, we systematically investigate how shifting the position of a variant within an MPRA probe influences its regulatory activity using models that predict expression in MPRAs from DNA sequence. We find that while the direction of variant effects is usually preserved across positions, the magnitude of expression changes can vary substantially depending on where the variant is placed within the construct. This positional bias appears to be largely explained by the strong position-dependent activity of TFs whose binding the variants perturb. In a subset of cases, interactions consistent with cooperativity between TFs also contribute to position-specific effects. ~1% of variants appear to disrupt RNA polymerase III (Pol III) promoters within Alu elements, resulting in position-specificity because both A and B boxes are required for function and exclusion of either motif due to window shifts disrupts the variants' effects. However, we saw little evidence to support the hypothesis that the positional dependence of variant effects resulted from the redundancy of motifs. Overall, our study demonstrates the complexity of cis-regulatory grammar and how it can confound the interpretation of regulatory variants. ### Competing Interest Statement R.T. has filed intellectual property related to MPRA and MPRA models. The other authors declare no competing interests.
Sambina Islam Aninta
@sambean12.bsky.social

MPRAs typically test variants in the center of ~200bp constructs. We shifted variant positions across the probe and found that while the direction of effects is usually preserved, the magnitude can vary substantially depending on placement. 2/6

Sambina Islam Aninta reposted

Carl de Boer
@carldeboer.bsky.social

SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...

Sambina Islam Aninta reposted

Carl de Boer
@carldeboer.bsky.social

Replying to @carldeboer.bsky.social

Thanks for reading! Please let us know what you think, and support GAME by contributing modules! Preprint: doi.org/10.1101/2025... GitHub: github.com/de-Boer-Lab/...

doi.orgGAME: Genomic API for Model EvaluationThe rapid expansion of genomics datasets and the application of machine learning has produced sequence-to-activity genomics models with ever-expanding capabilities. However, benchmarking these models ...

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