Many Faces of TRIM Proteins on the Road from Pluripotency to Neurogenesis

Nenasheva, Valentina V.; Tarantul, V. Z.

doi:10.1089/scd.2019.0152

Cited by 12 publications

(11 citation statements)

References 140 publications

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“…On 9q22.33, rs911934 is located in a region having a chromatin interaction with TRIM14 in adult cortex 46 (Supplementary Fig. 4 ), a gene which may activate Wnt/β-catenin signalling and affects mesodermal versus ectodermal differentiation of embryonic stem cells 58 . On 10p14, rs41298373 is a predicted deleterious missense coding variant in ITIH5 , which was previously reported to affect planum temporale volumetric asymmetry 35 .…”

Section: Resultsmentioning

confidence: 99%

The genetic architecture of structural left–right asymmetry of the human brain

et al. 2021

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Left–right hemispheric asymmetry is an important aspect of healthy brain organization for many functions including language, and it can be altered in cognitive and psychiatric disorders. No mechanism has yet been identified for establishing the human brain’s left–right axis. We performed multivariate genome-wide association scanning of cortical regional surface area and thickness asymmetries, and subcortical volume asymmetries, using data from 32,256 participants from the UK Biobank. There were 21 significant loci associated with different aspects of brain asymmetry, with functional enrichment involving microtubule-related genes and embryonic brain expression. These findings are consistent with a known role of the cytoskeleton in left–right axis determination in other organs of invertebrates and frogs. Genetic variants associated with brain asymmetry overlapped with those associated with autism, educational attainment and schizophrenia. Comparably large datasets will likely be required in future studies, to replicate and further clarify the associations of microtubule-related genes with variation in brain asymmetry, behavioural and psychiatric traits.

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Section: Resultsmentioning

confidence: 99%

The genetic architecture of structural left–right asymmetry of the human brain

et al. 2021

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“…On 9q22.33, rs911934 is located in a region having a chromatin interaction with TRIM14 in adult cortex 27 ( Supplementary Fig. 4), a gene which may activate Wnt/β-catenin signaling and affects mesodermal versus ectodermal differentiation of embryonic stem cells 28 . On 10p14, rs41298373 is a predicted deleterious missense coding variant in ITIH5, which was previously reported to affect planum temporale volumetric asymmetry 14 .…”

mentioning

confidence: 99%

The genetic architecture of structural left-right asymmetry of the human brain

Sha

Schijven

Carrión-Castillo

et al. 2020

Preprint

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Left-right hemispheric asymmetry is an important aspect of healthy brain organization for many functions including language, and can be altered in cognitive and psychiatric disorders1-8. No mechanism has yet been identified for establishing the human brain’s left-right axis9. We performed multivariate genome-wide association scanning (mvGWAS) of cortical regional surface area and thickness asymmetries, and subcortical volume asymmetries, using data from 32,256 participants from the UK Biobank. There were 21 significant loci affecting different aspects of brain asymmetry, with functional enrichment involving microtubule-related genes and embryonic brain expression. These findings are consistent with a known role of the cytoskeleton in left-right axis determination in other organs of invertebrates and frogs10-12. Genetic variants affecting brain asymmetry overlapped with those influencing autism, educational attainment and schizophrenia.

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“…Biological Process GO:0097150 (neuronal stem cell population maintenance) Understanding the functions of different TRIM proteins in this regard is an area of cutting-edge research, as discoveries that TRIM proteins have regulatory functions in neural development and maintenance have only recently been made 98 . As with stem cell differentiation, autophagy is an important process in stem cell maintenance 91 , and TRIM proteins have important roles in autophagy 99,100 .…”

Section: Detailed Validation Of Our Single Highest Naf Predictionmentioning

confidence: 99%

“…TRIM25 is expressed and contributes to stem cell maintenance in mouse embryos 102 by ensuring genomic stability following DNA replication 103 . A recent survey 98 states that TRIM25's function in stem cells appears to be the least well understood out of all TRIM family proteins, and makes no mention of a role for TRIM25 in neurological processes. The indirect evidence presented above, along with its high NAF score, suggests that TRIM25's role in this area be further investigated.…”

Section: Detailed Validation Of Our Single Highest Naf Predictionmentioning

confidence: 99%

SANA: Cross-Species Prediction of Gene Ontology GO Annotations via Topological Network Alignment

Wang,

Atkinson,

Hayes

2022

Preprint

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Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two Protein-Protein Interaction (PPI) networks should thus expose protein pairs with similar interaction partners allowing, for example, the prediction of common Gene Ontology (GO) terms. Unfortunately, no network alignment algorithm based on topology alone has been able to achieve this aim, though those that include sequence similarity have seen some success. We argue that this failure of topology alone is due to the sparsity and incompleteness of the PPI network data of almost all species, which provides the network topology with a small signal-to-noise ratio that is effectively swamped when sequence information is added to the mix. Here we show that the weak signal can be detected using multiple stochastic samples of "good" topological network alignments, which allows us to observe regions of the two networks that are robustly aligned across multiple samples. The resulting Network Alignment Frequency (NAF) strongly correlates with GO-based Resnik semantic similarity and enables the first successful cross-species predictions of GO terms based on topology-only network alignments. Our best predictions have an AUPR of about 0.4, which is competitive with state-of-the-art algorithms, even when there is no observable sequence similarity and no known homology relationship. While our results provide only a "proof of concept" on existing network data, we hypothesize that predicting GO terms from topology-only network alignments will become increasingly practical as the volume and quality of PPI network data increase.

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Many Faces of TRIM Proteins on the Road from Pluripotency to Neurogenesis

Cited by 12 publications

References 140 publications

The genetic architecture of structural left–right asymmetry of the human brain

The genetic architecture of structural left–right asymmetry of the human brain

The genetic architecture of structural left-right asymmetry of the human brain

SANA: Cross-Species Prediction of Gene Ontology GO Annotations via Topological Network Alignment

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