A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Boxem, Mike; Maliga, Zoltan; Klitgord, Niels; Li, Na; Lemmens, Irma; Mana, Miyeko; Lichtervelde, Lorenzo de; Mul, Joram D.; Peut, Diederik van de; DEVOS, M. J.; Simonis, Nicolas; Yıldırım, Muhammed A.; Çokol, Murat; Kao, Huey Ling; Smet, Anne Sophie de; Wang, Haidong; Schlaitz, Anne Lore; Hao, Tong; Milstein, Stuart; Fan, Changyu; Tipsword, Mike; Drew, Kevin; Galli, Matilde; Rhrissorrakrai, Kahn; Drechsel, David; Koller, Daphne; Roth, Frederick P.; Iakoucheva, Lilia M.; Dunker, A. Keith; Bonneau, Richard; Gunsalus, Kristin C.; Hill, David E.; Piano, Fabio; Tavernier, Jan; Heuvel, Sander van den; Hyman, Anthony A.; Vidal, Marc

doi:10.1016/j.cell.2012.11.042

Cited by 32 publications

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“…Using individual SH3 domains as baits is known to increase interactome mapping coverage (Tong et al , 2002; Tonikian et al , 2009). Indeed, previous worm interactome mapping efforts using full‐length proteins as baits (Li et al , 2004; Simonis et al , 2009) or protein fragments as baits (Boxem et al , 2008) retrieved ∼2.3 and ∼3.1 interactors per bait on average, respectively, while we retrieved ∼12. Further, the WI8 data contain 64 PPIs involving 21 proteins with SH3 domains also present in our network, while our data set contains 457 interactions involving individual SH3 domains from these 21 proteins as baits.…”

Section: Methodsmentioning

confidence: 81%

SH3 interactome conserves general function over specific form

Gfeller

Cheng

et al. 2013

Molecular Systems Biology

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Section: Methodsmentioning

confidence: 81%

SH3 interactome conserves general function over specific form

Gfeller

Cheng

et al. 2013

Molecular Systems Biology

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“…Two putative STIL orthologues, SAS5 and Ana2, were reported to interact with Caenorhabditis SAS6 (Leidel et al , 2005; Boxem et al , 2008) and Drosophila dSas6 (Stevens et al , 2010a), respectively. We next examined whether STIL interacts with human hSAS6 and several other centrosomal proteins including Plk4, CPAP, and Cep152 that are required for procentriole formation.…”

Section: Resultsmentioning

confidence: 99%

The human microcephaly protein STIL interacts with CPAP and is required for procentriole formation

et al. 2011

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Centriole duplication involves the growth of a procentriole next to the parental centriole. Mutations in STIL and CPAP/CENPJ cause primary microcephaly (MCPH). Here, we show that human STIL has an asymmetric localization to the daughter centriole and is required for procentriole formation. STIL levels oscillate during the cell cycle. Interestingly, STIL interacts directly with CPAP and forms a complex with hSAS6. A natural mutation of CPAP (E1235V) that causes MCPH in humans leads to significantly lower binding to STIL. Overexpression of STIL induced the formation of multiple procentrioles around the parental centriole. STIL depletion inhibited normal centriole duplication, Plk4-induced centriole amplification, and CPAP-induced centriole elongation, and resulted in a failure to localize hSAS6 and CPAP to the base of the nascent procentriole. Furthermore, hSAS6 depletion hindered STIL targeting to the procentriole, implying that STIL and hSAS6 are mutually dependent for their centriolar localization. Together, our results indicate that the two MCPH-associated proteins STIL and CPAP interact with each other and are required for procentriole formation, implying a central role of centriole biogenesis in MCPH.

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“…Screening matrices will grow as the square of the number of clones, with more clones needed to cover splice isoforms (Corominas et al , ) and other coding sequence variants (Sahni et al , ). Further adding to the dimension of the search space, it is now clear that screening with fragments can increase the assay sensitivity (Boxem et al , ), for example, by eliminating repressive domains. While significant improvements have been made to reduce the cost and effort required to screen large libraries of genes, state‐of‐the‐art Y2H methods still require manual colony picking and multiple PCR steps for each Y2H‐positive colony (Yu et al , ; Rolland et al , ).…”

Section: Discussionmentioning

confidence: 99%

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

Yachie

Petsalaki

Mellor

et al. 2016

Molecular Systems Biology

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High‐throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome‐scale interaction mapping. Here, we report Barcode Fusion Genetics‐Yeast Two‐Hybrid (BFG‐Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG‐Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein‐pair barcodes that can be quantified via next‐generation sequencing. We applied BFG‐Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG‐Y2H increases the efficiency of protein matrix screening, with quality that is on par with state‐of‐the‐art Y2H methods.

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A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Cited by 32 publications

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SH3 interactome conserves general function over specific form

SH3 interactome conserves general function over specific form

The human microcephaly protein STIL interacts with CPAP and is required for procentriole formation

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

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