Biology subjects

Alerasool, N.

Publications and source records attributed to Alerasool, N..

4 recordsLinked to original sources

bioRxiv2022

Proteome-scale induced proximity screens reveal highly potent protein degraders and stabilizers

Targeted protein degradation and stabilization are promising therapeutic modalities due to their potency and versatility. However, only few E3 ligases and deubiquitinases have been harnessed for this purpose. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation. Here, we used a proteome-scale platform to identify hundreds of human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. This allowed us to comprehensively compare the activities of human E3s and deubiquitinases, characterize non-canonical protein degraders and stabilizers, and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3s CBRN and VHL. Our study provides a functional catalogue of effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for discovery of novel proximity-dependent protein modulators.

molecular biology↗

bioRxiv2022

The kinetic landscape of human transcription factors

Cell-to-cell variability is shaped by transcription dynamics because genes are transcribed in bursts interspersed with inactive periods. The stochasticity of bursting means that genes transcribed in rare bursts exhibit more heterogeneity at the single cell level than genes that burst often 1, 2. Transcription starts with the binding of Transcription Factors (TFs) to specific sequence motifs where they recruit the transcription machinery 3. In some systems, individual TF binding events temporally correlate with the firing of transcriptional bursts, defining the target genes frequency and duration 4-6. However, in the absence of methods that assess the impact of different TFs on transcription dynamics at the same genetic loci, it remains unclear whether DNA binding kinetics are the sole determinant of bursting. Here we develop an imaging-based synthetic recruitment assay, CRISPRburst, and measure how 92 human TFs impact bursting kinetics. We show that TFs recruited to chromatin under identical conditions generate diverse bursting signatures, some TFs increasing the probability of the gene turning on while others increase the number of mRNA molecules transcribed per burst. We find that the association of TFs with specific protein partners determines their bursting output, and train a model to predict the kinetic signatures of all human TFs. These kinetic signatures can be used as a TF classification system complementary to existing families based on DNA binding domains. Additionally, kinetic signatures provide a rational framework to design synthetic activators, model transcription regulation, and understand expression heterogeneity.

biophysics↗

bioRxiv2021

Identification and functional characterization of transcriptional activators in human cells

Transcription is orchestrated by thousands of transcription factors and chromatin-associated proteins, but how these are causally connected to transcriptional activation or repression is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. We also identify potent transactivation domains among the hits. By combining interaction proteomics and chemical inhibitors, we delineate the preference of both known and novel transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct co-factors. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent activator. SRF-C3orf62 activates transcription in a CBP/p300-dependent manner and promotes proliferative and myogenic transcriptional programs. Our work provides a functional catalogue of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.

molecular biology↗

bioRxiv2021

Recurrent chromosomal translocations in sarcomas create a mega-complex that mislocalizes NuA4/TIP60 to Polycomb target loci

Chromosomal translocations frequently promote carcinogenesis by producing gain-of-function fusion proteins. Recent studies have identified highly recurrent chromosomal translocations in patients with Endometrial Stromal Sarcomas (ESS) and Ossifying FibroMyxoid Tumors (OFMT) leading to an in-frame fusion of PHF1 (PCL1) to six different subunits of the NuA4/TIP60 complex. While NuA4/TIP60 is a co-activator that acetylates chromatin and loads the H2A.Z histone variant, PHF1 is part of the Polycomb repressive complex 2 (PRC2) linked to transcriptional repression of key developmental genes through methylation of histone H3 on lysine 27. In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation. The chimeric protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically- associating domain including part of the HOXD cluster. This is linked to aberrant gene expression, most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1, implicated with a PRC2 component in the most frequent translocation in ESS, JAZF1-SUZ12, is a potent transcription activator that physically associates with NuA4/TIP60, its fusion creating similar outcomes as EPC1-PHF1. Importantly, the specific increased expression of PRC2 targets/HOX genes was also confirmed with ESS patient samples. Altogether, these results indicate that most chromosomal translocations linked to these sarcomas employ the same molecular oncogenic mechanism through a physical merge of NuA4/TIP60 and PRC2 complexes leading to mislocalization of histone marks and aberrant polycomb target gene expression.

molecular biology↗