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Article: Identification and functional characterization of transcriptional activators in human cells

Alerasool, Nader / Leng, He / Lin, Zhen-Yuan / Gingras, Anne-Claude / Taipale, Mikko

Molecular cell. 2022 Feb. 03, v. 82, no. 3

2022

Abstract: Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to ... ...

Abstract	Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. 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 p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
Keywords	chromatin ; genome ; humans ; proteome ; proteomics ; transactivators ; transcription (genetics) ; transcriptional activation
Language	English
Dates of publication	2022-0203
Size	p. 677-695.e7.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.12.008
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Article ; Online: An efficient KRAB domain for CRISPRi applications in human cells.

Alerasool, Nader / Segal, Dmitri / Lee, Hunsang / Taipale, Mikko

Nature methods

2020 Volume 17, Issue 11, Page(s) 1093–1096

Abstract: Clustered regularly interspaced short palindromic repeat interference (CRISPRi), based on the fusion of inactive Cas9 (dCas9) to the Krüppel-associated box (KRAB) repressor, is a powerful platform for silencing gene expression. However, it suffers from ... ...

Abstract	Clustered regularly interspaced short palindromic repeat interference (CRISPRi), based on the fusion of inactive Cas9 (dCas9) to the Krüppel-associated box (KRAB) repressor, is a powerful platform for silencing gene expression. However, it suffers from incomplete silencing of target genes. We assayed 57 KRAB domains for their repressive potency and identified the ZIM3 KRAB domain as an exceptionally potent repressor. We establish that ZIM3 KRAB-dCas9 fusion silences gene expression more efficiently than existing platforms.
MeSH term(s)	CRISPR-Associated Protein 9/genetics ; CRISPR-Cas Systems/genetics ; Catalytic Domain ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genes, Reporter ; HEK293 Cells ; Humans ; K562 Cells ; Kruppel-Like Transcription Factors/genetics ; Promoter Regions, Genetic ; Repressor Proteins/genetics ; Transcription, Genetic ; RNA, Guide, CRISPR-Cas Systems
Chemical Substances	Kruppel-Like Transcription Factors ; Repressor Proteins ; CRISPR-Associated Protein 9 (EC 3.1.-)
Language	English
Publishing date	2020-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-020-0966-x
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Article ; Online: Identification and functional characterization of transcriptional activators in human cells.

Alerasool, Nader / Leng, He / Lin, Zhen-Yuan / Gingras, Anne-Claude / Taipale, Mikko

Molecular cell

2022 Volume 82, Issue 3, Page(s) 677–695.e7

Abstract	Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. 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 p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
MeSH term(s)	Animals ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Line ; Gene Expression Regulation, Neoplastic ; HEK293 Cells ; Humans ; Intercellular Signaling Peptides and Proteins/genetics ; Intercellular Signaling Peptides and Proteins/metabolism ; K562 Cells ; Mice ; Myofibroma/genetics ; Myofibroma/metabolism ; NIH 3T3 Cells ; Proteome ; Proteomics ; Serum Response Factor/genetics ; Serum Response Factor/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic ; Transcriptional Activation
Chemical Substances	BRD4 protein, human ; C3orf62 protein, human ; Cell Cycle Proteins ; Intercellular Signaling Peptides and Proteins ; Proteome ; SRF protein, human ; Serum Response Factor ; Transcription Factors
Language	English
Publishing date	2022-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.12.008
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Article ; Online: Proteome-scale discovery of protein degradation and stabilization effectors.

Poirson, Juline / Cho, Hanna / Dhillon, Akashdeep / Haider, Shahan / Imrit, Ahmad Zoheyr / Lam, Mandy Hiu Yi / Alerasool, Nader / Lacoste, Jessica / Mizan, Lamisa / Wong, Cassandra / Gingras, Anne-Claude / Schramek, Daniel / Taipale, Mikko

Nature

2024 Volume 628, Issue 8009, Page(s) 878–886

Abstract: Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target ... ...

Abstract	Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space
MeSH term(s)	Humans ; Deubiquitinating Enzymes/analysis ; Deubiquitinating Enzymes/metabolism ; Protein Stability ; Proteolysis ; Proteome/metabolism ; Proteomics ; Ubiquitin-Protein Ligases/analysis ; Ubiquitin-Protein Ligases/metabolism ; Substrate Specificity ; Proteolysis Targeting Chimera/metabolism ; Von Hippel-Lindau Tumor Suppressor Protein/metabolism
Chemical Substances	Deubiquitinating Enzymes (EC 3.4.19.12) ; Proteome ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proteolysis Targeting Chimera ; VHL protein, human (EC 6.3.2.-) ; Von Hippel-Lindau Tumor Suppressor Protein (EC 2.3.2.27)
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07224-3
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Article ; Online: Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active genes.

Devoucoux, Maëva / Fort, Victoire / Khelifi, Gabriel / Xu, Joshua / Alerasool, Nader / Galloy, Maxime / Wong, Nicholas / Bourriquen, Gaëlle / Fradet-Turcotte, Amelie / Taipale, Mikko / Hope, Kristin / Hussein, Samer M I / Côté, Jacques

Cell reports

2022 Volume 39, Issue 11, Page(s) 110947

Abstract: A recurrent chromosomal translocation found in acute myeloid leukemia leads to an in-frame fusion of the transcription repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase complex. To understand the abnormal molecular events ... ...

Abstract	A recurrent chromosomal translocation found in acute myeloid leukemia leads to an in-frame fusion of the transcription repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase complex. To understand the abnormal molecular events that ZMYND11-MBTD1 expression can create, we perform a biochemical and functional characterization comparison to each individual fusion partner. ZMYND11-MBTD1 is stably incorporated into the endogenous NuA4/TIP60 complex, leading to its mislocalization on the body of genes normally bound by ZMYND11. This can be correlated to increased chromatin acetylation and altered gene transcription, most notably on the MYC oncogene, and alternative splicing. Importantly, ZMYND11-MBTD1 expression favors Myc-driven pluripotency during embryonic stem cell differentiation and self-renewal of hematopoietic stem/progenitor cells. Altogether, these results indicate that the ZMYND11-MBTD1 fusion functions primarily by mistargeting the NuA4/TIP60 complex to the body of genes, altering normal transcription of specific genes, likely driving oncogenesis in part through the Myc regulatory network.
MeSH term(s)	Acetylation ; Cell Cycle Proteins/metabolism ; Chromatin ; Chromosomal Proteins, Non-Histone/metabolism ; Co-Repressor Proteins/metabolism ; DNA-Binding Proteins/metabolism ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Humans ; Lysine Acetyltransferase 5/genetics ; Lysine Acetyltransferase 5/metabolism ; Oncogene Proteins, Fusion/genetics ; Oncogene Proteins, Fusion/metabolism ; Open Reading Frames/genetics ; Translocation, Genetic
Chemical Substances	Cell Cycle Proteins ; Chromatin ; Chromosomal Proteins, Non-Histone ; Co-Repressor Proteins ; DNA-Binding Proteins ; MBTD1 protein, human ; Oncogene Proteins, Fusion ; ZMYND11 protein, human ; Histone Acetyltransferases (EC 2.3.1.48) ; Lysine Acetyltransferase 5 (EC 2.3.1.48)
Language	English
Publishing date	2022-06-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110947
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Article ; Online: MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions.

Devoucoux, Maëva / Roques, Céline / Lachance, Catherine / Lashgari, Anahita / Joly-Beauparlant, Charles / Jacquet, Karine / Alerasool, Nader / Prudente, Alexandre / Taipale, Mikko / Droit, Arnaud / Lambert, Jean-Philippe / Hussein, Samer M I / Côté, Jacques

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 7, Page(s) 100253

Abstract: MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain (CHD) recognizing methylation of lysine 36 on histone H3 (H3K36me3) in chromatin. Intriguingly, it has been reported in the literature to interact with several ... ...

Abstract	MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain (CHD) recognizing methylation of lysine 36 on histone H3 (H3K36me3) in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing, and DNA repair by homologous recombination. To get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the CHD, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4/TIP60 histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L histone methyltransferase, and PALB2-BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15/X-MRGBP-BRD8-EP400NL (EP400 N-terminal like) that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4/TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the H3K36me3-binding CHD of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG proteins-associated protein complexes, which are essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes.
MeSH term(s)	Chromatin/metabolism ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Histones/metabolism ; Humans ; Nucleosomes/metabolism ; Transcription Factors/metabolism
Chemical Substances	Chromatin ; Histones ; MORF4L1 protein, human ; MORF4L2 protein, human ; Nucleosomes ; Transcription Factors ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2022-05-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100253
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Article: Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains

Piette, Benjamin L. / Alerasool, Nader / Lin, Zhen-Yuan / Lacoste, Jessica / Lam, Mandy Hiu Yi / Qian, Wesley Wei / Tran, Stephanie / Larsen, Brett / Campos, Eric / Peng, Jian / Gingras, Anne-Claude / Taipale, Mikko

Molecular cell. 2021 June 17, v. 81, no. 12

2021

Abstract: Hsp70s comprise a deeply conserved chaperone family that has a central role in maintaining protein homeostasis. In humans, Hsp70 client specificity is provided by 49 different co-factors known as J domain proteins (JDPs). However, the cellular function ... ...

Abstract	Hsp70s comprise a deeply conserved chaperone family that has a central role in maintaining protein homeostasis. In humans, Hsp70 client specificity is provided by 49 different co-factors known as J domain proteins (JDPs). However, the cellular function and client specificity of JDPs have largely remained elusive. We have combined affinity purification-mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID) to characterize the interactome of all human JDPs and Hsp70s. The resulting network suggests specific functions for many uncharacterized JDPs, and we establish a role of conserved JDPs DNAJC9 and DNAJC27 in histone chaperoning and ciliogenesis, respectively. Unexpectedly, we find that the J domain of DNAJC27 but not of other JDPs can fully replace the function of endogenous DNAJC27, suggesting a previously unappreciated role for J domains themselves in JDP specificity. More broadly, our work expands the role of the Hsp70-regulated proteostasis network and provides a platform for further discovery of JDP-dependent functions.
Keywords	biotinylation ; histones ; homeostasis ; humans ; spectroscopy
Language	English
Dates of publication	2021-0617
Size	p. 2549-2565.e8.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.04.012
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Article: Tetra-Primer ARMS PCR Optimization for Detection of IVS-II-I (G-A) and FSC 8/9 InsG Mutations in β-Thalassemia Major Patients in Isfahan Population.

Hajihoseini, Samaneh / Motovali-Bashi, Majid / Honardoost, Mohammad Amin / Alerasool, Nader

Iranian journal of public health

2015 Volume 44, Issue 3, Page(s) 380–387

Abstract: Background: β-thalassemia, a monogenic autosomal recessive disorder, is prevalent in Middle East, particularly in Iran. In Iran, near to 20 mutations in the β-globin gene are introduced as common mutations with varying incidence frequencies in each city. ...

Abstract	Background: β-thalassemia, a monogenic autosomal recessive disorder, is prevalent in Middle East, particularly in Iran. In Iran, near to 20 mutations in the β-globin gene are introduced as common mutations with varying incidence frequencies in each city. Therefore, detection and screening for couples at high risk can help to solve the problems of this disease. In this study, optimized genotyping of two common mutations in Isfahan Province, IVSII-I (G-A) and FSC-8/9 insG, was performed using the T-ARMS method. Methods: In this case-control study, 10 healthy individuals and 30 patients affected by β-thalassemia major with a mean 24.76 ± 4.5 years were selected from Omid Hospital in Isfahan Province. After designing tetra primers for two prevalent mutations IVSII-I (G-A) and FSC-8/9 insG, samples were genotyped using tetra-primers ARMS PCR technique. Results: We have developed a sensitive single tube tetra-primers PCR assay to detect both IVSII-1 (G-A) and FS8-9 insG mutations. Moreover, we have distinguished homozygous and heterozygous forms of these mutations successfully. The frequency of IVSII-1 (G-A) mutation from 30 patients in Isfahan was 86.6% (33.3% heterozygote, and 53.3% mutant homozygote) and for FS8-9 insG mutation was 16.6% (13.3% heterozygote, and 3.3% mutant homozygote). Conclusion: Tetra-primers ARMS PCR could be a reliable, accurate and simple technique for genotyping SNP and different mutations. So far, no study was done on optimization methods for genotyping mutations in β-thalassemia by T-ARMS. Here, we successfully adjusted and enhanced this method for recognizing two common mutations (FSC-8/9 insG and IVSII-I (G-A)) of β-thalassemia in Isfahan population.
Language	English
Publishing date	2015-04-23
Publishing country	Iran
Document type	Journal Article
ISSN	2251-6085 ; 0304-4556
ISSN	2251-6085 ; 0304-4556
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Article ; Online: Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains.

Piette, Benjamin L / Alerasool, Nader / Lin, Zhen-Yuan / Lacoste, Jessica / Lam, Mandy Hiu Yi / Qian, Wesley Wei / Tran, Stephanie / Larsen, Brett / Campos, Eric / Peng, Jian / Gingras, Anne-Claude / Taipale, Mikko

Molecular cell

2021 Volume 81, Issue 12, Page(s) 2549–2565.e8

Abstract	Hsp70s comprise a deeply conserved chaperone family that has a central role in maintaining protein homeostasis. In humans, Hsp70 client specificity is provided by 49 different co-factors known as J domain proteins (JDPs). However, the cellular function and client specificity of JDPs have largely remained elusive. We have combined affinity purification-mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID) to characterize the interactome of all human JDPs and Hsp70s. The resulting network suggests specific functions for many uncharacterized JDPs, and we establish a role of conserved JDPs DNAJC9 and DNAJC27 in histone chaperoning and ciliogenesis, respectively. Unexpectedly, we find that the J domain of DNAJC27 but not of other JDPs can fully replace the function of endogenous DNAJC27, suggesting a previously unappreciated role for J domains themselves in JDP specificity. More broadly, our work expands the role of the Hsp70-regulated proteostasis network and provides a platform for further discovery of JDP-dependent functions.
MeSH term(s)	HEK293 Cells ; HSP40 Heat-Shock Proteins/metabolism ; HSP40 Heat-Shock Proteins/physiology ; HSP70 Heat-Shock Proteins/metabolism ; HSP70 Heat-Shock Proteins/physiology ; HeLa Cells ; Humans ; Molecular Chaperones/metabolism ; Protein Binding ; Protein Domains ; Protein Interaction Domains and Motifs/physiology ; rab GTP-Binding Proteins/metabolism
Chemical Substances	DNAJC9 protein, human ; HSP40 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins ; Molecular Chaperones ; DNAJC27 protein, human (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2021-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.04.012
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Article ; Online: A universal deep-learning model for zinc finger design enables transcription factor reprogramming.

Nature biotechnology

2023 Volume 41, Issue 8, Page(s) 1117–1129

Abstract: ... ...

Abstract	Cys
MeSH term(s)	Humans ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Deep Learning ; Zinc Fingers/genetics ; Gene Expression Regulation ; DNA/genetics
Chemical Substances	Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2023-01-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01624-4
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