Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis

Gillespie, Mark A.; Palii, Carmen G.; Sánchez-Taltavull, Daniel; Shannon, Paul; Longabaugh, William J.R.; Downes, Damien J.; Sivaraman, Karthi; Hughes, Jim R.; Price, Nathan D.; Perkins, Theodore J.; Ranish, Jeffrey A.; Brand, Marjorie

doi:10.1101/812123

Cited by 21 publications

(34 citation statements)

References 82 publications

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“…We have previously shown that TFII-I interacts with HDAC3 and functions as a repressor of adult β-globin gene expression in erythroleukemia cell lines ( Crusselle-Davis et al, 2006 ). Gillespie et al (2020) recently performed a proteomic study in primary differentiating erythroid cells. The relative expression data for TFII-I demonstrate that it is up-regulated during differentiation of erythroid cells and declines in expression concomitant with the up-regulation of adult β-globin gene expression ( Figure 1A ).…”

Section: Resultsmentioning

confidence: 99%

“…(A) Relative protein expression levels for TFII-I, β-globin, and TBP during differentiation of erythroid cells. Data were extracted from a proteomic study by Gillespie et al (2020) . MPP, multiple progenitor population; CMP, common myeloid progenitors; MEP, myeloid erythroid progenitors; CFU-E, colony forming unite-erythroid; ProEB, proerythroblast; Baso EB, basophilic erythroblast.…”

Section: Resultsmentioning

confidence: 99%

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TFII-I/Gtf2i and Erythro-Megakaryopoiesis

Gurumurthy

Nar

et al. 2020

Front. Physiol.

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TFII-I is a ubiquitously expressed transcription factor that positively or negatively regulates gene expression. TFII-I has been implicated in neuronal and immunologic diseases as well as in thymic epithelial cancer. Williams-Beuren Syndrome (WBS) is caused by a large hemizygous deletion on chromosome 7q11.23 which encompasses 26-28 genes, including GTF2I, the human gene encoding TFII-I. A subset of WBS patients has recently been shown to present with macrocytosis, a mild anemia characterized by enlarged erythrocytes. We conditionally deleted the TFII-I/Gtf2i gene in adult mice by tamoxifen induced Cre-recombination. Bone marrow cells revealed defects in erythro-megakaryopoiesis and an increase in expression of the adult β-globin gene. The data show that TFII-I acts as a repressor of β-globin gene transcription and that it is implicated in the differentiation of erythro-megakaryocytic cells.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

TFII-I/Gtf2i and Erythro-Megakaryopoiesis

Gurumurthy

Nar

et al. 2020

Front. Physiol.

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“…Another example of clustered homotypic TF binding sites associated with gene control is the binding of ZFP64 to the MLL gene promoter, activating the expression of the chromatin regulator MLL, although in this case ZFP64 shows a limited set of additional direct target genes 32 . CHD4 is an especially abundant nuclear protein in erythroid precursors 33 .…”

Section: Discussionmentioning

confidence: 99%

ZNF410 represses fetal globin by devoted control of CHD4/NuRD

Vinjamur¹,

Yao²,

Cole³

et al. 2020

Preprint

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Major effectors of adult-stage fetal globin silencing include the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to the γ-globin genes but rather its chromatin occupancy is solely concentrated at CHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for ZNF410’s effects on γ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. These studies identify a new rational target for HbF induction for the β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex.

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“…Thus, in principle DIA should offer a more comprehensive analysis of peptides and as a consequence could be more suitable for MS analysis of chromatin (domains). Finally, when specific chromatin factors or TFs are subject of study, selective reaction monitoring (SRM) can be used to specifically measure the abundance of tens to hundreds of pre-selected proteins over a wide range of abundances (72). Further research is required to optimise and implement these mass spectrometry data acquisition methods for low input chromatin proteomics studies, but important lessons can perhaps be learned from the emerging field of single-cell proteomics, which deals with extremely low amount of input sample (73).…”

Section: The Biochemical Challenges and Opportunitiesmentioning

confidence: 99%

Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

Mierlo

Vermeulen

2021

Molecular & Cellular Proteomics

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Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. Mass spectrometry-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analysed using mass spectrometry or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analysed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made towards identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared to conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease.

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Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis

Cited by 21 publications

References 82 publications

TFII-I/Gtf2i and Erythro-Megakaryopoiesis

TFII-I/Gtf2i and Erythro-Megakaryopoiesis

ZNF410 represses fetal globin by devoted control of CHD4/NuRD

Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

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