Reprogramming competence of OCT factors is determined by transactivation domains

OCT4 (also known as POU5F1) plays an essential role in reprogramming. It is the only member of the POU (Pit-Oct-Unc) family of transcription factors that can induce pluripotency despite sharing high structural similarities to all other members. Here, we discover that OCT6 (also known as POU3F1) can elicit reprogramming specifically in human cells. OCT6-based reprogramming does not alter the mesenchymal-epithelial transition but is attenuated through the delayed activation of the pluripotency network in comparison with OCT4-based reprogramming. Creating a series of reciprocal domain-swapped chimeras and mutants across all OCT factors, we clearly delineate essential elements of OCT4/OCT6-dependent reprogramming and, conversely, identify the features that prevent induction of pluripotency by other OCT factors. With this strategy, we further discover various chimeric proteins that are superior to OCT4 in reprogramming. Our findings clarify how reprogramming competences of OCT factors are conferred through their structural components.

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Biological importance of OCT transcription factors in reprogramming and development

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00637-4 ◽

2021 ◽

Author(s):

Kee-Pyo Kim ◽

Dong Wook Han ◽

Johnny Kim ◽

Hans R. Schöler

Keyword(s):

Stem Cells ◽

Transcription Factors ◽

Induced Pluripotent Stem Cells ◽

Pluripotent Stem Cells ◽

Ectopic Expression ◽

Donor Cell ◽

Structural Components ◽

Oct4 Expression ◽

Reprogramming Factors ◽

Induced Pluripotent

AbstractEctopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Attempts to identify genes or chemicals that can functionally replace each of these four reprogramming factors have revealed that exogenous Oct4 is not necessary for reprogramming under certain conditions or in the presence of alternative factors that can regulate endogenous Oct4 expression. For example, polycistronic expression of Sox2, Klf4 and c-Myc can elicit reprogramming by activating endogenous Oct4 expression indirectly. Experiments in which the reprogramming competence of all other Oct family members tested and also in different species have led to the decisive conclusion that Oct proteins display different reprogramming competences and species-dependent reprogramming activity despite their profound sequence conservation. We discuss the roles of the structural components of Oct proteins in reprogramming and how donor cell epigenomes endow Oct proteins with different reprogramming competences.

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DOT1L Complex Regulates Transcriptional Initiation 1 in Human Cells

10.1101/2020.12.07.414722 ◽

2020 ◽

Author(s):

Ming Yu ◽

Robert Roeder ◽

Aiwei Wu ◽

Junhong Zhi ◽

Tian Tian ◽

...

Keyword(s):

Transcription Factors ◽

Elongation Factor ◽

Elongation Rate ◽

Human Cells ◽

Mixed Lineage Leukemia ◽

Transcriptional Elongation ◽

Saga Complex ◽

Transcriptional Initiation ◽

Pol Ii ◽

General Transcription Factors

DOT1L, the only H3K79 methyltransferase in human cells and a homolog of the yeast Dot1, normally forms a complex with AF10, AF17 and ENL/AF9, is dysregulated in most of the cases of mixed lineage leukemia (MLL) and is believed to regulate transcriptional elongation without much evidence. Here we show that DOT1L depletion reduced the global occupancy without affecting the traveling ratio or the elongation rate of Pol II, suggesting it not a major elongation factor. An examination of general transcription factors binding revealed globally reduced TBP and TFIIA occupancies near promoters after DOT1L loss, pointing to a role in transcriptional initiation. Proteomic studies uncovered that DOT1L regulates transcriptional initiation likely by facilitating the recruitment of TFIID. Moreover, ENL, a DOT1L complex subunit with a known role in DOT1L recruitment, also regulates transcriptional initiation. Furthermore, DOT1L stimulates H2B monoubiquitination by limiting the recruitment of human SAGA complex, and the connection between Dot1/DOT1L and SAGA complex is conserved between yeast and human. These results advanced current understanding of roles of DOT1L complex in transcriptional regulation and MLL.

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KLF4 Induces Mesenchymal–Epithelial Transition (MET) by Suppressing Multiple EMT-Inducing Transcription Factors

Cancers ◽

10.3390/cancers13205135 ◽

2021 ◽

Vol 13 (20) ◽

pp. 5135

Author(s):

Ayalur Raghu Subbalakshmi ◽

Sarthak Sahoo ◽

Isabelle McMullen ◽

Aaditya Narayan Saxena ◽

Sudhanva Kalasapura Venugopal ◽

...

Keyword(s):

Transcription Factors ◽

Patient Survival ◽

Dynamic Processes ◽

State Transitions ◽

Specific Manner ◽

Context Specific ◽

Phenotypic Shift ◽

Acting In Concert ◽

Epithelial State ◽

Mesenchymal Epithelial Transition

Epithelial–Mesenchymal Plasticity (EMP) refers to reversible dynamic processes where cells can transition from epithelial to mesenchymal (EMT) or from mesenchymal to epithelial (MET) phenotypes. Both these processes are modulated by multiple transcription factors acting in concert. While EMT-inducing transcription factors (TFs)—TWIST1/2, ZEB1/2, SNAIL1/2/3, GSC, and FOXC2—are well-characterized, the MET-inducing TFs are relatively poorly understood (OVOL1/2 and GRHL1/2). Here, using mechanism-based mathematical modeling, we show that transcription factor KLF4 can delay the onset of EMT by suppressing multiple EMT-TFs. Our simulations suggest that KLF4 overexpression can promote a phenotypic shift toward a more epithelial state, an observation suggested by the negative correlation of KLF4 with EMT-TFs and with transcriptomic-based EMT scoring metrics in cancer cell lines. We also show that the influence of KLF4 in modulating the EMT dynamics can be strengthened by its ability to inhibit cell-state transitions at the epigenetic level. Thus, KLF4 can inhibit EMT through multiple parallel paths and can act as a putative MET-TF. KLF4 associates with the patient survival metrics across multiple cancers in a context-specific manner, highlighting the complex association of EMP with patient survival.

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Sequence and functional characterization of hypoxia-inducible factors, HIF1α, HIF2αa, and HIF3α, from the estuarine fish, Fundulus heteroclitus

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00402.2016 ◽

2017 ◽

Vol 312 (3) ◽

pp. R412-R425 ◽

Cited By ~ 7

Author(s):

Ian K. Townley ◽

Sibel I. Karchner ◽

Elena Skripnikova ◽

Thomas E. Wiese ◽

Mark E. Hahn ◽

...

Keyword(s):

Transcription Factors ◽

Fundulus Heteroclitus ◽

Phylogenetic Analyses ◽

Functional Characterization ◽

Hypoxia Inducible Factor ◽

Estuarine Fish ◽

Low Oxygen ◽

Aryl Hydrocarbon ◽

Transactivation Domains

The hypoxia-inducible factor (HIF) family of transcription factors plays central roles in the development, physiology, pathology, and environmental adaptation of animals. Because many aquatic habitats are characterized by episodes of low dissolved oxygen, fish represent ideal models to study the roles of HIF in the response to aquatic hypoxia. The estuarine fish Fundulus heteroclitus is found in habitats prone to hypoxia. It responds to low oxygen via behavioral, physiological, and molecular changes, and one member of the HIF family, HIF2α, has been previously described. Herein, cDNA sequencing, phylogenetic analyses, and genomic approaches were used to determine other members of the HIFα family from F. heteroclitus and their relationships to HIFα subunits from other vertebrates. In vitro and cellular approaches demonstrated that full-length forms of HIF1α, HIF2α, and HIF3α independently formed complexes with the β-subunit, aryl hydrocarbon receptor nuclear translocator, to bind to hypoxia response elements and activate reporter gene expression. Quantitative PCR showed that HIFα mRNA abundance varied among organs of normoxic fish in an isoform-specific fashion. Analysis of the F. heteroclitus genome revealed a locus encoding a second HIF2α—HIF2αb—a predicted protein lacking oxygen sensing and transactivation domains. Finally, sequence analyses demonstrated polymorphism in the coding sequence of each F. heteroclitus HIFα subunit, suggesting that genetic variation in these transcription factors may play a role in the variation in hypoxia responses among individuals or populations.

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Differential Contribution of N- and C-Terminal Regions of HIF1α and HIF2α to Their Target Gene Selectivity

International Journal of Molecular Sciences ◽

10.3390/ijms21249401 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9401

Author(s):

Antonio Bouthelier ◽

Florinda Meléndez-Rodríguez ◽

Andrés A. Urrutia ◽

Julián Aragonés

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Cellular Response ◽

Target Gene ◽

Target Genes ◽

Transactivation Domain ◽

Transactivation Domains ◽

Relative Contribution

Cellular response to hypoxia is controlled by the hypoxia-inducible transcription factors HIF1α and HIF2α. Some genes are preferentially induced by HIF1α or HIF2α, as has been explored in some cell models and for particular sets of genes. Here we have extended this analysis to other HIF-dependent genes using in vitro WT8 renal carcinoma cells and in vivo conditional Vhl-deficient mice models. Moreover, we generated chimeric HIF1/2 transcription factors to study the contribution of the HIF1α and HIF2α DNA binding/heterodimerization and transactivation domains to HIF target specificity. We show that the induction of HIF1α-dependent genes in WT8 cells, such as CAIX (CAR9) and BNIP3, requires both halves of HIF, whereas the HIF2α transactivation domain is more relevant for the induction of HIF2 target genes like the amino acid carrier SLC7A5. The HIF selectivity for some genes in WT8 cells is conserved in Vhl-deficient lung and liver tissue, whereas other genes like Glut1 (Slc2a1) behave distinctly in these tissues. Therefore the relative contribution of the DNA binding/heterodimerization and transactivation domains for HIF target selectivity can be different when comparing HIF1α or HIF2α isoforms, and that HIF target gene specificity is conserved in human and mouse cells for some of the genes analyzed.

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TNF-inducible expression of lymphotoxin-β in hepatic cells: An essential role for NF-κB and Ets1 transcription factors

Cytokine ◽

10.1016/j.cyto.2012.05.029 ◽

2012 ◽

Vol 60 (2) ◽

pp. 498-504 ◽

Cited By ~ 4

Author(s):

Lily S. Subrata ◽

Dominic C. Voon ◽

George C.T. Yeoh ◽

Daniela Ulgiati ◽

Elizabeth A. Quail ◽

...

Keyword(s):

Transcription Factors ◽

Essential Role ◽

Inducible Expression ◽

Hepatic Cells

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Broadly Applicable Methodology for the Rapid and Dosable Small Molecule-Mediated Regulation of Transcription Factors in Human Cells

Journal of the American Chemical Society ◽

10.1021/ja402756p ◽

2013 ◽

Vol 135 (22) ◽

pp. 8129-8132 ◽

Cited By ~ 30

Author(s):

Matthew D. Shoulders ◽

Lisa M. Ryno ◽

Christina B. Cooley ◽

Jeffery W. Kelly ◽

R. Luke Wiseman

Keyword(s):

Transcription Factors ◽

Small Molecule ◽

Human Cells ◽

Regulation Of Transcription

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Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Genome Research ◽

10.1101/gr.127597.111 ◽

2011 ◽

Vol 22 (1) ◽

pp. 9-24 ◽

Cited By ~ 77

Author(s):

B.-K. Lee ◽

A. A. Bhinge ◽

A. Battenhouse ◽

R. M. McDaniell ◽

Z. Liu ◽

...

Keyword(s):

Transcription Factors ◽

Human Cells ◽

Cell Type ◽

Binding Studies ◽

Genome Wide ◽

Cell Type Specific

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Probing Target Search Mechanisms of Transcription Factors in Human Cells

Biophysical Journal ◽

10.1016/j.bpj.2010.12.550 ◽

2011 ◽

Vol 100 (3) ◽

pp. 64a

Author(s):

Davide Normanno ◽

Lydia Boudarene ◽

Claire Dugast-Darzacq ◽

Xavier Darzacq ◽

Maxime Dahan

Keyword(s):

Transcription Factors ◽

Human Cells ◽

Target Search

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TGF-β-activated Kinase 1 (TAK1) and Apoptosis Signal-regulating Kinase 1 (ASK1) Interact with the Promyogenic Receptor Cdo to Promote Myogenic Differentiation via Activation of p38MAPK Pathway

Journal of Biological Chemistry ◽

10.1074/jbc.m112.351601 ◽

2012 ◽

Vol 287 (15) ◽

pp. 11602-11615 ◽

Cited By ~ 25

Author(s):

Phong Tran ◽

Seok-Man Ho ◽

Bok-Geon Kim ◽

Tuan Anh Vuong ◽

Young-Eun Leem ◽

...

Keyword(s):

Transcription Factors ◽

Essential Role ◽

Myogenic Differentiation ◽

C2c12 Cells ◽

Myoblast Differentiation ◽

Surface Molecule ◽

Cell Surface Molecule ◽

Cell Systems ◽

Myotube Formation ◽

P38mapk Pathway

p38MAPK plays an essential role in the transition of myoblasts to differentiated myotubes through the activation of MyoD family transcription factors. A promyogenic cell surface molecule, Cdo, promotes myogenic differentiation mainly through activation of the p38MAPK pathway. Two MAP3Ks, TAK1 and ASK1, can activate p38MAPK via MKK6 in various cell systems. Moreover TAK1 has been shown to promote myogenic differentiation via p38MAPK activation. In this study, we hypothesized that TAK1 and ASK1 might function as MAP3Ks in Cdo-mediated p38MAPK activation during myoblast differentiation. Both ASK1 and TAK1 were expressed in myoblasts and interacted with the cytoplasmic tail of Cdo and a scaffold protein, JLP. The depletion of TAK1 or ASK1 in C2C12 cells decreased myoblast differentiation, whereas overexpression of TAK1 or ASK1 in C2C12 cells enhanced myotube formation. In agreement with this, overexpression of ASK1 or TAK1 resulted in enhanced p38MAPK activation, and their knockdown inhibited p38MAPK in C2C12 cells. Overexpression of TAK1 or ASK1 in Cdo−/− myoblasts and Cdo-depleted C2C12 cells restored p38MAPK activation as well as myotube formation. Furthermore, ASK1 and TAK1 compensated for each other in p38MAPK activation and myoblast differentiation. Taken together, these findings suggest that ASK1 and TAK1 function as MAP3Ks in Cdo-mediated p38MAPK activation to promote myogenic differentiation.

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