What do Transcription Factors Interact With?

Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces

(2021) Nitika Badjatia et al.   Cell Reports

A high-resolution protein architecture of the budding yeast genome

(2021) Matthew J. Rossi et al.   NATURE

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA

(2020) Rafal Donczew et al.   eLife

Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury

(2020) Julia Wilflingseder et al.   Nature Communications

Identification of the human DPR core promoter element using machine learning

(2020) Long Vo ngoc et al.   NATURE

Transcription imparts architecture, function and logic to enhancer units

(2020) Nathaniel D. Tippens et al.   NATURE GENETICS

Molecular determinants of MED1 interaction with the DNA bound VDR–RXR heterodimer

(2020) Anna Y Belorusova et al.   NUCLEIC ACIDS RESEARCH

Systematic interrogation of human promoters

(2019) Shira Weingarten-Gabbay et al.   GENOME RESEARCH

Twenty years of Mediator complex structural studies

(2019) Alexis Verger et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The RNA Polymerase II Core Promoter in Drosophila

(2019) Long Vo Ngoc et al.   GENETICS

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

Mediator complex interaction partners organize the transcriptional network that defines neural stem cells

(2019) Marti Quevedo et al.   Nature Communications

Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

(2019) Iris Steinparzer et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Multiple direct interactions of TBP with the MYC oncoprotein

(2019) Yong Wei et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TADs and Their Borders: Free Movement or Building a Wall?

(2019) Li-Hsin Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

Developing in 3D: the role of CTCF in cell differentiation

(2018) Rodrigo G. Arzate-Mejía et al.   DEVELOPMENT

Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock

(2018) Vinesh Vinayachandran et al.   GENOME RESEARCH

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Simplified ChIP-exo assays

(2018) Matthew J. Rossi et al.   Nature Communications

Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex

(2018) Lisa M. Tuttle et al.   Cell Reports

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

(2018) Ryan Raisner et al.   Cell Reports

Phase Separation, Protein Disorder, and Enhancer Function

(2018) Steven Hahn   CELL

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Transcription factor dimerization activates the p300 acetyltransferase

(2018) Esther Ortega et al.   NATURE

Structure of human TFIID and mechanism of TBP loading onto promoter DNA

(2018) Avinash B. Patel et al.   SCIENCE

Brd4’s Bromodomains Mediate Histone H3 Acetylation and Chromatin Remodeling in Pluripotent Cells through P300 and Brg1

(2018) Tao Wu et al.   Cell Reports

p53 Dynamically Directs TFIID Assembly on Target Gene Promoters

(2017) R. A. Coleman et al.   MOLECULAR AND CELLULAR BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4

(2016) Emi Hibino et al.   PROTEIN SCIENCE

Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development

(2016) Zhen Liu et al.   Nature Communications

Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics

(2016) Zachary C. Poss et al.   Cell Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

p53 modulates the activity of the GLI1 oncogene through interactions with the shared coactivator TAF9

(2015) Joon Won Yoon et al.   DNA REPAIR

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis

(2015) Petros Papadopoulos et al.   MOLECULAR AND CELLULAR BIOLOGY

Mediator kinase inhibition further activates super-enhancer-associated genes in AML

(2015) Henry E. Pelish et al.   NATURE

Architecture of the RNA polymerase II–Mediator core initiation complex

(2015) C. Plaschka et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The BET Family Member BRD4 Interacts with OCT4 and Regulates Pluripotency Gene Expression

(2015) Tao Wu et al.   Stem Cell Reports

MYC interacts with the human STAGA coactivator complex via multivalent contacts with the GCN5 and TRRAP subunits

(2014) Na Zhang et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

Liver Med23 ablation improves glucose and lipid metabolism through modulating FOXO1 activity

(2014) Yajing Chu et al.   CELL RESEARCH

Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module

(2014) Hui Wang et al.   CELL RESEARCH

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

(2014) Jennifer L. Plank et al.   MOLECULAR CELL

Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D

(2014) S. Bhattacharya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mediator subunit Med23 contributes to controlling T-cell activation and prevents autoimmunity

(2014) Yang Sun et al.   Nature Communications

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

(2014) Jason A. West et al.   Nature Communications

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

The Mediator complex and transcription regulation

(2013) Zachary C. Poss et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A TAF4 coactivator function for E proteins that involves enhanced TFIID binding

(2013) W.-Y. Chen et al.   GENES & DEVELOPMENT

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation

(2013) Madhanagopal Anandapadamanaban et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Signaling by Nuclear Receptors

(2013) R. Sever et al.   Cold Spring Harbor Perspectives in Biology

Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

(2012) J.-w. Yin et al.   GENES & DEVELOPMENT

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Selective requirement for Mediator MED23 in Ras-active lung cancer

(2012) X. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mediator and SAGA Have Distinct Roles in Pol II Preinitiation Complex Assembly and Function

(2012) Xiao-Fen Chen et al.   Cell Reports

Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation

(2011) A. M. Pilon et al.   BLOOD

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Oct4 links multiple epigenetic pathways to the pluripotency network

(2011) Junjun Ding et al.   CELL RESEARCH

The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex

(2011) Peter S. Brzovic et al.   MOLECULAR CELL

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between subunits of the Mediator complex with gene-specific transcription factors

(2011) Tilman Borggrefe et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases

(2010) David C. Bedford et al.   Epigenetics

Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription

(2010) Justin H. Layer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation

(2010) Gabor Papai et al.   NATURE

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains

(2009) Jonathan M Wojciak et al.   EMBO JOURNAL

Structures of three distinct activator-TFIID complexes

(2009) W.-L. Liu et al.   GENES & DEVELOPMENT

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Distinct modes of gene regulation by a cell-specific transcriptional activator

(2009) T. Sengupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multivalent Binding of p53 to the STAGA Complex Mediates Coactivator Recruitment after UV Damage

(2008) A. M. Gamper et al.   MOLECULAR AND CELLULAR BIOLOGY

Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation

(2007) Philippe Collas   Frontiers in Bioscience-Landmark