The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors

Helix–loop–helix proteins and the advent of cellular diversity: 30 years of discovery

(2019) Cornelis Murre   GENES & DEVELOPMENT

MYC2 Regulates the Termination of Jasmonate Signaling via an Autoregulatory Negative Feedback Loop

(2019) Yuanyuan Liu et al.   PLANT CELL

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

(2019) Marti Quevedo et al.   Nature Communications

PhaSePro: the database of proteins driving liquid–liquid phase separation

(2019) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Mapping Hidden Residual Structure within the Myc bHLH-LZ Domain Using Chemical Denaturant Titration

(2019) Stanislava Panova et al.   STRUCTURE

Transcription Activation Domains of the Yeast Factors Met4 and Ino2: Tandem Activation Domains with Properties Similar to the Yeast Gcn4 Activator

(2018) Derek Pacheco et al.   MOLECULAR AND CELLULAR BIOLOGY

The Arabidopsis thaliana Mediator subunit MED8 regulates plant immunity to Botrytis Cinerea through interacting with the basic helix-loop-helix (bHLH) transcription factor FAMA

(2018) Xiaohui Li et al.   PLoS One

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Oncogenic transcriptional program driven by TAL1 in T-cell acute lymphoblastic leukemia

(2018) Tze King Tan et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

(2018) Jonathon A. Ditlev et al.   JOURNAL OF MOLECULAR BIOLOGY

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Kinase-controlled phase transition of membraneless organelles in mitosis

(2018) Arpan Kumar Rai et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

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

(2018) Ann Boija et al.   CELL

Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin

(2017) Chunpeng An et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically Disordered Proteome of Human Membrane-Less Organelles

(2017) April L. Darling et al.   PROTEOMICS

Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body

(2017) Robert J. Duronio et al.   RNA Biology

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Temporal regulation of chromatin during myoblast differentiation

(2017) Akihito Harada et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain

(2017) Bede Portz et al.   Nature Communications

VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

(2017) Xiaosai Yao et al.   Cancer Discovery

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

Targeted Disruption of TCF12 Reveals HEB as Essential in Human Mesodermal Specification and Hematopoiesis

(2017) Yang Li et al.   Stem Cell Reports

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Phase separation in biology; functional organization of a higher order

(2016) Diana M. Mitrea et al.   Cell Communication and Signaling

Molecular functions of the transcription factors E2A and E2-2 in controlling germinal center B cell and plasma cell development

(2016) Miriam Wöhner et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Deciphering the molecular mechanisms underlying the binding of the TWIST1/E12 complex to regulatory E-box sequences

(2016) Charlotte Bouard et al.   NUCLEIC ACIDS RESEARCH

Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression

(2016) Tusar T. Saha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tcf12, A Member of Basic Helix-Loop-Helix Transcription Factors, Mediates Bone Marrow Mesenchymal Stem Cell Osteogenic Differentiation In Vitro and In Vivo

(2016) Siqi Yi et al.   STEM CELLS

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

(2016) Diana M Mitrea et al.   eLife

Inhibitor of differentiation 4 (ID4) acts as an inhibitor of ID-1, -2 and -3 and promotes basic helix loop helix (bHLH) E47 DNA binding and transcriptional activity

(2015) Pankaj Sharma et al.   BIOCHIMIE

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

Inverse Size Scaling of the Nucleolus by a Concentration-Dependent Phase Transition

(2015) Stephanie C. Weber et al.   CURRENT BIOLOGY

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA transcription modulates phase transition-driven nuclear body assembly

(2015) Joel Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

(2015) Alexandre A.S.F. Raposo et al.   Cell Reports

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Phosphorylation in intrinsically disordered regions regulates the activity of Neurogenin2

(2014) Gary S McDowell et al.   BMC BIOCHEMISTRY

Transcription factor 4 (TCF4) and schizophrenia: integrating the animal and the human perspective

(2014) Boris B. Quednow et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

(2014) Zhenling Peng et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

The Quantitative Nuclear Matrix Proteome as a Biochemical Snapshot of Nuclear Organization

(2014) Rudolf Engelke et al.   JOURNAL OF PROTEOME RESEARCH

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

The DynaMine webserver: predicting protein dynamics from sequence

(2014) Elisa Cilia et al.   NUCLEIC ACIDS RESEARCH

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling

(2013) Frank Wippich et al.   CELL

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

Mechanisms of Mediator complex action in transcriptional activation

(2013) Suraiya A. Ansari et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Mediator complex and transcription regulation

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

A decade and a half of protein intrinsic disorder: Biology still waits for physics

(2013) Vladimir N. Uversky   PROTEIN SCIENCE

From protein sequence to dynamics and disorder with DynaMine

(2013) Elisa Cilia et al.   Nature Communications

Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites

(2012) Joshua K Sailsbery et al.   BMC EVOLUTIONARY BIOLOGY

Hypoxia-Inducible Factors in Physiology and Medicine

(2012) Gregg L. Semenza   CELL

The Arabidopsis Mediator Subunit MED25 Differentially Regulates Jasmonate and Abscisic Acid Signaling through Interacting with the MYC2 and ABI5 Transcription Factors

(2012) R. Chen et al.   PLANT CELL

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity

(2012) J. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors

(2012) Julia Heisig et al.   PLoS Genetics

Function and regulation of the Mediator complex

(2011) Ronald C Conaway et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Phylogenetic Analysis and Classification of the Fungal bHLH Domain

(2011) J. K. Sailsbery et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Basic Helix−Loop−Helix Region of Human Neurogenin 1 Is a Monomeric Natively Unfolded Protein Which Forms a “Fuzzy” Complex upon DNA Binding

(2010) David Aguado-Llera et al.   BIOCHEMISTRY

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

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

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature

(2010) Michael K. Skinner et al.   DIFFERENTIATION

Coactivation of the CLOCK-BMAL1 complex by CBP mediates resetting of the circadian clock

(2010) Y. Lee et al.   JOURNAL OF CELL SCIENCE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Heterodimer of two bHLH-PAS proteins mediates juvenile hormone-induced gene expression

(2010) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Analysis of Zebrafish Basic Helix-Loop-Helix Transcription Factors

(2009) Yong Wang et al.   JOURNAL OF MOLECULAR EVOLUTION

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

(2009) N. Pires et al.   MOLECULAR BIOLOGY AND EVOLUTION

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

Structure and Signaling Mechanism of Per-ARNT-Sim Domains

(2009) Andreas Möglich et al.   STRUCTURE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Differential nuclear scaffold/matrix attachment marks expressed genes†

(2008) Amelia K. Linnemann et al.   HUMAN MOLECULAR GENETICS

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

(2008) Andrew Campen et al.   PROTEIN AND PEPTIDE LETTERS

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

(2007) Peter Tompa et al.   TRENDS IN BIOCHEMICAL SCIENCES