Collaboration through chromatin: motors of transcription and chromatin structure

RNA polymerase I (Pol I) passage through nucleosomes depends on Pol I subunits binding its lobe structure

(2020) Philipp E. Merkl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing

(2020) Yan Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

(2020) Anand Ranjan et al.   eLife

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms

(2020) Nazar Mashtalir et al.   CELL

Enzymatic Reactions inside Biological Condensates

(2020) Yi Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers

(2020) Jun Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability

(2020) Lisa Prendergast et al.   Nature Communications

The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

(2020) A Elizabeth Hildreth et al.   eLife

Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation

(2020) Saurabh K. Bhardwaj et al.   Nature Communications

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

(2019) Haruhiko Ehara et al.   SCIENCE

Mechanism of DNA translocation underlying chromatin remodelling by Snf2

(2019) Meijing Li et al.   NATURE

Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

(2019) Josefina Ocampo et al.   GENOME RESEARCH

Transcription initiation factor TBP: old friend new questions

(2019) Kevin Kramm et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Dynamic chromatin organization without the 30-nm fiber

(2019) Kazuhiro Maeshima et al.   CURRENT OPINION IN CELL BIOLOGY

The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo

(2019) Christine E Cucinotta et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

(2019) Jean Paul Armache et al.   eLife

Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

(2019) Sangjin Kim et al.   CELL

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

(2019) Razvan V Chereji et al.   GENOME RESEARCH

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

FACT caught in the act of manipulating the nucleosome

(2019) Yang Liu et al.   NATURE

Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family

(2019) Manu Shubhdarshan Shukla et al.   Scientific Reports

A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing

(2019) Hai T. Dao et al.   Nature Chemical Biology

Transcription through the nucleosome

(2019) Tomoya Kujirai et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3′ end processing

(2018) Simei Yu et al.   NUCLEIC ACIDS RESEARCH

The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome

(2018) Joshua M Tokuda et al.   NUCLEIC ACIDS RESEARCH

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

(2018) Giovanni B Brandani et al.   NUCLEIC ACIDS RESEARCH

Structural rearrangements of the histone octamer translocate DNA

(2018) Silvija Bilokapic et al.   Nature Communications

The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h

(2018) Nathan Gamarra et al.   eLife

A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA

(2018) Jessica Winger et al.   eLife

Molecular mechanism of promoter opening by RNA polymerase III

(2018) Matthias K. Vorländer et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

(2018) Peter R Cook et al.   NUCLEIC ACIDS RESEARCH

Dissociation of Rpb4 from RNA polymerase II is important for yeast functionality

(2018) Lea Duek et al.   PLoS One

Intracellular nucleosomes constrain a DNA linking number difference of −1.26 that reconciles the Lk paradox

(2018) Joana Segura et al.   Nature Communications

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

(2018) Ramasubramanian Sundaramoorthy et al.   eLife

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

(2018) Sandipan Brahma et al.   MOLECULAR CELL

Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast

(2018) Gunjan D. Mehta et al.   MOLECULAR CELL

Nucleosome structure and dynamics are coming of age

(2018) Keda Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of the nucleosome transition during RNA polymerase II passage

(2018) Tomoya Kujirai et al.   SCIENCE

Structure and dynamics of the yeast SWR1-nucleosome complex

(2018) Oliver Willhoft et al.   SCIENCE

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates

(2017) Srinivas Ramachandran et al.   MOLECULAR CELL

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

(2017) Răzvan V. Chereji et al.   MOLECULAR CELL

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair

(2017) Jun Xu et al.   NATURE

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure

(2017) Xiaoyu Liu et al.   NATURE

Nucleosome–Chd1 structure and implications for chromatin remodelling

(2017) Lucas Farnung et al.   NATURE

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

(2017) Geoffrey P. Dann et al.   NATURE

Histone octamer rearranges to adapt to DNA unwrapping

(2017) Silvija Bilokapic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome

(2017) John B. Crickard et al.   NUCLEIC ACIDS RESEARCH

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

(2017) Kalyan K. Sinha et al.   SCIENCE

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

(2017) Sandipan Brahma et al.   Nature Communications

Histone octamer rearranges to adapt to DNA unwrapping

(2017) Silvija Bilokapic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones

(2017) Coral Y. Zhou et al.   Cell Reports

Crosstalk within a functional INO80 complex dimer regulates nucleosome sliding

(2017) Oliver Willhoft et al.   eLife

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

(2016) Coral Y. Zhou et al.   Annual Review of Biophysics

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

Recognition of the nucleosome by chromatin factors and enzymes

(2016) Robert K McGinty et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome-wide uniformity of human ‘open’ pre-initiation complexes

(2016) William K.M. Lai et al.   GENOME RESEARCH

Structure and regulation of the chromatin remodeller ISWI

(2016) Lijuan Yan et al.   NATURE

Structure of chromatin remodeler Swi2/Snf2 in the resting state

(2016) Xian Xia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms of backtrack recovery by RNA polymerases I and II

(2016) Ana Lisica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme"

(2016) F. Wang et al.   SCIENCE

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes

(2016) Sergei Rudnizky et al.   Nature Communications

Structure of chromatin remodeler Swi2/Snf2 in the resting state

(2016) Xian Xia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

(2016) Zhenhai Li et al.   Scientific Reports

Stepwise nucleosome translocation by RSC remodeling complexes

(2016) Bryan T Harada et al.   eLife

The Chd1 chromatin remodeler shifts hexasomes unidirectionally

(2016) Robert F Levendosky et al.   eLife

Dynamic enhancer–gene body contacts during transcription elongation

(2015) Kiwon Lee et al.   GENES & DEVELOPMENT

A Nucleotide-Driven Switch Regulates Flanking DNA Length Sensing by a Dimeric Chromatin Remodeler

(2015) John D. Leonard et al.   MOLECULAR CELL

INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation

(2015) Anne Lafon et al.   MOLECULAR CELL

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility inDrosophila melanogaster

(2015) Răzvan V. Chereji et al.   NUCLEIC ACIDS RESEARCH

H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast

(2015) Anand Ranjan et al.   eLife

Dynamic regulation of transcription factors by nucleosome remodeling

(2015) Ming Li et al.   eLife

Structure of transcribed chromatin is a sensor of DNA damage

(2015) N. A. Pestov et al.   Science Advances

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Nucleosome Structure and Function

(2014) Robert K. McGinty et al.   CHEMICAL REVIEWS

A method for evaluating nucleosome stability with a protein-binding fluorescent dye

(2014) Hiroyuki Taguchi et al.   METHODS

Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA

(2014) William L. Hwang et al.   NATURE

Histone variants at the transcription start-site

(2014) Tatiana A. Soboleva et al.   TRENDS IN GENETICS

The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

(2014) Peter J Skene et al.   eLife

A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes

(2013) Yatendra Kumar et al.   BMC GENOMICS

ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps

(2013) Sebastian Deindl et al.   CELL

Nucleosome-free Region Dominates Histone Acetylation in Targeting SWR1 to Promoters for H2A.Z Replacement

(2013) Anand Ranjan et al.   CELL

SWR-C and INO80 Chromatin Remodelers Recognize Nucleosome-free Regions Near +1 Nucleosomes

(2013) Kuangyu Yen et al.   CELL

The NuRD architecture

(2013) Hillary F. Allen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Quantitative Proteomics Demonstrates That the RNA Polymerase II Subunits Rpb4 and Rpb7 Dissociate during Transcriptional Elongation

(2013) Amber L. Mosley et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone chaperone FACT action during transcription through chromatin by RNA polymerase II

(2013) F.-K. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

(2013) Maxim Y. Sheinin et al.   Nature Communications

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

(2013) Manchuta Dangkulwanich et al.   eLife

Structural Analysis of the Hexasome, Lacking One Histone H2A/H2B Dimer from the Conventional Nucleosome

(2012) Yasuhiro Arimura et al.   BIOCHEMISTRY

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

CHD1 remodelers regulate nucleosome spacingin vitroand align nucleosomal arrays over gene coding regions inS. pombe

(2012) Julia Pointner et al.   EMBO JOURNAL

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

(2012) Bianca P Hennig et al.   EMBO REPORTS

Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1

(2012) J.-S. Lee et al.   GENES & DEVELOPMENT

Histone ADP-Ribosylation Facilitates Gene Transcription by Directly Remodeling Nucleosomes

(2012) R. Martinez-Zamudio et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes

(2012) Cedric R. Clapier et al.   NATURE

Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro

(2012) B. G. Kuryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Regulation of H2A.Z Localization by the INO80 Chromatin-Remodeling Enzyme Is Essential for Genome Integrity

(2011) Manolis Papamichos-Chronakis et al.   CELL

Evolution of Two Modes of Intrinsic RNA Polymerase Transcript Cleavage

(2011) Wenjie Ruan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1

(2011) J. N. McKnight et al.   MOLECULAR AND CELLULAR BIOLOGY

Structure and mechanism of the chromatin remodelling factor ISW1a

(2011) Kazuhiro Yamada et al.   NATURE

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

(2011) Lacramioara Bintu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation

(2011) Daria A. Gaykalova et al.   NUCLEIC ACIDS RESEARCH

Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome

(2010) Ed Luk et al.   CELL

Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II

(2010) Fu-Kai Hsieh et al.   EMBO REPORTS

SWI/SNF Has Intrinsic Nucleosome Disassembly Activity that Is Dependent on Adjacent Nucleosomes

(2010) Mekonnen Lemma Dechassa et al.   MOLECULAR CELL

The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor

(2010) Glenn Hauk et al.   MOLECULAR CELL

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

(2010) Jing Jin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome accessibility governed by the dimer/tetramer interface

(2010) Vera Böhm et al.   NUCLEIC ACIDS RESEARCH

Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer

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

RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones

(2010) O. I. Kulaeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Insight into the Sequence Dependence of Nucleosome Positioning

(2010) Bin Wu et al.   STRUCTURE

Active RNA Polymerases: Mobile or Immobile Molecular Machines?

(2010) Argyris Papantonis et al.   PLOS BIOLOGY

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

FACT facilitates chromatin transcription by RNA polymerases I and III

(2009) Joanna L Birch et al.   EMBO JOURNAL

Histone Chaperone Spt16 Promotes Redeposition of the Original H3-H4 Histones Evicted by Elongating RNA Polymerase

(2009) Adil Jamai et al.   MOLECULAR CELL

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes

(2009) Lisa R. Racki et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

(2009) Olga I Kulaeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Structure of Eukaryotic RNA Polymerases

(2008) P. Cramer et al.   Annual Review of Biophysics

Histone N-terminal Tails Interfere with Nucleosome Traversal by RNA Polymerase II

(2008) Andrea Újvári et al.   JOURNAL OF BIOLOGICAL CHEMISTRY