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Steven Henikoff

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https://www.readbyqxmd.com/read/27797823/mediator-binding-to-uass-is-broadly-uncoupled-from-transcription-and-cooperative-with-tfiid-recruitment-to-promoters
#1
Sebastian Grünberg, Steven Henikoff, Steven Hahn, Gabriel E Zentner
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes...
November 15, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27503998/mechanisms-of-nucleosome-dynamics-in-vivo
#2
REVIEW
Steven Henikoff
Nucleosomes function to tightly package DNA into chromosomes, but the nucleosomal landscape becomes disrupted during active processes such as replication, transcription, and repair. The realization that many proteins responsible for chromatin regulation are frequently mutated in cancer has drawn attention to chromatin dynamics; however, the basic mechanisms whereby nucleosomes are disrupted and reassembled is incompletely understood. Here, I present an overview of chromatin dynamics as has been elucidated in model organisms, in which our understanding is most advanced...
2016: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/27458904/epigenetics-cellular-memory-and-gene-regulation
#3
Steven Henikoff, John M Greally
The field described as 'epigenetics' has captured the imagination of scientists and the lay public. Advances in our understanding of chromatin and gene regulatory mechanisms have had impact on drug development, fueling excitement in the lay public about the prospects of applying this knowledge to address health issues. However, when describing these scientific advances as 'epigenetic', we encounter the problem that this term means different things to different people, starting within the scientific community and amplified in the popular press...
July 25, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27384170/cenpt-bridges-adjacent-cenpa-nucleosomes-on-young-human-%C3%AE-satellite-dimers
#4
Jitendra Thakur, Steven Henikoff
Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. Two components of the CCAN, CENPC and the histone-fold protein CENPT, provide independent connections from the ∼171-bp centromeric α-satellite repeat units to the outer kinetochore. However, the spatial relationship between CENPA nucleosomes and these two branches remains unclear...
September 2016: Genome Research
https://www.readbyqxmd.com/read/27062929/transcriptional-regulators-compete-with-nucleosomes-post-replication
#5
Srinivas Ramachandran, Steven Henikoff
Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, we have developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. We find that the characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication...
April 21, 2016: Cell
https://www.readbyqxmd.com/read/26933790/nucleosome-dynamics-during-chromatin-remodeling-in-vivo
#6
Srinivas Ramachandran, Steven Henikoff
Precise positioning of nucleosomes around regulatory sites is achieved by the action of chromatin remodelers, which use the energy of ATP to slide, evict or change the composition of nucleosomes. Chromatin remodelers act to bind nucleosomes, disrupt histone-DNA interactions and translocate the DNA around the histone core to reposition nucleosomes. Hence, remodeling is expected to involve nucleosomal intermediates with a structural organization that is distinct from intact nucleosomes. We describe the identification of a partially unwrapped nucleosome structure using methods that map histone-DNA contacts genome-wide...
2016: Nucleus
https://www.readbyqxmd.com/read/26877204/evolutionary-turnover-of-kinetochore-proteins-a-ship-of-theseus
#7
REVIEW
Ines A Drinnenberg, Steven Henikoff, Harmit S Malik
The kinetochore is a multiprotein complex that mediates the attachment of a eukaryotic chromosome to the mitotic spindle. The protein composition of kinetochores is similar across species as divergent as yeast and human. However, recent findings have revealed an unexpected degree of compositional diversity in kinetochores. For example, kinetochore proteins that are essential in some species have been lost in others, whereas new kinetochore proteins have emerged in other lineages. Even in lineages with similar kinetochore composition, individual kinetochore proteins have functionally diverged to acquire either essential or redundant roles...
July 2016: Trends in Cell Biology
https://www.readbyqxmd.com/read/26669278/corrigendum-chec-seq-kinetics-discriminates-transcription-factor-binding-sites-by-dna-sequence-and-shape-in-vivo
#8
Gabriel E Zentner, Sivakanthan Kasinathan, Beibei Xin, Remo Rohs, Steven Henikoff
No abstract text is available yet for this article.
2015: Nature Communications
https://www.readbyqxmd.com/read/26490019/chec-seq-kinetics-discriminates-transcription-factor-binding-sites-by-dna-sequence-and-shape-in-vivo
#9
Gabriel E Zentner, Sivakanthan Kasinathan, Beibei Xin, Remo Rohs, Steven Henikoff
Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to map budding yeast transcription factor (TF) binding. Temporal analysis of ChEC-seq data reveals two classes of sites for TFs, one displaying rapid cleavage at sites with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs...
October 22, 2015: Nature Communications
https://www.readbyqxmd.com/read/26275423/inner-kinetochore-protein-interactions-with-regional-centromeres-of-fission-yeast
#10
Jitendra Thakur, Paul B Talbert, Steven Henikoff
Centromeres of the fission yeast Schizosaccharomyces pombe lack the highly repetitive sequences that make most other "regional" centromeres refractory to analysis. To map fission yeast centromeres, we applied H4S47C-anchored cleavage mapping and native and cross-linked chromatin immunoprecipitation with paired-end sequencing. H3 nucleosomes are nearly absent from the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle that are mostly unpositioned and are more widely spaced than nucleosomes elsewhere...
October 2015: Genetics
https://www.readbyqxmd.com/read/26269799/replicating-nucleosomes
#11
Srinivas Ramachandran, Steven Henikoff
Eukaryotic replication disrupts each nucleosome as the fork passes, followed by re-assembly of disrupted nucleosomes and incorporation of newly synthesized histones into nucleosomes in the daughter genomes. In this review, we examine this process of replication-coupled nucleosome assembly to understand how characteristic steady state nucleosome landscapes are attained. Recent studies have begun to elucidate mechanisms involved in histone transfer during replication and maturation of the nucleosome landscape after disruption by replication...
August 7, 2015: Science Advances
https://www.readbyqxmd.com/read/26170439/the-genetic-map-enters-its-second-century
#12
Steven Henikoff
The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the past 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics and exemplify the ingenuity of GSA members. The 2015 recipient is Steven Henikoff, whose achievements include major contributions to Drosophila genetics and epigenetics, Arabidopsis genetics and epigenetics, population and evolutionary genetics, genomic technologies, computational biology, and transcription and chromatin biology...
July 2015: Genetics
https://www.readbyqxmd.com/read/26087157/epigenomic-landscapes-reflect-neuronal-diversity
#13
COMMENT
Steven Henikoff
Epigenomic profiling of complex tissues obscures regulatory elements that distinguish one cell type from another. In this issue of Neuron, Mo et al. (2015) apply cell-type-specific profiling to mouse neuronal subtypes and discover an unprecedented level of neuronal diversity.
June 17, 2015: Neuron
https://www.readbyqxmd.com/read/26079792/a-simple-method-for-generating-high-resolution-maps-of-genome-wide-protein-binding
#14
COMPARATIVE STUDY
Peter J Skene, Steven Henikoff
Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require significant experimental alterations and complex bioinformatics. Previously, we have used a new crosslinking ChIP-seq protocol (X-ChIP-seq) to perform high-resolution mapping of RNA Polymerase II (Skene et al., 2014). Here, we build upon this work and compare X-ChIP-seq to existing methodologies...
2015: ELife
https://www.readbyqxmd.com/read/26057978/epigenome-editing-made-easy
#15
Gabriel E Zentner, Steven Henikoff
No abstract text is available yet for this article.
June 2015: Nature Biotechnology
https://www.readbyqxmd.com/read/25956076/diversity-in-the-organization-of-centromeric-chromatin
#16
REVIEW
Florian A Steiner, Steven Henikoff
Centromeric chromatin is distinguished primarily by nucleosomes containing the histone variant cenH3, which organizes the kinetochore that links the chromosome to the spindle apparatus. Whereas budding yeast have simple 'point' centromeres with single cenH3 nucleosomes, and fission yeast have 'regional' centromeres without obvious sequence specificity, the centromeres of most organisms are embedded in highly repetitive 'satellite' DNA. Recent studies have revealed a remarkable diversity in centromere chromatin organization among different lineages, including some that have lost cenH3 altogether...
April 2015: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/25927077/a-unique-chromatin-complex-occupies-young-%C3%AE-satellite-arrays-of-human-centromeres
#17
Jorja G Henikoff, Jitendra Thakur, Sivakanthan Kasinathan, Steven Henikoff
The intractability of homogeneous α-satellite arrays has impeded understanding of human centromeres. Artificial centromeres are produced from higher-order repeats (HORs) present at centromere edges, although the exact sequences and chromatin conformations of centromere cores remain unknown. We use high-resolution chromatin immunoprecipitation (ChIP) of centromere components followed by clustering of sequence data as an unbiased approach to identify functional centromere sequences. We find that specific dimeric α-satellite units shared by multiple individuals dominate functional human centromeres...
February 12, 2015: Science Advances
https://www.readbyqxmd.com/read/25827087/mapping-regulatory-factors-by-immunoprecipitation-from-native-chromatin
#18
Guillermo A Orsi, Sivakanthan Kasinathan, Gabriel E Zentner, Steven Henikoff, Kami Ahmad
Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin (ORGANIC) is a high-resolution method that can be used to quantitatively map protein-DNA interactions with high specificity and sensitivity. This method uses micrococcal nuclease (MNase) digestion of chromatin and low-salt solubilization to preserve protein-DNA complexes, followed by immunoprecipitation and paired-end sequencing for genome-wide mapping of binding sites. In this unit, we describe methods for isolation of nuclei and MNase digestion of unfixed chromatin, immunoprecipitation of protein-DNA complexes, and high-throughput sequencing to map sites of bound factors...
2015: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/25826366/methylation-sensitive-expression-of-a-dna-demethylase-gene-serves-as-an-epigenetic-rheostat
#19
Ben P Williams, Daniela Pignatta, Steven Henikoff, Mary Gehring
Genomes must balance active suppression of transposable elements (TEs) with the need to maintain gene expression. In Arabidopsis, euchromatic TEs are targeted by RNA-directed DNA methylation (RdDM). Conversely, active DNA demethylation prevents accumulation of methylation at genes proximal to these TEs. It is unknown how a cellular balance between methylation and demethylation activities is achieved. Here we show that both RdDM and DNA demethylation are highly active at a TE proximal to the major DNA demethylase gene ROS1...
March 2015: PLoS Genetics
https://www.readbyqxmd.com/read/25561719/histone-variants-and-epigenetics
#20
REVIEW
Steven Henikoff, M Mitchell Smith
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes...
January 2015: Cold Spring Harbor Perspectives in Biology
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