Search Results - "Widom, Jonathan"

Poly(dA:dT) tracts: major determinants of nucleosome organization by Segal, Eran, Widom, Jonathan

“…Homopolymeric stretches of deoxyadenosine nucleotides (A's) on one strand of double-stranded DNA, referred to as poly(dA:dT) tracts or A-tracts, are…”
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A map of nucleosome positions in yeast at base-pair resolution by Brogaard, Kristin, Xi, Liqun, Wang, Ji-Ping, Widom, Jonathan

“…The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function. However, existing methods for mapping nucleosomes do…”
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Dynamics of Nucleosome Invasion by DNA Binding Proteins by Tims, Hannah S., Gurunathan, Kaushik, Levitus, Marcia, Widom, Jonathan

“…Nucleosomes sterically occlude their wrapped DNA from interacting with many large protein complexes. How proteins gain access to nucleosomal DNA target sites…”
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Controls of nucleosome positioning in the human genome by Gaffney, Daniel J, McVicker, Graham, Pai, Athma A, Fondufe-Mittendorf, Yvonne N, Lewellen, Noah, Michelini, Katelyn, Widom, Jonathan, Gilad, Yoav, Pritchard, Jonathan K

“…Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes…”
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Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity by Small, Eliza C, Xi, Liqun, Wang, Ji-Ping, Widom, Jonathan, Licht, Jonathan D

“…Nucleosomes, the basic unit of chromatin, have a critical role in the control of gene expression. Nucleosome positions have generally been determined by…”
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Predicting nucleosome positioning using a duration Hidden Markov Model by Xi, Liqun, Fondufe-Mittendorf, Yvonne, Xia, Lei, Flatow, Jared, Widom, Jonathan, Wang, Ji-Ping

“…The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions…”
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Distinct modes of regulation by chromatin encoded through nucleosome positioning signals by Field, Yair, Kaplan, Noam, Fondufe-Mittendorf, Yvonne, Moore, Irene K, Sharon, Eilon, Lubling, Yaniv, Widom, Jonathan, Segal, Eran

“…The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the…”
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Dynamics and function of compact nucleosome arrays by Poirier, Michael G, Widom, Jonathan, Oh, Eugene, Tims, Hannah S

“…Nucleosomes can interfere with DNA binding by factors, but previous work showed that protein-binding sites on a single nucleosome are accessible. Dynamics in…”
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Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning by Moyle-Heyrman, Georgette, Zaichuk, Tetiana, Xi, Liqun, Zhang, Quanwei, Uhlenbeck, Olke C., Holmgren, Robert, Widom, Jonathan, Wang, Ji-Ping

“…Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair…”
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High flexibility of DNA on short length scales probed by atomic force microscopy by Nelson, Philip C, Wiggins, Paul A, van der Heijden, Thijn, Moreno-Herrero, Fernando, Spakowitz, Andrew, Phillips, Rob, Widom, Jonathan, Dekker, Cees

“…The mechanics of DNA bending on intermediate length scales (5-100 nm) plays a key role in many cellular processes, and is also important in the fabrication of…”
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H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state by Brickner, Donna Garvey, Cajigas, Ivelisse, Fondufe-Mittendorf, Yvonne, Ahmed, Sara, Lee, Pei-Chih, Widom, Jonathan, Brickner, Jason H

“…Many genes are recruited to the nuclear periphery upon transcriptional activation. The mechanism and functional significance of this recruitment is unclear. We…”
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Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome by Moyle-Heyrman, Georgette, Tims, Hannah S., Widom, Jonathan

“…Cooperativity in transcription factor (TF) binding is essential in eukaryotic gene regulation and arises through diverse mechanisms. Here, we focus on one…”
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Using DNA mechanics to predict in vitro nucleosome positions and formation energies by Morozov, Alexandre V, Fortney, Karissa, Gaykalova, Daria A, Studitsky, Vasily M, Widom, Jonathan, Siggia, Eric D

“…In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for…”
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High nucleosome occupancy is encoded at human regulatory sequences by Tillo, Desiree, Kaplan, Noam, Moore, Irene K, Fondufe-Mittendorf, Yvonne, Gossett, Andrea J, Field, Yair, Lieb, Jason D, Widom, Jonathan, Segal, Eran, Hughes, Timothy R

“…Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low…”
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Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization by Lubling, Yaniv, Moore, Irene K, Fondufe-Mittendorf, Yvonne, Field, Yair, Widom, Jonathan, Mieczkowski, Piotr, Lieb, Jason D, Segal, Eran, Kaplan, Noam

“…Eran Segal and colleagues report that promoters driving expression of cellular respiration genes in aerobic yeast species encode relatively open chromatin,…”
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The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo by Henikoff, Steven, Ramachandran, Srinivas, Krassovsky, Kristina, Bryson, Terri D, Codomo, Christine A, Brogaard, Kristin, Widom, Jonathan, Wang, Ji-Ping, Henikoff, Jorja G

“…In budding yeast, a single cenH3 (Cse4) nucleosome occupies the ∼120-bp functional centromere, however conflicting structural models for the particle have been…”
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Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs by Nalabothula, Narasimharao, Xi, Liqun, Bhattacharyya, Sucharita, Widom, Jonathan, Wang, Ji-Ping, Reeve, John N, Santangelo, Thomas J, Fondufe-Mittendorf, Yvonne N

“…Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a…”
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Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity by Garcia, Hernan G., Grayson, Paul, Han, Lin, Inamdar, Mandar, Kondev, Jané, Nelson, Philip C., Phillips, Rob, Widom, Jonathan, Wiggins, Paul A.

“…The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in…”
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Collaborative Competition Mechanism for Gene Activation In Vivo by Miller, Joanna A., Widom, Jonathan

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells by Sebeson, Amy, Xi, Liqun, Zhang, Quanwei, Sigmund, Audrey, Wang, Ji-Ping, Widom, Jonathan, Wang, Xiaozhong

“…The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode…”
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