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Full-Text Articles in Molecular Biology

Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh May 2017

Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh

GSBS Dissertations and Theses

Chromatin packages eukaryotic genomes via a hierarchical series of folding steps, encrypting multiple layers of epigenetic information, which are capable of regulating nuclear transactions in response to complex signals in environment. Besides the 1-dimensinal chromatin landscape such as nucleosome positioning and histone modifications, little is known about the secondary chromatin structures and their functional consequences related to transcriptional regulation and DNA replication. The family of chromosomal conformation capture (3C) assays has revolutionized our understanding of large-scale chromosome folding with the ability to measure relative interaction probability between genomic loci in vivo. However, the suboptimal resolution of the typical 3C techniques ...


The Mitotic Genome: Accessibility And Transcriptional Control, Chris Hsiung Jan 2016

The Mitotic Genome: Accessibility And Transcriptional Control, Chris Hsiung

Publicly Accessible Penn Dissertations

Mitosis entails dramatic global alterations to genome structure and regulation, including

chromosome condensation, dissociation of the transcriptional machinery from chromosomes, and transcriptional silencing. Here I report studies that address the macromolecular accessibility of the mitotic genome and the control of transcriptional reactivation upon mitotic exit in a mammalian cell line. The results obtained from measuring the sensitivity of chromatin to DNase I cleavage by sequencing (DNase-seq) in pure mitotic cell populations demonstrate that macromolecular accessibility of the mitotic genome is widely preserved. Thus, steric hindrance from chromatin condensation is insufficient for explaining the eviction of transcription factors from mitotic chromatin ...


Comparative Genomics Reveals Chd1 As A Determinant Of Nucleosome Spacing In Vivo, Amanda Hughes, Oliver J. Rando Jul 2015

Comparative Genomics Reveals Chd1 As A Determinant Of Nucleosome Spacing In Vivo, Amanda Hughes, Oliver J. Rando

Open Access Articles

Packaging of genomic DNA into nucleosomes is nearly universally conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species because, for example, the average length of linker DNA between nucleosomes can differ significantly even between closely related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species-Saccharomyces cerevisiae and Kluyveromyces lactis-is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and ...


The Role Of Histone H3 And H4 In Centromere Function And Genome Integrity, Payel Chaudhuri Dec 2013

The Role Of Histone H3 And H4 In Centromere Function And Genome Integrity, Payel Chaudhuri

Theses and Dissertations

Histone H2A plays an important role in chromosomal segregation among parent and daughter cells during mitosis. While it is established that this histone is important in maintaining chromosome number in cell, further work is carried out to explore the role of other histones like H3 and H4 for similar effects. A systematic study is initiated by screening a library based on mutation of different amino acid residues in these histones. This detailed screening identified specific regions within H3 and H4, which are critically important for centromeric function. These histones residing near the DNA entry/exit region of nucleosome effects the ...


Lysine Post-Translational Modifications Of Saccharomyces Cerevisiae Chromatin Proteins, Christopher Richard Edwards Jan 2012

Lysine Post-Translational Modifications Of Saccharomyces Cerevisiae Chromatin Proteins, Christopher Richard Edwards

Publicly Accessible Penn Dissertations

DNA exists within the cell as part of a complex structure called chromatin which is comprised of many proteins, including histones, and participates in and influences every DNA-related process. Chromatin's proteins are modified post-translationally and this impacts their functions and in turn, the DNA processes in which they participate. However, the repertoire of post-translational modifications (PTMs), the enzymes that create and remove them, and their roles in chromosome biology are not fully understood. We have used the budding yeast Saccharomyces cerevisiae to investigate chromatin PTMs, specifically lysine modifications, through three avenues: the enzymes that regulate lysine PTMs, the histone ...


The Jil-1 Histone H3s10 Kinase Regulates Dimethyl H3k9 Modifications And Heterochromatic Spreading In Drosophila, Weiguo Zhang, Huai Deng, Xiaomin Bao, Stephanie Lerach, Jack Girton, Jorgen Johansen, Kristen M. Johansen Jan 2006

The Jil-1 Histone H3s10 Kinase Regulates Dimethyl H3k9 Modifications And Heterochromatic Spreading In Drosophila, Weiguo Zhang, Huai Deng, Xiaomin Bao, Stephanie Lerach, Jack Girton, Jorgen Johansen, Kristen M. Johansen

Biochemistry, Biophysics and Molecular Biology Publications

In this study, we show that a reduction in the levels of the JIL-1 histone H3S10 kinase results in the spreading of the major heterochromatin markers dimethyl H3K9 and HP1 to ectopic locations on the chromosome arms, with the most pronounced increase on the X chromosomes. Genetic interaction assays demonstrated that JIL-1 functions in vivo in a pathway that includes Su(var)3-9, which is a major catalyst for dimethylation of the histone H3K9 residue, HP1 recruitment, and the formation of silenced heterochromatin. We further provide evidence that JIL-1 activity and localization are not affected by the absence of Su ...


The Characterization Of Ribosomal Rna Gene Chromatin From Physarum Polycephalum, Sally A. Amero, Vicky L. Montoya, Wendy L. Murdoch, Roy C. Ogle, John L. Keating, Robert M. Grainger Aug 1988

The Characterization Of Ribosomal Rna Gene Chromatin From Physarum Polycephalum, Sally A. Amero, Vicky L. Montoya, Wendy L. Murdoch, Roy C. Ogle, John L. Keating, Robert M. Grainger

Medical Diagnostics & Translational Sciences Faculty Publications

We have isolated ribosomal RNA gene (rDNA) chromatin from Physarum polycephalum using a nucleolar isolation procedure that minimizes protein loss from chromatin and, subsequently, either agarose gel electrophoresis or metrizamide gradient centrifugation to purify this chromatin fraction (Amero, S. A., Ogle, R. C., Keating, J. L., Montoya, V. L., Murdoch, W. L., and Grainger, R. M. (1988) J. Biol. Chem. 263, 10725-10733). Metrizamide-purified rDNA chromatin obtained from nucleoli isolated according to the new procedure has a core histone/DNA ratio of 0.77:1. The major core histone classes comigrate electrophoretically with their nuclear counterparts on Triton-acid-urea/sodium dodecyl sulfate ...


The Purification Of Ribosomal Rna Gene Chromatin From Physarum Polycephalum, Sally A. Amero, Roy C. Ogle, John L. Keating, Vicky L. Montoya, Wendy L. Murdoch, Robert M. Grainger Jan 1988

The Purification Of Ribosomal Rna Gene Chromatin From Physarum Polycephalum, Sally A. Amero, Roy C. Ogle, John L. Keating, Vicky L. Montoya, Wendy L. Murdoch, Robert M. Grainger

Medical Diagnostics & Translational Sciences Faculty Publications

We have undertaken the purification of ribosomal RNA gene (rDNA) chromatin from the slime mold Physarum polycephalum, in order to study its chromatin structure. In this organism rDNA exists in nucleoli as highly repeated minichromosomes, and one can obtain crude chromatin fractions highly enriched in rDNA from isolated nucleoli. We first developed a nucleolar isolation method utilizing polyamines as stabilization agents that results in a chromatin fraction containing far more protein than is obtained by the more commonly used divalent cation isolation methods. The latter method appears to result in extensive histone loss during chromatin isolations. Two methods were then ...