DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin

Murugesapillai, Divakaran; McCauley, Micah J.; Huo, Ran; Holte, Molly H. Nelson; Stepanyants, Armen; Maher, L. James; Israeloff, N. E.; Williams, Mark C.

doi:10.1093/nar/gku635

Cited by 58 publications

(120 citation statements)

References 51 publications

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“…To test this, we used AFM imaging in liquid to determine the extent of TFAM-CTΔ26 binding under the conditions of this study. Because the persistence length of mtDNA decreases upon TFAM binding, persistence length can be used to determine if and when TFAM-CTΔ26 is bound to mtDNA (Murugesapillai et al, 2014;Rivetti et al, 1996;Zhang et al, 2009). As expected, a value of 50 ± 2 nm was measured in the absence of TFAM ( Fig.…”

Section: Resultssupporting

confidence: 61%

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Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter

Uchida

Murugesapillai

Wang

et al. 2017

Preprint

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Section: Resultssupporting

confidence: 61%

“…This value was 17 ± 2 pN (N=15). This is similar to the force required to break loops formed by the yeast HMG-box protein, HMO1 (Murugesapillai et al, 2014).…”

Section: Resultsmentioning

confidence: 61%

Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter

Uchida

Murugesapillai

Wang

et al. 2017

Preprint

Self Cite

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“…6) (151). However, the looped DNA structure formed by HMO1 is dynamic and is predicted to be easily disrupted by the force generated by a transcribing RNA polymerase (151). HMO1 has also been implicated in (151).…”

Section: Hmo1 Is a Component Of The Pol I Transcription Machinerymentioning

confidence: 99%

“…However, the looped DNA structure formed by HMO1 is dynamic and is predicted to be easily disrupted by the force generated by a transcribing RNA polymerase (151). HMO1 has also been implicated in (151). Such topological domains may also be mediated by the concerted action of HMO1 and Top2 (195).…”

Section: Hmo1 Is a Component Of The Pol I Transcription Machinerymentioning

confidence: 99%

Yeast HMO1: Linker Histone Reinvented

Panday

Grove

2017

Microbiol Mol Biol Rev

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SUMMARY Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or “fragile” nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.

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“…We observed the repeated occurrence of BAS1-RTT107, BAS1-TYE7, YAP6-BAS1 and ASK10-HMO1 in consecutive time-points of S288c sub-networks. We observed apart from BAS1 (discussed above), genes associated with mitotic functions as end nodes of these weak ties, such as RTT107 for DNA repair (Leung et al 2011), TYE7 for glycolytic gene expression (Sato et al 2000), YAP6 for carbohydrate metabolism (Hanlon et al 2011), ASK10 for glycerol transport (Beese et al 2009) and HMO1 for DNA structure modification (Murugesapillai et al 2014) (Fig. 3B).…”

Section: Longitudinal Transcriptional Regulatory Network Of S288c Inmentioning

confidence: 82%

Longitudinal network theory approaches identify crucial factors affecting sporulation efficiency in yeast

Sarkar

Gupta

Verma

et al. 2016

Preprint

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Integrating network theory approaches over longitudinal genome-wide gene expression data is a robust approach to understand the molecular underpinnings of a dynamic biological process. Here, we performed a network-based investigation of longitudinal gene expression changes during sporulation of a yeast strain, SK1. Using global network attributes, viz.clustering coefficient, degree distribution of a node, degree-degree mixing of the connected nodes and disassortativity, we observed dynamic changes in these parameters indicating a highly connected network with inter-module crosstalk. Analysis of local attributes, such as clustering coefficient, hierarchy, betweenness centrality and Granovetter's weak ties showed that there was an inherent hierarchy under regulatory control that was determined by specific nodes. Biological annotation of these nodes indicated the role of specifically linked pairs of genes in meiosis. These genes act as crucial regulators of sporulation in the highly sporulating SK1 strain. An independent analysis of these network properties in a less efficient sporulating strain helped to understand the heterogeneity of network profiles. We show that comparison of network properties has the potential to identify candidate nodes contributing to the phenotypic diversity of developmental processes in natural populations. Therefore, studying these network parameters as described in this work for dynamic developmental processes, such as sporulation in yeast and eventually in disease progression in humans, can help in identifying candidate factors which are potential regulators of differences between normal and perturbed processes and can be causal targets for intervention.

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DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin

Cited by 58 publications

References 51 publications

Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter

Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter

Yeast HMO1: Linker Histone Reinvented

Longitudinal network theory approaches identify crucial factors affecting sporulation efficiency in yeast

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