FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells

Autor: Ying Zheng, Eric Batchelor, Craig J. Benham, Wendy Dubois, David Levens

Publikováno v: Communications Biology
Communications Biology, Vol 3, Iss 1, Pp 1-11 (2020)

Physiologically, MYC levels must be precisely set to faithfully amplify the transcriptome, but in cancer MYC is quantitatively misregulated. Here, we study the variation of MYC amongst single primary cells (B-cells and murine embryonic fibroblasts, M

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c17180228d71ef90494108e680d663fd
https://doi.org/10.1038/s42003-020-01264-x

Theoretical analysis of competing conformational transitions in superhelical DNA.

Autor: Dina Zhabinskaya, Craig J Benham

Publikováno v: PLoS Computational Biology, Vol 8, Iss 4, p e1002484 (2012)

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologi

Externí odkaz: https://doaj.org/article/7c6280fa9c1a40f182468cf888f189f0

Theoretical analysis of the stress induced B-Z transition in superhelical DNA.

Autor: Dina Zhabinskaya, Craig J Benham

Publikováno v: PLoS Computational Biology, Vol 7, Iss 1, p e1001051 (2011)

We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-f

Externí odkaz: https://doaj.org/article/bbc27df43f764aa4a4e5cb0d3638278b

Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins.

Autor: Prashanth Ak, Craig J Benham

Publikováno v: PLoS Computational Biology, Vol 1, Iss 1, p e7 (2005)

Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo. Rather, superhelical

Externí odkaz: https://doaj.org/article/c150a87cddd94976addb5b8b64b2099a

Interplay between DNA sequence and negative superhelicity drives R-loop structures

Autor: Frédéric Chédin, Shaheen Sulthana, Robert Stolz, Maika Malig, Stella R. Hartono, Craig J. Benham

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 13
Proceedings of the National Academy of Sciences of the United States of America

Significance Three-stranded R-loop structures form during transcription when the nascent RNA transcript rehybridizes to the template DNA strand. This creates an RNA:DNA hybrid and forces the nontemplate DNA strand into a single-stranded, looped-out s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d85573e5cfad6ce4d573c07cc6464937
https://escholarship.org/uc/item/0vz4t8b4