TY - JOUR
T1 - Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning
AU - Gent, Jonathan I.
AU - Schneider, Kevin L.
AU - Topp, Christopher N.
AU - Rodriguez, Carmen
AU - Presting, Gernot G.
AU - Dawe, R. Kelly
N1 - Funding Information:
This work was supported by grants from: the National Science Foundation (0421671 and 092270) to RKD; from the National Institutes of Health (NIGMS-F32-GM095223) to JIG; and by a University of Georgia Graduate School Dissertation Completion Award to CNT. We thank Richard Meagher for helping to inspire the project and Sarah Wolf for technical help.
PY - 2011
Y1 - 2011
N2 - Background: Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent. Results: In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ∼156-bp centromeric satellite sequence (tandem repeat) CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ∼10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2) lacked a detectable AA/TT periodicity but exhibited tightly phased positioning. Conclusions: These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres.
AB - Background: Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent. Results: In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ∼156-bp centromeric satellite sequence (tandem repeat) CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ∼10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2) lacked a detectable AA/TT periodicity but exhibited tightly phased positioning. Conclusions: These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres.
UR - http://www.scopus.com/inward/record.url?scp=79951955695&partnerID=8YFLogxK
U2 - 10.1186/1756-8935-4-3
DO - 10.1186/1756-8935-4-3
M3 - Article
AN - SCOPUS:79951955695
SN - 1756-8935
VL - 4
JO - Epigenetics and Chromatin
JF - Epigenetics and Chromatin
IS - 1
M1 - 3
ER -