TY - JOUR
T1 - Beyond Sequence
T2 - Internucleosomal Interactions Dominate Array Assembly
AU - Wang, Yaqing
AU - Stormberg, Tommy
AU - Hashemi, Mohtadin
AU - Kolomeisky, Anatoly B.
AU - Lyubchenko, Yuri L.
N1 - Publisher Copyright:
© 2022 American Chemical Society.
PY - 2022/12/29
Y1 - 2022/12/29
N2 - The organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here, we investigated the contributions of the DNA sequence and internucleosomal interactions on the organization of the nucleosomal arrays in compact structures using atomic force microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of close positioning with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.
AB - The organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here, we investigated the contributions of the DNA sequence and internucleosomal interactions on the organization of the nucleosomal arrays in compact structures using atomic force microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of close positioning with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.
UR - http://www.scopus.com/inward/record.url?scp=85144174454&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85144174454&partnerID=8YFLogxK
U2 - 10.1021/acs.jpcb.2c05321
DO - 10.1021/acs.jpcb.2c05321
M3 - Article
C2 - 36516875
AN - SCOPUS:85144174454
SN - 1520-6106
VL - 126
SP - 10813
EP - 10821
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 51
ER -