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Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove
M E Ludérus1, J L den Blaauwen, O J de Smit
1E. C. Slater Institute, University of Amsterdam, The Netherlands.
Abstract:
Chromatin in eukaryotic nuclei is thought to be partitioned into functional loop domains that are generated by the binding of defined DNA sequences, named MARs (matrix attachment regions), to the nuclear matrix. We have previously identified B-type lamins as MAR-binding matrix components (M. E. E. Ludérus, A. de Graaf, E. Mattia, J. L. den Blaauwen, M. A. Grande, L. de Jong, and R. van Driel, Cell 70:949-959, 1992). Here we show that A-type lamins and the structurally related proteins desmin and NuMA also specifically bind MARs in vitro. We studied the interaction between MARs and lamin polymers in molecular detail and found that the interaction is saturable, of high affinity, and evolutionarily conserved. Competition studies revealed the existence of two different types of interaction related to different structural features of MARs: one involving the minor groove of double-stranded MAR DNA and one involving single-stranded regions. We obtained similar results for the interaction of MARs with intact nuclear matrices from rat liver. A model in which the interaction of nuclear matrix proteins with single-stranded MAR regions serves to stabilize the transcriptionally active state of chromatin is discussed.
Insights
Matrix attachment regions (MARs) bind to nuclear matrix proteins, including A-type and B-type lamins. This interaction, crucial for chromatin organization, involves MAR DNA
Area of Science:
- Molecular Biology
- Cell Biology
- Genetics
Background:
- Eukaryotic chromatin is organized into functional loop domains attached to the nuclear matrix via matrix attachment regions (MARs).
- B-type lamins were previously identified as MAR-binding nuclear matrix components.
Purpose of the Study:
- To investigate the binding of A-type lamins, desmin, and NuMA to MARs.
- To characterize the molecular interactions between MARs and lamin polymers.
- To explore the role of these interactions in chromatin organization and transcriptional regulation.
Main Methods:
- In vitro binding assays to study the interaction between MARs and A-type lamins, desmin, and NuMA.
- Detailed molecular studies of MAR-lamin polymer interactions, including affinity and saturation.
- Competition studies to differentiate interaction types based on MAR structural features.
- Experiments using intact nuclear matrices from rat liver to validate in vitro findings.
Main Results:
- A-type lamins, desmin, and NuMA specifically bind MARs in vitro, extending the known MAR-binding proteins.
- The interaction between MARs and lamin polymers is saturable, high-affinity, and evolutionarily conserved.
- Two distinct MAR-protein interaction types were identified: one involving the minor groove of double-stranded DNA and another involving single-stranded regions.
Conclusions:
- Nuclear matrix proteins, including various lamins and related proteins, play a significant role in MAR binding.
- The specific interactions between MARs and nuclear matrix proteins contribute to the structural organization of chromatin.
- A model is proposed where MAR-protein interactions, particularly with single-stranded MAR regions, stabilize transcriptionally active chromatin.