Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure
| Autor: | Alexey A. Gavrilov, Elena S. Philonenko, Sergey V. Razin, Inna Zukher, Olga V. Iarovaia |
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| Rok vydání: | 2010 |
| Předmět: |
Transcription factories
Gene Regulation Chromatin and Epigenetics Biology Cell Fractionation Cell Line chemistry.chemical_compound Transcription (biology) Genetics medicine Animals Nuclear Matrix Promoter DNA DNA Restriction Enzymes Nuclear matrix Molecular biology Chromatin Globins Housekeeping gene Cell biology Cell nucleus medicine.anatomical_structure chemistry CpG Islands Chickens |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkq712 |
| Popis: | We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments. This protocol, referred to as Matrix 3C (M3C), includes a high salt extraction of nuclei, the removal of distal parts of unfolded DNA loops using restriction enzyme treatment, ligation of the nuclear matrix-bound DNA fragments and a subsequent analysis of ligation frequencies. Using the M3C procedure, we have demonstrated that CpG islands of at least three housekeeping genes that surround the chicken α-globin gene domain are assembled into a complex (presumably, a transcription factory) that is stabilized by the nuclear matrix in both erythroid and non-erythroid cells. In erythroid cells, the regulatory elements of the α-globin genes are attracted to this complex to form a new assembly: an active chromatin hub that is linked to the pre-existing transcription factory. The erythroid-specific part of the assembly is removed by high salt extraction. Based on these observations, we propose that mixed transcription factories that mediate the transcription of both housekeeping and tissue-specific genes are composed of a permanent compartment containing integrated into the nuclear matrix promoters of housekeeping genes and a ‘guest’ compartment where promoters and regulatory elements of tissue-specific genes can be temporarily recruited. |
| Databáze: | OpenAIRE |
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