Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure.
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.
Gavrilov
Alexey A
AA
Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia.
Zukher
Inna S
IS
Philonenko
Elena S
ES
Razin
Sergey V
SV
Iarovaia
Olga V
OV
D000818:Animals; D002458:Cell Fractionation; D002460:Cell Line; D002645:Chickens / Q000235:genetics; D002843:Chromatin / Q000737:chemistry*; D018899:CpG Islands; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification; D004262:DNA Restriction Enzymes; D005914:Globins / Q000235:genetics; D015530:Nuclear Matrix / Q000235:genetics*
D002843:Chromatin; D005914:Globins; D004247:DNA; D004262:DNA Restriction Enzymes