Abstract
Induction of gene expression is correlated with alterations in nuclear organization, including proximity to other active genes, to the nuclear cortex, and to cytologically distinct domains of the nucleus. Chromosomes are tethered to the insoluble nuclear scaffold/matrix through interaction with Scaffold/Matrix Attachment Region (SAR/MAR) binding proteins. Identification and characterization of proteins involved in establishing or maintaining chromosome-scaffold interactions is necessary to understand how the nucleus is organized and how dynamic changes in attachment are correlated with alterations in gene expression. We identified and characterized one such scaffold attachment factor, a Drosophila homolog of mammalian SAF-B. The large nuclei and chromosomes of Drosophila have allowed us to show that SAF-B inhabits distinct subnuclear compartments, forms weblike continua in nuclei of salivary glands, and interacts with discrete chromosomal loci in interphase nuclei. These interactions appear mediated either by DNA-protein interactions, or through RNA-protein interactions that can be altered during changes in gene expression programs. Extraction of soluble nuclear proteins and DNA leaves SAF-B intact, showing that this scaffold/matrix-attachment protein is a durable component of the nuclear matrix. Together, we have shown that SAF-B links the nuclear scaffold, chromosomes, and transcriptional activity.
Highlights
In the eukaryotic nucleus, gene expression is thought to be a multistep process that involves changes in chromatin organization and chromatin structure followed by maturation of the polymerase complex and rearrangements of the transcription unit within the volume of the nucleus
Activities of Scaffold/Matrix Attachment Region (SAR/MAR) binding proteins have been characterized biochemically; it is still unclear how are they are involved in gene regulation, they have been proposed to contribute to chromatin structure by mediating the attachment of chromatin to the nuclear scaffold thereby folding chromatin into topologically independent loop domains[14,17]
Since these proteins are thought to link gene regulation and the nuclear scaffold, we expected SAF-B homologs in all eukaryotes, and were curious whether Drosophila contained one or more genes belonging to the saf-b family. saf-b family members are distinctive because they possess a DNAbinding SAP domain similar to that found in Ku70/Ku80 and Protein Inhibitor of Activated STAT[33,34], an RNA-recognizing RRM motif, and K-rich, R/E-rich, and G-rich domains
Summary
Gene expression is thought to be a multistep process that involves changes in chromatin organization and chromatin structure followed by maturation of the polymerase complex and rearrangements of the transcription unit within the volume of the nucleus. Activities of Scaffold/Matrix Attachment Region (SAR/MAR) binding proteins have been characterized biochemically; it is still unclear how are they are involved in gene regulation, they have been proposed to contribute to chromatin structure by mediating the attachment of chromatin to the nuclear scaffold thereby folding chromatin into topologically independent loop domains[14,17]. This view may be an oversimplification of a group of proteins with diverse functions, as many have been shown to affect transcription, replication, RNA processing, and RNA transport[18,19,20,21,22]. More work is needed to define the role of SARs/MARs and their binding proteins in chromatin remodeling and transcriptional regulation
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