RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization

Abstract

Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%–5% of total chromatin-associated nucleic acids, are polyA− and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s) are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with α-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

RNA regulation of epigenetic processes

“…(14) Many aspects of the regulation of chromatin structure have been shown to be directed by RNA (Fig. 1).…”

Hidden treasures in unspliced EST data

“…Chromatin-associated RNAs (CARs) are predominantly non-polyadenylated [23]. Recently, deep sequencing was used to characterize 141 intronic regions and 74 intergenic regions harboring CARs [24].…”

Teachings from the egg: New and unexpected functions of RNAs

“…Recently, RNA was found to play a structural role in the organization of chromatin from chicken liver and Drosophila S2 cell nuclei (Rodrıguez-Campos and Azorın, 2007). These authors showed that the RNA is an integral component of chromatin and that the removal of chromatin-associated RNAs (which account for 2-5% of total chromatin-associated nucleic acids) results in fragmentation of the chromatin (euchromatin and heterochromatin) without loss of histone H1 and other core histone proteins (Rodrıguez-Campos and Azorın, 2007).…”

“…Recently, RNA was found to play a structural role in the organization of chromatin from chicken liver and Drosophila S2 cell nuclei (Rodrıguez-Campos and Azorın, 2007). These authors showed that the RNA is an integral component of chromatin and that the removal of chromatin-associated RNAs (which account for 2-5% of total chromatin-associated nucleic acids) results in fragmentation of the chromatin (euchromatin and heterochromatin) without loss of histone H1 and other core histone proteins (Rodrıguez-Campos and Azorın, 2007). Although further studies are needed to understand the structural role of RNA in chromatin structure, the authors suggested that RNA might stabilize the binding of structural nonhistone proteins, stabilize high-order chromatin structures by facilitating folding of chromatin fibers, or bind to multiple sites to facilitate long-distance chromatin-chromatin interaction (Rodrıguez-Campos and Azorın, 2007).…”

“…These authors showed that the RNA is an integral component of chromatin and that the removal of chromatin-associated RNAs (which account for 2-5% of total chromatin-associated nucleic acids) results in fragmentation of the chromatin (euchromatin and heterochromatin) without loss of histone H1 and other core histone proteins (Rodrıguez-Campos and Azorın, 2007). Although further studies are needed to understand the structural role of RNA in chromatin structure, the authors suggested that RNA might stabilize the binding of structural nonhistone proteins, stabilize high-order chromatin structures by facilitating folding of chromatin fibers, or bind to multiple sites to facilitate long-distance chromatin-chromatin interaction (Rodrıguez-Campos and Azorın, 2007). Studies from another laboratory showed that G-rich RNA present in the nucleus is involved in the recruitment of the origin recognition complex (ORC), which determines the initiation sites of DNA replication (Norseen et al, 2008).…”