Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
Highlights
The standard approach has been to investigate these interactions in the context of peptide fragments of the histones. Though these studies have revealed a great deal about post-translational modification (PTM) specificity, they preclude the ability to identify contacts outside the histone tails that might contribute to chromatin association
In addition to histone binding, three of these, the hPHF1 Tudor, 53BP1 Tandem-Tudor domains (TTD) and scESA1 knotted-Tudor have been identified to interact with nucleic acids
We focus on the SANT/Myb domains from c-Myb, coREST1, ISW1a, and S. cerevisiae Chd1, which are known to associate with domains from c-Myb, coREST1, ISW1a, and S. cerevisiae Chd1, which are known to associate with histones and/or are part of histone modifying complexes and represent each of the two known histones and/or are part of histone modifying complexes and represent each of the two known
Summary
The eukaryotic genome exists in the cell nucleus in the form of chromatin. The basic subunit of chromatin is the nucleosome, a complex of ~147 base pairs (bp) of DNA wrapped around an octamer of histones H2A, H2B, H3, and H4. A large number of histone PTMs have been discovered along with a plethora of protein domains that can recognize them [4,5,6,7,8]. The standard approach has been to investigate these interactions in the context of peptide fragments of the histones Though these studies have revealed a great deal about PTM specificity, they preclude the ability to identify contacts outside the histone tails that might contribute to chromatin association. A growing subset of known histone reader domains have been shown to interact with DNA and/or RNA. We review what is known about the mechanism and function of reader domain nucleic acid binding
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