Abstract
Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins’ preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications.
Highlights
With the advent of genomics techniques, the understanding of the many roles of histone proteins and their modifications has increased rapidly [1,2]
Genomic location and loss of function experiments challenge the view that Hmga proteins act as local modulators of transcriptional regulation but rather argue for a role as structural components of chromatin
We aimed to investigate the in vivo DNA and chromatin-binding preferences of Hmga1 and Hmga2 proteins
Summary
With the advent of genomics techniques, the understanding of the many roles of histone proteins and their modifications has increased rapidly [1,2]. Comparably little attention has been given to the second most abundant class of nuclear proteins after histones [3], the high mobility group proteins [4]. High mobility group proteins are highly conserved and have been divided into 3 families (A, B, N) based on their different structural features [6]. The two members of the A group, Hmga and Hmga, are ~100 amino acids (AA) long intrinsically disordered proteins, which possess 3 DNA-binding domains (DBD) and a short acidic tail [7]. Compared to Hmga, Hmga harbors a smaller linker between the first and the second DBD and a longer AA sequence between the third DBD and the acidic tail. Within the 3 DBDs there is high conservation between both proteins with 74% identity and 15% similarity (S1A Fig)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
