UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

Abstract

BackgroundH3.3 is an ancient and conserved H3 variant and plays essential roles in transcriptional regulation. HIRA complex, which is composed of HIRA, UBN1 or UBN2, and Cabin1, is a H3.3 specific chaperone complex. However, it still remains largely uncharacterized how HIRA complex specifically recognizes and deposits H3.3 to the chromatin, such as promoters and enhancers.ResultsIn this study, we demonstrate that the UBN1 or UBN2 subunit is mainly responsible for specific recognition and direct binding of H3.3 by the HIRA complex. While the HIRA subunit can enhance the binding affinity of UBN1 toward H3.3, Cabin1 subunit cannot. We also demonstrate that both Ala87 and Gly90 residues of H3.3 are required and sufficient for the specific recognition and binding by UBN1. ChIP-seq studies reveal that two independent HIRA complexes (UBN1-HIRA and UBN2-HIRA) can cooperatively deposit H3.3 to cis-regulatory regions, including active promoters and active enhancers in mouse embryonic stem (mES) cells. Importantly, disruption of histone chaperone activities of UBN1 and UBN2 by FID/AAA mutation results in the defect of H3.3 deposition at promoters of developmental genes involved in neural differentiation, and subsequently causes the failure of activation of these genes during neural differentiation of mES cells.ConclusionTogether, our results provide novel insights into the mechanism by which the HIRA complex specifically recognizes and deposits H3.3 at promoters and enhancers of developmental genes, which plays a critical role in neural differentiation of mES cells.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0573-9) contains supplementary material, which is available to authorized users.

Histone Variants: Guardians of Genome Integrity

“…Several histone variants, including macroH2A, H2A.Z, and H3.3, strongly impact the balance between cell differentiation and self-renewal by regulating the expression of pluripotency and developmental genes. The deposition of H3.3 at the promoters of developmental genes indeed drives the differentiation of embryonic stem cells and regulates neuronal differentiation programs [237][238][239]. Similarly, macroH2A variants stimulate the differentiation of pluripotent cells in mammals [240,241] and, in agreement with these findings, macroH2A loss enhances cell stemness in liver and bladder cancer [166,242].…”

Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA

“…Our data thus delineate two independent pathways, HIRA-ASF1B-ATF3 and HIRA-ASF1B-UBN2, which both contribute to transcription recovery post UV damage. Regarding UBN2, in addition to binding and depositing H3.3 at regulatory elements of developmental genes in mouse embryonic stem cells 58 , we now show that UBN2 also promotes de novo deposition of H3.3 at UV damage sites in human cells. Nevertheless, this histone deposition activity is not involved in transcription recovery post UV damage, arguing that transcription restart relies on another function of UBN2, yet to be identified.…”

“…Indeed, this histone chaperone complex comprises HIRA 56 , Ubinuclein 1 (UBN1) 57 or the less characterized UBN2 58 , and CABIN1 subunits 59 (Fig. 1a), and coordinates with Anti-silencing function 1A (ASF1A) 42,60 to promote H3.3 deposition (reviewed in 41 ).…”

“…Considering that the effect of ATF3 knockdown on alleviating the transcription defect in HIRA-depleted cells was only partial, we assumed that additional, ATF3-independent pathways might mediate HIRA function on transcription recovery post UVC. During the course of our studies, UBN2 was characterized as an alternative subunit to UBN1 within the HIRA complex, chaperoning H3.3 in mouse embryonic stem cells 58 . We confirmed the contribution of UBN2 to new H3.3 deposition at UVC damage sites in human cells (Fig.…”

Epigenetic Mechanisms of Learning and Memory: Implications for Aging

“…This high level of specialization contributes to the positioning of variants in both euchromatin and heterochromatin and the mediation of different downstream functions. For example, H3.3 can be deposited into chromatin at highly transcribed regions by the histone regulator A (HIRA) complex [ 57 , 58 ], but can also be found at telomeres and repetitive heterochromatic regions where it is deposited by a complex comprising alpha thalassemia, mental retardation syndrome X-linked (ATRX), and death domain associated protein (DAXX) [ 59 , 60 , 61 ]. Notably, histone variant chaperones act in large chromatin remodeling complexes that often carry other proteins involved in transcription.…”