Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.04.14.536936

SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes

Godneeva, B.·Ninova, M.·Fejes Toth, K.·Aravin, A.
View original source ↗Export metadata ↓

Abstract

The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonuss repressive activity. SUMOylation influences Bonuss subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Godneeva, B., Ninova, M., Fejes Toth, K., Aravin, A.. 2023-04-15. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. https://doi.org/10.1101/2023.04.14.536936

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The C-terminus of the KREH1 helicase is important for RNA binding and association with mitochondrial RNA editing complexes in T. brucei

Mitochondrial pre-mRNA editing in kinetoplastids, a clade that includes human-infective parasitic protists such as Trypanosoma and Leishmania, is required to produce translatable, functional gene products from otherwise nonfunctional mitochondrial precursor transcripts of essential respiratory chain complex subunits. RNA editing is a template-guided process in which cognate guide RNAs (gRNAs) anneal to specific sites at the pre-mRNA and direct the complementary insertion and/or deletion of uridines. Large multi-modular complexes - like the RNA-Editing Substrate-binding Complex (RESC) and the RNA-Editing Catalytic Complexes (RECC) - organize and catalyze RNA editing, respectively. Within these assemblies, Kinetoplast RNA Editing Helicases (KREHs) play an important role in ribonucleoprotein complex remodeling, particularly in pan-editing, when transcripts are extensively modified throughout their length by multiple gRNAs. However, the mechanisms by which KREH RNA helicases facilitate pan-editing, and their specific roles in this process, remain unclear. Here, we define the molecular properties of the Trypanosoma brucei DEAD-box RNA editing helicase KREH1. Cellular co-proteome analyses reveal that KREH1 interacts with subunits of the RESC complex and biochemical experiments show that KREH1 is an RNA-dependent ATPase that unwinds double-stranded RNA substrates. We show that the flexible C-terminus of KREH1 is important for RNA binding and, consequently, for enzymatic activity in vitro and interactions with the RESC complex in vivo. Overall, our experiments refine the role of KREH1 in the pan-editing process and establish its utility as a molecular tool for investigating higher-order RNA editing complexes in the cellular context.

molecular biology↗
bioRxiv2026

Structural basis of nucleosome remodeling by archaeal RNA polymerase during transcription elongation

Transcription occurs in the context of histone-based chromatin in eukaryotes and most archaea. The archaeal RNA polymerase and histones are ancestral to their eukaryotic counterparts, yet how RNA polymerase traverses histone-bound DNA in archaea remains poorly understood. Here, we reconstitute a nucleosome-associated transcription elongation complex (TEC) from Pyrococcus furiosus and capture its structure across multiple elongation states by cryo-electron microscopy (cryo-EM). High-resolution structures reveal that the RNA polymerase engages a three-dimer HPfB nucleosome positioned downstream. We identify direct physical interactions between HPfB and Rpo1N RNA polymerase subunit, establishing a defined polymerase-histone interface during transcription. Structural comparisons across defined elongation states demonstrate that RNA polymerase first translocates on DNA using the proximal histone dimer as an anchor, followed by destabilisation of the distal dimer. The DNA exiting the nucleosome is partially unwrapped and is redirected traversing the Rpo4/7 stalk. At extended transcript lengths nucleosome organisation is lost, indicating that transcription elongation ultimately disrupts histone-DNA interactions. This work provides the first structural insight into transcription through chromatin in archaea, revealing a mechanism in which the archaeal RNA polymerase actively remodels nucleosomes via DNA redirection and histone displacement, aided by direct polymerase-histone contacts.

molecular biology↗
bioRxiv2026

Structural mechanism of Gasdermin E-mediated mtDNA release from apoptotic mitochondria

During apoptosis, the permeabilization of the mitochondrial inner membrane (MIM) through still-unclear mechanisms releases mtDNA into the cytosol, triggering the inflammatory cGAS/STING pathway under low caspase activity. Here, we report that, in apoptosis, the active form of the pore-forming protein Gasdermin E (GSDME-N) damages mitochondria before plasma membrane disruption. We visualize GSDME-N pore-like nano-assemblies in the MIM of apoptotic cells and of isolated mitochondria, which we bridge with the cryo-EM structure of the GSDME-N pore in mitochondria-like membranes. Deep membrane insertion of the anchor domain, which acts as a determinant of GSDME-N cardiolipin binding preferences, supports a role in pore formation. Notably, GSDME depletion results in a reduction in cristae swelling, MIM extrusion and mtDNA release during apoptosis. Subsequently, this decreases STING activation and inflammatory responses under caspase inhibition. Our findings reveal that GSDME mediates MIM permeabilization and mtDNA release during apoptosis and define the mechanism of GSDME-mediated membrane damage.

molecular biology↗