Biology subjects

Mars, J.-C.

Publications and source records attributed to Mars, J.-C..

3 recordsLinked to original sources

bioRxiv2025

Nuclear RNA cap-chaperones eIF4E and NCBP2 govern distinct fates for 1000s of mRNAs uncovering an unexpected regulatory point in gene expression

mRNA processing constitutes a series of steps in the nucleus to generate mature mRNAs that can be translated into protein. This relies on the methyl-7-guanosine (m7G) "cap" on the 5end of mRNAs which is bound by the nuclear cap-binding protein NCBP2 with its cofactor NCBP1. The NCBP1/2 complex chaperones capped mRNA through these processing steps. NCBP2 is considered the sole nuclear cap-binding factor and thus its cap-chaperone role is thought to be a constitutive, housekeeping activity. However, another cap-binding protein, the eukaryotic translation initiation factor eIF4E, is also found in the nucleus. Two cap-binding factors co-existing in the nucleus intimate an undiscovered regulatory point in gene expression or, alternatively, redundancy to ensure gene expression fidelity. Consistent with the former possibility, eIF4E and NCBP2 drove distinct gene expression, transcriptomic, and splicing signatures impacting [~]2500 transcripts involved in distinct biological programmes with only [~]360 transcripts in common and of these only 79 common splicing events. Thus, each cap-chaperone designates distinct mRNA populations for specific processing revealing a new step in gene expression. We denote this mRNA specification of cap-chaperones (SOCCS). We uncovered multiple molecular mechanisms that contribute to SOCCS: distinct spatial localization of eIF4E and NCBP2 within the nucleus, identification of sequence motifs within targeted mRNAs segregated by eIF4E or NCBP2 sensitivity, distinct protein partners for these cap-chaperones and differential impacts on the production of key spliceosome components e.g. U2AF1, PRP31, SF3B1 and SNRNP200 indicative of distinct transcriptomic landscapes produced by eIF4E or NCBP2 overexpression. In all, the realization that multiple cap-binding proteins coexist in the nucleus led us to identify an unexpected gene-expression regulatory point which engaged distinct biological programmes.

genetics↗

bioRxiv2021

The human RNA polymerase I structure reveals an HMG-like transcription factor docking domain specific to metazoans

Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP-fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This dock II domain resembles a truncated HMG-box incapable of DNA-binding which may serve as a downstream-transcription factor binding platform in metazoans. Biochemical analysis and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG-box domain containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.

biochemistry↗

bioRxiv2021

Bidirectional cooperation between Ubtf1 and SL1 determines RNA Polymerase I promoter recognition in cell and is negatively affected in the UBTF-E210K neuroregression syndrome.

Transcription of the [~]200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAFI factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the Taf1b subunit of SL1 causes a striking depletion UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and -2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation.

molecular biology↗