Biology subjects

Szczesniak, M. W.

Publications and source records attributed to Szczesniak, M. W..

3 recordsLinked to original sources

bioRxiv2023

Interplay between m6A modification and overall transcripts quantity: Impacts on mRNA composition in plant stress granules

Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. They contain a rich pool of RNA, including non-translated mRNA. The mechanisms governing transcripts accumulation in SGs is only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs composition and assembly remains elusive. We examined the formation of SGs, the presence of m6A, and the transcription-level-dependent localization of selected mRNAs within these granules during hypoxia in the roots of Lupinus angustifolius and Arabidopsis thaliana. In lupine, SGs exhibit a distinctive bi-zonal structure, comprising of a ring and a central area with differences in ultrastructure and composition. Following the transcriptome analysis, mRNAs were selected for examination of their localization in SGs and m6A levels. Transcripts from genes responsive to hypoxia (ADH1 and HUP7) exhibited significant lower levels of m6A compared to housekeeping genes but only ADH1 was not present in SGs. HUP7 mRNA with low quantity of m6A, is present both in the SGs and cytoplasm probably due to extremely high expression level. It was also shown that the amount of m6A in SGs was higher than in the cytoplasm only in the first hours of hypoxia and then decreased. In mutants of A. thaliana with reduced level of m6A, formation and quantity of SGs were studied. In this line, ECT2 was not observed and poly(A) RNA levels were slightly reduced in SGs. Additionally the number of SGs was lower than that of the wild type. In summary, our findings demonstrate the limited impact of m6A modification on SGs assembly. However the interplay between m6A modification and the overall transcript quantity in the cytoplasm plays a regulatory role in mRNA partitioning into SGs.

cell biology↗

bioRxiv2023

Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells

U7 snRNA is part of U7 snRNP, a complex required for the 3end processing of replication-dependent histone pre-mRNAs in the S phase of the cell cycle. During this maturation event, the 5 region of U7 snRNA hybridizes with the highly complementary sequence present in the 3UTR of histone pre-mRNAs, called histone downstream element, HDE. This base-pair interaction triggers subsequent reactions that eventually result in cleavage and release of mature histone transcripts. Intriguingly, U7 snRNP is constitutively expressed throughout the cell cycle and in nondividing cells, suggesting another function of U7 snRNA/snRNP in cells. Here, we show that several human endogenous retroviruses (HERVs) are significantly upregulated in HEK293T cells with U7 snRNA knockdown. They predominantly belong to the LTR12 class. Interestingly, some of them are located within long intergenic noncoding RNAs (lincRNAs), which in turn are upregulated in U7 snRNA knockdown cells as well. Significantly, both these HERV1/LTR12s and lincRNAs contain two or more sequence motifs that perfectly match the 5 end of U7 snRNA, which we called HDE-like motifs. We confirmed that mutations within the HDE-like motifs abrogate U7 snRNA regulatory function and stimulate the expression of selected lincRNAs. Furthermore, we demonstrate that U7 snRNA inhibits HERV1/LTR12 and lincRNA expression at the transcription level. We propose a mechanism in which U7 snRNA hampers binding/activity of NF-Y transcription factor to CCAAT motifs that are frequently found in LTRs as well as in a close proximity to HDE-like motifs. The expression of many HERV1/LTR12s and lincRNAs regulated by U7 snRNA seems to be tissue specific, therefore, we suggest that U7 snRNA plays a protective role in keeping deleterious genetic elements in silence in selected types of cells.

molecular biology↗

bioRxiv2022

FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression

FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this paper, we show that FUS depletion results in differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2-O methylation (2-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and/or progression.

molecular biology↗