Michal Gdula

Adam Mickiewicz University in Poznań | UAM · Faculty of Biology

Defining the beginning of a eukaryotic protein-coding gene is relatively simple. It corresponds to the first ribonucleotide incorporated by RNA polymerase II (Pol II) into the nascent RNA molecule. This nucleotide is protected by capping and maintained in the mature messenger RNA (mRNA). However, in higher eukaryotes, the end of mRNA is separated f...

Usage of alternative mRNA 3′ ends has profound functional consequences, particularly in the nervous system. In this issue of Neuron, LaForce et al. (2022) dissect the effect of CLP1 on mRNA 3′ end diversity in motor neuron models of neurodegeneration.

DNA damage through endogenous and environmental toxicants is a constant threat to both a human’s ability to pass on intact genetic information to its offspring as well as in somatic cells for its own survival. To counter these threats posed by DNA damage, cells have evolved a series of highly choreographed mechanisms—collectively defined as the DNA...

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for...

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, co...

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for...

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), and formation of two mega-domains. In this study we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contribute...

Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the geno...

5C data correction and normalization for the keratinocyte library replicate 2. In all heatmaps the reverse probes shown in columns and forward probes shown in rows. (a) Raw data (b) Data after 5C probe cis-purge. Grey stripes represent probes that were removed (c) Data after singleton interaction removal. Grey stripes are the primers removed in the...

(a) Relative mRNA expression levels in freshly plated murine keratinocytes and thymocytes aligned to the schematic map of the 5,3 Mb locus analyzed using 5C technologyin this study. (b) Heatmaps representing raw 5C data for both TC replicates. Reverse probes are plotted as columns and the forward probes as rows. Pearson’s correlation coefficient is...

5C data correction and normalization for the thymocyte library replicate 1. In all heatmaps the reverse probes shown in columns and forward probes shown in rows. (a) Raw data (b) Data after 5C probe cis-purge. Grey stripes represent probes that were removed (c) Data after singleton interaction removal. Grey stripes are the primers removed in the pr...

5C data correction and normalization for the thymocyte library replicate 2. In all heatmaps the reverse probes shown in columns and forward probes shown in rows. (a) Raw data (b) Data after 5C probe cis-purge. Grey stripes represent probes that were removed (c) Data after singleton interaction removal. Grey stripes are the primers removed in the pr...

5C data correction and normalization for the keratinocyte library replicate 1. In all heatmaps the reverse probes shown in columns and forward probes shown in rows. (a) Raw data (b) Data after 5C probe cis-purge. Grey stripes represent probes that were removed (c) Data after singleton interaction removal. Grey stripes are the primers removed in the...

(a) Heatmap representing the 5C data after the normalization and binning (bin size 150 kb, step size 15kb) in TCs. The position of TAD border midpoints (average for the midpoints calculated based on the insulation index analysis in two replicates independently) are identified by green lines under the heatmaps. Schematic map of the studied locus and...

BAC probes used for the 3D FISH analysis. (XLSX)

Micro-array expression data in keratinocytes and thymocytes. (XLSX)

3D FISH inter-probe distances. (XLSX)

All significant 5C looping interactions reproducible in both keratinocyte library replicates. (XLSX)

Keratinocyte-specific 5C interactions. (XLSX)

Thymocyte-specific 5C interactions. (XLSX)

All significant 5C looping interactions reproducible in both thymocyte library replicates. (XLSX)

5C interactions common in keratinocytes and thymocytes. (XLSX)

Gene enhancers identified by H3K4me1 and H3K27ac ChIP-seq. (XLSX)

5C interactions between gene promoters and enhancers. (XLSX)

All 5C interactions involving gene enhancers. (XLSX)

5C probes removed in probe filtering step. (XLSX)

5C interactions between gene enhancers and promoters in different TADs. (XLSX)

Individual interactions removed in singleton removal step. (XLSX)

Polycomb steps to inactivate X XX females silence one of their X chromosomes. This involves a process whereby a noncoding RNA known as Xist coats one of the X chromosomes and recruits chromatin silencing factors. The Polycomb complexes PRC1 and PRC2 are also known to be involved in X chromosome inactivation. Almeida et al. elucidate a key role of a...

The Polycomb repressive complexes PRC1 and PRC2 are key mediators of heritable gene silencing in multicellular organisms. Here we characterise AEBP2, a known PRC2 cofactor which, in vitro, has been shown to stimulate PRC2 activity. We show that AEBP2 localises specifically to PRC2 target loci, including the inactive X chromosome. Proteomic analysis...

In Saccharomyces cerevisiae, short noncoding RNA (ncRNA) generated by RNA polymerase II (Pol II) are terminated by the NRD complex consisting of Nrd1, Nab3, and Sen1. We now show that Pcf11, a component of the cleavage and polyadenylation complex (CPAC), is also generally required for NRD-dependent transcription termination through the action of it...

Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation...

Significance Polycomb repressor proteins are recruited to the inactive X chromosome in mammals, and this has been attributed to a biochemical interaction between the non–protein-coding RNA X-inactive specific transcript (Xist), which initiates the X inactivation process, and core polycomb subunits. We have studied this using a combination of genome...

DNA damage through endogenous and environmental toxicants is a constant threat to both a human's ability to pass on intact genetic information to its offspring as well as somatic cells for their own survival. To counter these threats posed by DNA damage, cells have evolved a series of highly choreographed mechanisms-collectively defined as the DNA...

The nucleus of epidermal keratinocytes is a complex and highly compartmentalized organelle, whose structure is markedly changed during terminal differentiation and transition of the genome from a transcriptionally active state seen in the basal and spinous epidermal cells to a fully inactive state in the keratinized cells of the cornified layer. He...

The nucleus is a complex and highly compartmentalized organelle, which undergoes major organization changes during cell differentiation, allowing cells to become specialized and fulfill their functions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes a programmed transformation from active status, associated wi...

The relevance of preconceptional and prenatal toxicant exposures for genomic stability in offspring is difficult to analyze in human populations, because gestational exposures usually cannot be separated from preconceptional exposures. To analyze the roles of exposures during gestation and conception on genomic stability in the offspring, stability...

Current immunisation programmes against hepatitis B virus (HBV) increasingly often involve novel tri-component vaccines containing—together with the small (S-HBsAg)—also medium and large surface antigens of HBV (M- and L-HBsAg). Plants producing all HBsAg proteins can be a source of components for a potential oral ‘triple’ anti-HBV vaccine. The obj...

Supplementary Fig. 1. PCR analysis of the M-HBs or L-HBs transgene in plants. a M-HBs in 18-month-old tobacco plants, b L-HBs in 18-month-old tobacco plants, c M-HBs in lettuce plants of T1 generation, d L-HBs in lettuce plants of T1 generation The transgenes were amplified using primers designed to M-HBsAg coding sequence (a, c) to amplify a 864 b...

Supplemetary Fig. 2. Southern blot analysis of integrated T-DNA in genomic DNA using a probe complementary to the M- or L-HBs sequence. a M-HBs in 18-month-old tobacco plants, b L-HBs in 18-month-old tobacco plants, c M-HBs in lettuce plants of T1 generation, d L-HBs in lettuce plants of T1 generation Lanes 1–19 (a), 23A-90 (b), 1E/4–18A/31 (c) and...

During development, multipotent progenitor cells establish tissue-specific programs of gene expression. In this paper, we show that p63 transcription factor, a master regulator of epidermal morphogenesis, executes its function in part by directly regulating expression of the genome organizer Satb1 in progenitor cells. p63 binds to a proximal regula...

Efficient immunization against hepatitis B virus (HBV) and other pathogens with plant-based oral vaccines requires appropriate plant expressors and the optimization of vaccine compositions and administration protocols. Previous immunization studies were mainly based on a combination of the injection of a small surface antigen of HBV (S-HBsAg) and t...