Biology subjects

Wozniak, T.

Publications and source records attributed to Wozniak, T..

5 recordsLinked to original sources

bioRxiv2026

Reconstructing their genomes confirms the historically attested genealogy of the two medieval emperors Otto I (the Great) and Heinrich II (Saint Henry)

The Medieval Ottonian dynasty had a lasting impact on European history. We obtained ancient genomic DNA from the purported remains of Otto I (912-973) and Heinrich (Henry) II (973-1024), the first and last emperors of this dynasty, preserved in the cathedrals of Magdeburg and Bamberg, respectively. Historical records attest that they were related as a great-uncle and a grandnephew via the paternal line. Whole-genome sequencing confirms such a relationship between the two individuals, as we identify a third-degree genetic relationship based on shared DNA segments and infer matching Y haplogroups. This genetic relatedness effectively identifies the remains of the two emperors. The authentication yields a valuable resource for refining and calibrating bio-archaeological methods. Because historical records provide the precise lifespans and dates of death of these individuals, their remains can serve as a "ground-truth" for methods such as radiocarbon dating and age-at-death estimates. They can provide calibration data to improve our understanding of the radiocarbon reservoir effects of Medieval elites. As the Ottonian lineage was closely linked to the mating networks of elites across Europe, the genomes of the two emperors are valuable resources for identifying other potential elite burials.

genetics↗

bioRxiv2022

TransCRISPR - sgRNA design tool for CRISPR/Cas9 experiments targeting transcription factor motifs

Eukaryotic genomes contain several types of recurrent DNA motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial DNA motifs. We present transCRISPR, the first online tool dedicated to search for DNA sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen DNA motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sites, and others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/

molecular biology↗

bioRxiv2021

CRISPR/Cas9 screen for functional MYC binding sites reveals MYC-dependent vulnerabilities in K562 cells

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell type- and developmental stage-specific manner. To date, a comprehensive analysis of direct MYC targets with essential roles in different types of cancer is missing. To enable identification of functional MYC binding sites and corresponding target genes, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knockout protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines: K562, ST486, HepG2 and MCF7, which revealed several essential E-boxes and genes. Among them we pinpointed crucial known and novel MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach in K562 cells confirmed that E-box disruption affects MYC binding, target genes expression and cell proliferation. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.

molecular biology↗

bioRxiv2020

RNAlign2D, a novel RNA structural alignment tool based on pseudo-amino acid substitution matrix

BackgroundThe functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs. ResultsHere, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE. ConclusionsRNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.

bioinformatics↗

bioRxiv2019

Human PUM1 and PUM2 exhibit regulation of divergent mRNA targets in male germ cells

Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding proteins with wide-ranging roles, including germ cell development that has functional implications in fertility. Although human PUM1 and PUM2 are closely related to each other and recognize the same RNA binding motif, there is some evidence for functional diversity, particularly related to their roles in fertility. Here, by RNA sequencing (RNA-Seq) approaches, we identified separate mRNA pools regulated by PUM1 and PUM2 proteins in human male germ cells. Using global mass spectrometry-based profiling, we identified distinct PUM1- and PUM2-bound putative protein cofactors, most of them involved in RNA processing. Combinatorial analysis of RNA-Seq and mass spectrometry findings revealed that PUM1 and PUM2 may form distinct RNA-regulatory networks, with different roles in human reproduction and testicular tumorigenesis. Our findings highlight the functional divergence and versatility of PUM paralogue-based post-transcriptional regulation, offering insight into the mechanisms underlying their diverse biological roles and diseases resulting from their dysfunction.

molecular biology↗