Piotr Ziolkowski

Piotr Ziolkowski
Adam Mickiewicz University | UAM · Laboratory of Genome Biology, http://dgb.amu.edu.pl

PhD

About

96
Publications
9,124
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1,376
Citations
Citations since 2016
46 Research Items
1088 Citations
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2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
Introduction
I am interested in understanding molecular mechanisms responsible for regulation of gene expression at the level of chromatin remodeling and modification. Another research area which has been recently established in my lab is genetic control of meiotic recombination in plants. This research will add to our understanding of plant sexual reproduction, but will also find applications in modern plant breeding and biotechnology.
Additional affiliations
January 2016 - November 2017
Adam Mickiewicz University
Position
  • Principal Investigator
June 2000 - September 2005

Publications

Publications (96)
Article
Full-text available
It is believed that recombination in meiosis serves to reshuffle genetic material from both parents to increase genetic variation in the progeny. At the same time, the number of crossovers is usually kept at a very low level. As a consequence, many organisms need to make the best possible use from the one or two crossovers that occur per chromosome...
Article
Full-text available
During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained...
Article
Full-text available
The influence of the histone variant H2A.Z on transcription remains a long-standing conundrum. Here, by analyzing the actin-related protein6 mutant, which is impaired in H2A.Z deposition, and by H2A.Z profiling in stress conditions, we investigated the impact of this histone variant on gene expression in Arabidopsis thaliana. We demonstrate that th...
Article
Full-text available
During meiosis homologous chromosomes undergo crossover recombination. Sequence differences between homologs can locally inhibit crossovers. Despite this, nucleotide diversity and population-scaled recombination are positively correlated in eukaryote genomes. To investigate interactions between heterozygosity and recombination we crossed Arabidopsi...
Article
Full-text available
Significance The majority of eukaryotes reproduce sexually, creating genetic variation within populations. Sexual reproduction requires gamete production via meiotic cell division. During meiosis, homologous chromosomes pair and undergo exchange, called crossover. Crossover is vital for crop breeding and remains a major tool to combine useful trait...
Article
Full-text available
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and...
Article
Full-text available
Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloropl...
Chapter
The number of crossovers during meiosis is relatively low, so multiple meioses need to be analyzed to accurately measure crossover frequency. In Arabidopsis, systems based on the segregation of fluorescent T-DNA reporters that are expressed in seeds (fluorescent-tagged lines, FTLs) allow for an accurate measurement of crossover frequency in specifi...
Chapter
Investigating the process of gamete formation in plants often requires the use of mutants of selected genes in various genetic backgrounds. For example, analysis of meiotic recombination based on sequencing or genotyping requires the generation of hybrids between two lines. Although T-DNA mutant collections of Arabidopsis thaliana are vast and easi...
Article
Full-text available
The complexity of the subcellular processes that take place during meiosis requires a significant remodeling of cellular metabolism and dynamic changes in the organization of chromosomes and the cytoskeleton. Recently, investigations of meiotic transcriptomes have revealed additional noncoding RNA factors (ncRNAs) that directly or indirectly influe...
Article
Full-text available
Significance Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified...
Article
Full-text available
Zjawisko crossing-over (CO) polega na wzajemnej wymianie fragmentów chromatyd pomiędzy chromosomami homologicznymi i zachodzi podczas pierwszego podziału mejotycznego. Na ostateczną lokalizację i częstość crossing-over na chromosomie wpływa wiele czynników, m.in. aktywność modyfikatorów działających in trans, stopień metylacji chromatyny czy obecno...
Article
Full-text available
During meiosis, DNA double-strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects cross-overs, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, sh...
Poster
Full-text available
During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchanges via the crossovers, enabling to create novel genetic diversity all the while ensuring the formation of well-balanced gametes. Despite the critical functions of crossovers, their number and distribution vary extensively within and between species. Natural recombinat...
Preprint
Full-text available
NuA4, an essential histone acetyltransferase complex, is required for efficient transcription in eukaryotes. Using genome editing, genomic approaches and biochemical assays, we characterized plant homologues of two key components of this complex, EPL1 and EAF1 in Arabidopsis thaliana . Surprisingly, we found that loss of AtEPL1, which is necessary...
Article
Full-text available
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oli...
Article
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequencedArabidopsis thalianaSPO11-1-oligo...
Article
Full-text available
Chromatin Affinity Purification (ChAP) is widely used to study chromatin architecture and protein complexes interacting with DNA. Here we present an efficient method for ChAP from Arabidopsis thaliana rosette leaves, in which in vivo biotinylation system is used. The chromatin is digested by Micrococcal Nuclease (MNase), hence the distribution of n...
Preprint
Full-text available
Meiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleo...
Article
Full-text available
Meiosis is fundamental to sexual reproduction and creates genetic variation in progeny. During meiosis paired homologous chromosomes undergo recombination, which can result in reciprocal crossovers. This process can recombine independently arising mutations onto the same chromosome. Recombination locations are highly variable between meioses, altho...
Article
Full-text available
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) ge...
Data
Overlap of crossovers with NBS-LRR genes compared with other genes. (A) The distribution of distances between start coordinates for NBS-LRR genes (black) and sampled data (blue). (B) As for (A), but showing the distribution of gene widths. (C) Boxplot showing the distribution of the number of crossovers per gene from the sampled data. The red point...
Data
Validation of template specificity for RAC1 allele-specific oligonucleotides used for pollen-typing. Representative ethidium bromide stained agarose gels are shown with PCR amplification products generated using either Col or Ler genomic DNA as a template. Reactions were repeated using the gradient of annealing temperatures indicated at the top of...
Data
Crossover frequency within the MRC1 NBS-LRR supercluster region. The table lists marker coordinates used to genotype double-selected MRC1 crossover individuals, together with Col and Ler genotypes and interval lengths (bp). The number of crossovers identified in each interval is shown, together with cM/Mb. Eurasian and Swedish historical recombinat...
Data
Fine-mapping crossovers within the HRG4-HRG5 MRC1 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Measurement of I5a genetic distance using fluorescent pollen and flow cytometry. The first column lists the accession the I5a reporter (Col-0) was crossed to. In the case of Col-0 this represents data from Col-0/Col-0 homozygotes. The total number of pollen counted is listed, in addition to the number with red fluorescence alone (Red), yellow alone...
Data
RAC1 primer sequences used for allele-specific PCR amplification. Positions annealing to Col/Ler polymorphic bases in the allele-specific primers are indicated in red. The accession each primer anneals to is listed (Col or Ler), together with a code indicating whether the primer is forward or reverse (F or R) and used in the first or second round o...
Data
Identifying single locus KAN and BAR lines for MRC genetic mapping. (A) Representative Southern blots used to identify single copy SAIL and SGT lines. Replicate samples indicate DNA isolated from siblings. Single copy lines were identified for further experiments. (B) Self-fertilization of homozygous KAN or BAR lines should yield ~100% resistance p...
Data
RPP4-RPP5 structural diversity between Arabidopsis accessions analysed by Southern blotting and hybridization. Genomic DNA was isolated from the indicated accessions and digested with AseI. DNA was separated using gel electrophoresis, blotting and probing using radio-labelled RPP4 DNA. (TIFF)
Data
Arabidopsis thaliana NBS-LRR gene family annotation. For each gene, chromosome, transcriptional start site (TSS) and termination site (TTS) are listed according to TAIR10 representative gene models. Historical recombination (cM/Mb) and diversity parameters (θ and π) were calculated for intragenic regions between TSS and TTS, using Eurasian and Swed...
Data
Fine-mapping crossovers within the HRG1 MRC1 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Fine-mapping crossovers within the WRR4 MRC1 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Fine-mapping crossovers within the CW9 MRC1 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Fine-mapping crossovers within the HRG9 MRC5 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Measurement of RAC1 recombination rate via pollen-typing. A 9.419 kb amplicon (Chr1: 11,288,146–11,297,565 bp) containing the RAC1 gene was amplified using allele-specific oligonucleotides to estimate the number of parental (non-recombinant) and crossover molecules per μl of Col/Ler F1 pollen genomic DNA. Genetic distance was calculated as describe...
Data
HRG1 structural diversity between Arabidopsis accessions analysed by Southern blotting and hybridization. Genomic DNA was isolated from the indicated accessions and digested with EcoRV. DNA was separated using gel electrophoresis, blotting and probing using radio-labelled HRG1 DNA. (TIFF)
Data
RPP1 structural diversity between Arabidopsis accessions analysed by Southern blotting and hybridization. Genomic DNA was isolated from the indicated accessions and digested with HaeII and PstI. DNA was separated using gel electrophoresis, blotting and probing using radio-labelled RPP1 DNA. (TIFF)
Data
Fine-mapping crossovers within the HRG7-HRG8 MRC5 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Recombination rates of plant crossover hotspots. The mean and maximum crossover frequency (cM/Mb) measured at known plant hotspots is listed, together with the species studied, hotspot name, width of measured region, genetic distance (cM) and crossover frequency (cM/Mb), together with chromosome average recombination rates. (DOCX)
Data
Crossovers identified by genotyping by sequencing in a Col×Ler F2 population. 192 Col×Ler F2 individuals were analysed by genotyping-by-sequencing. The number of crossovers (CO) per F2 and in total are listed, for the whole genome and for each chromosome separately. (DOCX)
Data
Crossover distributions across the RAC1 R gene hotspot analysed via pollen typing. 181 single RAC1 crossover molecules were Sanger sequenced to identify recombination sites to the resolution of single polymorphisms. Col and Ler genotypes and number of crossovers per interval are listed, together with cM/Mb. (DOCX)
Data
RAC1 crossover read pair analysis pipeline. The number of read pairs surviving sequential analysis filters are listed in order to identify RAC1 crossover read pairs. Paired end reads (1 and 2) were separated and aligned to the Col or Ler RAC1 parental template sequences, allowing only exact matches (Mapped). Read pair ends that mapped to both Col a...
Data
CTT-repeat motifs associated with high and low MRC recombination NBS-LRR genes. NBS-LRR genes located within the MRC genetic maps were divided into two groups according to whether their interval had higher or lower crossover frequency (cM/Mb) compared with the male Col×Ler genome average (4.82 cM/Mb) [71]. We then matched the position weight matrix...
Data
Crossover frequency within the MRC5 NBS-LRR supercluster region. The table lists marker coordinates used to genotype double-selected MRC5 crossover individuals, together with Col and Ler genotypes and interval length (bp). The number of crossovers identified in each interval is shown, together with cM/Mb. Eurasian and Swedish historical recombinati...
Data
Fine-mapping crossovers within the HRG2 HRG3 MRC5 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Data
Fine-mapping crossovers within the HRG6 MRC1 map interval using dCAPs genotyping. The ‘Genotyping Assay’ column indicates whether a given marker coordinate was genotyped by KBiosciences (SNP), or via dCAPs assays. (DOCX)
Article
Full-text available
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) ge...
Article
During meiosis homologous chromosomes undergo crossover recombination. Sequence differences between homologs can locally inhibit crossovers. Despite this nucleotide diversity and population-scaled recombination are positively correlated in eukaryote genomes. To investigate interactions between heterozygosity and recombination we crossed Arabidopsis...
Article
Full-text available
Histone acetyltransferase complex NuA4 and histone variant exchanging complex SWR1 are two chromatin modifying complexes which act cooperatively in yeast and share some intriguing structural similarities. Protein subunits of NuA4 and SWR1-C are highly conserved across eukaryotes, but form different multiprotein arrangements. For example, the human...
Article
Full-text available
Ethylene plays a crucial role in various biological processes and therefore its biosynthesis is strictly regulated by multiple mechanisms. Post-translational regulation, which is pivotal in controlling ethylene biosynthesis, impacts 1-aminocyclopropane 1-carboxylate synthase (ACS) protein stability via the complex interplay of specific factors. Her...
Article
Full-text available
During meiosis, reciprocal exchange between homologous chromosomes occurs as a result of crossovers (COs). CO frequency varies within genomes and is subject to genetic, epigenetic and environmental control. As robust measurement of COs is limited by their low numbers, typically 1-2 per chromosome, we adapted flow cytometry for use with Arabidopsis...
Article
Full-text available
PRDM9 directs human meiotic crossover hot spots to intergenic sequence motifs, whereas budding yeast hot spots overlap regions of low nucleosome density (LND) in gene promoters. To investigate hot spots in plants, which lack PRDM9, we used coalescent analysis of genetic variation in Arabidopsis thaliana. Crossovers increased toward gene promoters a...
Article
Comparison of genome sequences has become an important approach to identify and understand biological significance of the variations and fluxes that occur through a genome. The main subject of the work concentrates on identification of indels and SNPs in large genomes and their potential application in biotechnology. Importantly, fine elaboration o...
Article
Full-text available
We further investigated genome macrosynteny for Brassica species and Arabidopsis thaliana. This work aimed at comparative map construction for B. oleracea and A. thaliana chromosomes based on 160 known A. thaliana probes: 147 expressed sequence tags (ESTs) and 13 full-length cDNA clones. Based on an in silico study of the A. thaliana genome, most o...
Article
Full-text available
Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (C...