Department of Biological DNA Modification

 VO1V0110bx Head
Saulius KLIMAŠAUSKAS 
Dr. Habil., FRSC
Distinguished Professor
ORCID;Google ScholarResearcherID
phone: +370 5 2234350
fax: +370 5 2234367
e-mail: saulius.klimasauskas (at) bti.vu.lt

Research Staff                            PhD students

Giedrius Vilkaitis, Ph.D.             Stasė Gasiulė, M.Sc.
Edita Kriukienė,  Ph.D.              Janina Ličytė, M.Sc.
Rasa Rakauskaitė, Ph.D.            Milda Mickutė, M.Sc.
Viktoras Masevičius, Ph.D.         Povilas Gibas, M.Sc.
Juozas Gordevičius, Ph.D.          Milda Narmontė, M.Sc.
Miglė Tomkuvienė, Ph.D.
Vaidotas Stankevičius, Ph.D.
Aleksandr Osipenko, Ph.D.
Zdislav Staševskij, M.Sc.

Giedrė Urbanavičiūtė, M.Sc.
Kotryna Kvederavičiūtė, M.Sc.
Audronė Rukšėnaitė, M.Sc.

 E Kurausko foto 0054x

Research Overview

AdoMet-dependent methyltransferases (MTases), which represent more than 3% of the proteins in the cell, catalyze the transfer of the methyl group from S-adenosyl-L-methionine (AdoMet) to N-, C-, O- or S-nucleophiles in DNA, RNA, proteins or small biomolecules.

In DNA, enzymatic methylation of nucleobases serves to expand the information content of the genome in organisms ranging from bacteria to mammals. Postreplicative methylation is accomplished by DNA methyltransferases yielding 5-methylcytosine, N4-methylcytosine or N6-methyladenine (Kweon et al., 2019). Genomic DNA methylation is a key epigenetic regulatory mechanism in high eukaryotes. Aberrant DNA methylation correlates with a number of pediatric syndromes and cancer, or predisposes individuals to various other human diseases. However, research into the epigenetic misregulation and its diagnostics is hampered by the limitations of available analytical techniques. 

 

Targeted covalent labeling of biopolymers

Besides their diverse biological roles, DNA MTases are attractive models to study the structural aspects of DNA-protein interaction. Bacterial enzymes recognize an impressive variety (over 200) of short sequences in DNA. Following detailed mechanistic and structural studies of MTases, we turned to repurposing these enzymes sequence-specific covalent modification of DNA and other biopolymers. Our strategy is based on designing novel synthetic analogues of the natural cofactor AdoMet. We have synthesized a series of model AdoMet analogs with sulfonium-bound extended side chains replacing the methyl group (Klimašauskas and Weinhold, 2007). This novel enabling technology named mTAG (methyltransferase-directed Transfer of Activated Groups) is a convenient and robust technique that is suitable for routine laboratory use. In particular, we demonstrated that propargylic side chains can be efficiently transferred by DNA MTases with high sequence- and base-specificity (Lukinavičius et al., 2007, 2012 and 2013; Masevičius et al., 2016; Tomkuvienė et al., 2016; Tomkuvienė et al., 2019) offering many potential applications for genomic (Neely et al., 2010) and epigenomic (see below) studies. Moreover, the newly developed cofactors are suitable for targeted transfer of functional groups or other chemical entities to RNA (Tomkuvienė et al., 2012; Plotnikova et al., 2014; Osipenko et al., 2017; Mickutė et al., 2018) using appropriate MTases as catalysts. 

In the absence of the S-adenosylmethionine cofactor, bacterial cytosine-5 MTases can catalyze catalyze reversible covalent addition of exogenous aliphatic aldehydes to their target residues in DNA, thus yielding corresponding 5-hydroxyalkylcytosines (Liutkevičiūtė et al., 2009). Moreover, our further studies demonstrated the ability of the MTases to direct condensation of aliphatic thiols and selenols with 5-hydroxymethylcytosine in DNA to yield 5-alkylchalcogenomethyl derivatives (Liutkevičiūtė et al., 2011) or decarboxylation of 5-carboxylcytosines (Liutkevičiūtė et al., 2014) in DNA. These atypical reactions demonstrate a surprizing catalytic versatility of these enzymes and pave new ways for the sequence-specific derivatization and analysis of 5-hydroxymethylcytosine, a recently discovered nucleobase in mammalian DNA (Kriukienė et al., 2012).

 

Novel approaches to epigenome profiling

Genomic DNA methylation is a prevalent epigenetic modification in mammals, which is brought about by three known DNA cytosine-5 methyltransferases (DNMTs). Although DNA methylation has been extensively investigated, many mechanistic aspects of the DNMT action remain obscure due limitations of current analytical techniques. We therefore aim to develop new experimental approaches to genome-wide profiling of DNA methylation for epigenome studies and improved diagnostics. Our approach is based on selective mTAG labeling and enrichment of unmethylated CpG sites (Gerasimaitė et al., 2009; Kriukienė et al. 2013; Labrie et al., 2016) in the genome followed by analysis of the enriched fractions on tiling microarrays (in collaboration with Prof. Art Petronis, CAMH, Toronto, Canada). Recently, we have advanced DNA methylome profiling by developing a high-resolution economical technique named Tethered Oligonucleotide-Primed sequencing, TOP-seq, which exploits non-homologous priming of the DNA polymerase at covalently tagged CpG sites to directly produce adjoining regions for their sequencing and precise genomic mapping (Staševskij et al., 2017). Our current ERC-supported studies seek to gain in-depth understanding of how the genomic methylation patterns are established and how they govern cell plasticity and variability during differentiation and development. These questions could be answered by precise determination of where and when methylation marks are deposited by the individual DNMTs, and how these methylation marks affect gene expression.

  Advanced Grant support for the EpiTrack project

 

Methylation of small non-coding RNA

MicroRNAs and siRNAs are small non-coding double-stranded RNA molecules that control gene activity in a homology-dependent manner - a process named RNA interference. Since their discovery in 1993, numerous microRNAs have been identified and recognized as important regulators of gene expression in both plants and animals. Many microRNAs have well-defined developmental and tissue-specific expression pattern, but a great number of microRNAs and their roles are still unknown.

Biogenesis of miRNAs and siRNAs in plants differs from that in animals as it involves an additional methylation step catalyzed by the HEN1 methyltransferase. HEN1 from Arabidopsis catalyzes the transfer methyl groups from AdoMet onto the 2'OH group of the 3'-terminal nucleotide of small RNAs, like miRNA/miRNA* and siRNA/siRNA*. The methylation is imperative in the biogenesis of microRNA in Arabidopsis. A number of biochemical approaches have been developed in our laboratory for examining the unique methyltransferase HEN1 (Yang et al., 2007; Vilkaitis et al., 2010; Plotnikova et al., 2013; Baranauskė et al., 2015).

 

Recent publications

S.-M. Kweon, Y. Chen, E. Moon, K. Kvederaviciute, S. Klimašauskas and D.E. Feldman
An adversarial DNA N6-methyladenine-sensor network preserves polycomb silencing.
Mol. Cell, 2019, 74: 1138-1147.e6.

M. Tomkuvienė, M. Mickutė, G. Vilkaitis, and S. Klimašauskas
Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA.
Curr. Opin. Biotechnol., 2019, 55: 114-123.

K. Daniūnaitė, S. Jarmalaitė, and E. Kriukienė
Epigenomic technologies for diciphering circulating tumor DNA.
Curr. Opin. Biotechnol., 2019, 55: 23-29.

M. Mickutė, M. Nainytė, L. Vasiliauskaitė. A. Plotnikova, V. Masevičius, S. Klimašauskas and G. Vilkaitis
Animal Hen1 2′-O-methyltransferases as tools for 3′-terminal functionalization and labelling of single-stranded RNAs.
Nucleic Acids Res., 2018, 46: 
e104.

M. Alexeeva, P. Guragain, A.N. Tesfahun, M. Tomkuvienė, A. Arshad, R. Gerasimaitė, A. Rukšėnaitė, G. Urbanavičiūtė, M. Bjørås, J.K. Laerdahl, A. Klungland, S. Klimašauskas and S. Bjelland
Excision of the double methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins.
Phil. Trans. R. Soc. B, 2018, 373(1748): 20170337.

J. Gordevičius, A. Kriščiūnas, D.E. Groot, S.M. Yip, M. Susic, A. Kwan, R. Kustra, A.M. Joshua, K.N. Chi, A. Petronis, and G. Oh.
Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients.
Clin. Cancer Res., 2018, 24(14): 3317-3324.

M. Tomkuvienė, J. Ličytė, I. Olendraitė, Z. Liutkevičiūtė, B. Clouet-d'Orval and S. Klimašauskas
Archaeal fibrillarin-Nop5 heterodimer 2'-O-methylates RNA independently of the C/D guide RNP particle.
RNA, 2017, 23(9): 1329-1337.

A. Osipenko, A. Plotnikova, M. Nainytė, V. Masevičius, S. Klimašauskas, and G. Vilkaitis 
Oligonucleotide-addressed covalent 3’-terminal derivatization of small RNA strands for enrichment and visualization.
Angew. Chem. Int. Ed., 2017, 56(23): 6507–6510.

Z. Staševskij, P. Gibas, J. Gordevičius, E. Kriukienė, and S. Klimašauskas
Tethered Oligonucleotide-Primed sequencing, TOP-seq: a high resolution economical approach for DNA epigenome profiling. 
Mol. Cell, 2017, 65(3): 554–564.

M. Tomkuvienė, E. Kriukienė, and S. Klimašauskas
DNA labeling using DNA methyltransferases.
Adv. Exp. Med. Biol., 2016, 945: 511-535.

V. Labrie, O. J. Buske, E. Oh, R. Jeremian, C. Ptak, G. Gasiūnas, A. Maleckas, R. Petereit, A. Žvirbliene, K. Adamonis, E. Kriukienė, K. Koncevičius, J. Gordevičius, A. Nair, A. Zhang, S. Ebrahimi, G. Oh, V. Šikšnys, L. Kupčinskas, M. Brudno, and A. Petronis
Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.
Nature Struct. Mol. Biol2016, 23(6): 566-573.

V. Myrianthopoulos, P. F. Cartron, Z. Liutkevičiūtė, S. Klimašauskas, D. Matulis, C. Bronner, N. Martinet, and E. Mikros
Tandem virtual screening targeting the SRA domain of UHRF1 identifies a novel chemical tool modulating DNA methylation.
Eur. J. Med. Chem., 2016, 114: 390–396.

V. Masevičius, M. Nainytė, and S. Klimašauskas
Synthesis of S-adenosyl-L-methionine analogs with extended transferable groups for methyltransferase-directed labeling of DNA and RNA. 
Curr. Protoc. Nucleic Acid Chem., 2016, 64: 1.36.1-1.36.13.

D. Esyunina, M. Turtola, D. Pupov, I. Bass, S. Klimašauskas, G. Belogurov, and A. Kulbachinskiy 
Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.
Nucleic Acids Res., 2016, 44(3): 1298–1308

R. Rakauskaitė, G. Urbanavičiūtė, A. Rukšėnaitė, Z. Liutkevičiūtė,  R. Juškėnas, V. Masevičius, and S. Klimašauskas
Biosynthetic selenoproteins with geneticallyencoded photocaged selenocysteines.
Chem. Commun., 2015, 51(39): 8245-8248.

S. Baranauskė, M. Mickutė, A. Plotnikova, A. Finke, Č. Venclovas, S. Klimašauskas, and G. Vilkaitis 
Functional mapping of the plant small RNAmethyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins.
Nucleic Acids Res., 2015, 43(5): 2802-2812.

A. Plotnikova, A. Osipenko,  V. Masevičius, G. Vilkaitis, and S. Klimašauskas
Selective covalent labeling of miRNA and siRNA duplexes using HEN1 methyltransferase.
J. Am. Chem. Soc., 2014, 136(39): 
13550–13553.

Z. Liutkevičiūtė, E. Kriukienė, J. Ličytė, M. Rudytė, G. Urbanavičiūtė, and S. Klimašauskas
Direct decarboxylation of 5-carboxylcytosine by DNA C5-methyltransferases.
J. Am. Chem. Soc
., 2014, 136(16): 5884−5887.

N. Miropolskaya, D. Esyunina, S. Klimašauskas, V. Nikiforov, I. Artsimovitch, and A. Kulbachinskiy 
Interplay between the trigger loop and the F loop during RNA polymerase catalysis.
Nucleic Acids Res., 2014, 42(1): 544–552

E. Kriukienė, V. Labrie, T. Khare, G. Urbanavičiūtė, A. Lapinaitė, K. Koncevičius, D. Li, T. Wang, S. Pai,C. Ptak, J. Gordevičius, S.C. Wang, A. Petronis, and S. Klimašauskas
DNA unmethylome profiling by covalent capture of CpG sites.
Nature Commun., 2013, 4: 2190.

A. Plotnikova, S. Baranauskė, A. Osipenko, S. Klimašauskas, and G. Vilkaitis
Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase.
Biochem J., 2013, 453: 281-290.

G. Lukinavičius, M. Tomkuvienė, V. Masevičius, and S. Klimašauskas
Enhanced chemical stability of AdoMet analogues for improved methyltransferase-directed labeling of DNA.
ACS Chem. Biol., 2013, 8: 1134-1139.

T. Khare, S. Pai, K. Koncevičius, M. Pal, E. Kriukienė, Z. Liutkevičiūtė, M. Irimia, P. Jia, C. Ptak, M. Xia, R. Tice, M. Tochigi, S. Moréra, A. Nazarians, D. Belsham, A.H.C. Wong, B.J. Blencowe, S.C. Wang, P. Kapranov, R. Kustra, V. Labrie, S. Klimašauskas, and A. Petronis
5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary.

Nature Struct. Mol. Biol., 2012, 19: (10) 1037–1043.

E. Kriukienė, Z. Liutkevičiūtė, and S. Klimašauskas
5-Hydroxymethylcytosine – the elusive epigenetic mark in mammalian DNA.

Chem. Soc. Rev., 2012, 41: (21) 69166930.

G. Lukinavičius, A. Lapinaitė, G. Urbanavičiūtė, R. Gerasimaitė, and S. Klimašauskas
Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA.
Nucleic Acids Res., 2012, 40, (22) 1159411602.

M. Tomkuvienė, B. Clouet-d'Orval, I. Černiauskas, E. Weinhold, and S. Klimašauskas
Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases.
Nucleic Acids Res., 2012, 40, (14) 6765-6773.

R. Sakaguchi, A. Giessing, Q. Dai, G. Lahoud, Z. Liutkevičiūtė, S. Klimašauskas, J. Piccirilli, F. Kirpekar, and Y.-M. Hou
Recognition of guanosine by dissimilar tRNA methyltransferases.

RNA, 2012, 18: 1687–1701.

Z. Liutkevičiūtė, E. Kriukienė, I. Grigaitytė, V. Masevičius and S. Klimašauskas
Methyltransferase-directed derivatization of 5-hydroxymethylcytosine in DNA.
Angew. Chem. Int. Ed., 2011, 50: 2090-2093.

R. Gerasimaitė, E. Merkienė and S. Klimašauskas 
Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase. 
Nucleic Acids Res., 2011, 39: 3771-3780.

R.K. Neely, P. Dedecker, J. Hotta, G. Urbanavičiūtė, S. Klimašauskas, and J. Hofkens
DNA fluorocode: A single molecule, optical map of DNA with nanometre resolution.
Chem. Sci., 2010, 1: 453-460.

G. Vilkaitis, A. Plotnikova, and S. Klimašauskas
Kinetic and functional analysis of the small RNA methyltransferase HEN1: 

The catalytic domain is essential for preferential modification of duplex RNA.
RNA, 2010, 16: 1935-1942.

N. Miropolskaya, I. Artsimovitch, S. Klimašauskas, V. Nikiforov, and A. Kulbachinskiy 
Allosteric control of catalysis by the F loop of RNA polymerase. 
Proc. Natl. Acad. Sci. USA, 2009, 106:
 
18942-18947
.

R. Gerasimaitė, G. Vilkaitis, and S. Klimašauskas
A directed evolution design of a GCG-specific DNA hemimethylase. 
Nucleic Acids Res.
2009, 37: 7332-7341.

Z. Liutkevičiūtė, G. Lukinavičius, V. Masevičius, D. Daujotytė, and S. Klimašauskas
Cytosine-5 methyltransferases add aldehydes to DNA.
Nature Chem. Biol., 2009, 5: 400-402.

D. Daujotytė, Z. Liutkevičiūtė, G. Tamulaitis and S. Klimašauskas 
Chemical mapping of cytosines enzymatically flipped out of the DNA helix. 
Nucleic Acids Res.
, 2008, 36: e57.

G. Lukinavičius, V. Lapienė, Z. Staševskij, C. Dalhoff, E. Weinhold, and S. Klimašauskas 
Targeted labeling of DNA by methyltransferase-directed Transfer of Activated Groups (mTAG). 
J. Am. Chem. Soc., 2007, 129: 2758-2759.

S. Klimašauskas and E. Weinhold
A new tool for biotechnology: AdoMet-dependent methyltransferases.
Trends Biotechnol., 2007, 25: 99-104.

 

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