APPLICATION FORM

YSP-Travel Fellowships for 13th FAOBMB Congress, Bangkok, 23-29 November, 2012.
Name of Applicant: Dr. Chotika Yokthongwattana Position: Lecturer

Address of Applicant: Department of Biochemistry Faculty of Science Kasetsart University

Email address: fscicks@ku.ac.th Membership of FAOBMB Constituent Society: Biochemistry and Molecular Biology Section, Science Society of Thailand (ID: 3367) Date of Birth: 27 January 1978

Proof of Age: (Certification by the Head of your Institution or Department is required) I certify on the basis of official documentation which I have seen (e.g. passport, birth certificate or drivers licence) that the date of birth of the applicant Dr Chotika Yokthongwattana is 27/01/1978.., as shown above. (DD/Month/Year)

Signed: Assist Prof Dr Kiattawee Choowongkomon Position: Head of Department

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Personal Statement
Over the past decades, the study of plant molecular biology has allowed us to understand into gene regulation and its function. In order to investigate gene function or to create plants with novel traits, for example to improve their agronomic properties by transgenic approach, it is essential to understand the mechanism that control transgene expression. Hence, the knowledge and skills related to epigenetic mechanisms of gene regulation are of great interest. My research interests focus on the study of gene regulation and expression through epigenetic process; specifically the change of gene expression during plant exposure to environmental stresses. My Ph.D. research was on regulation of gene silencing in Arabidopsis. The laboratory focused on identification of epigenetic components regulating expression of both endogenous as well as transgenes. Mutants for various epigenetic components such as DNA methyltransferases, histone methyltransferases had been generated and characterized. One of these components, MOM1, is a plant specific protein. Previously it was believed that gene silencing at transcription and post-transcriptional level are separately regulated. My doctoral thesis has established the relationships between transcriptional gene silencing and post-transcriptional silencing from the work of mom1 modifiers screening (Yokthongwattana et al. 2010). After obtaining my Ph.D., I joined, as a lecturer, at the Department of Biochemistry, Faculty of Science, Kasetsart University, Thailand, where I started my own research group. Since agricultural products generate a lot of incomes to the country, the ultimate goal of my research is to help enhance crop productivities. In general, productivity and quality of crop plants are significantly influenced by cultivating conditions. A high percentage of agricultural land areas in Thailand face the problem of soil salinity. Therefore, the knowledge of successful plant adaptation to salinity stress has become the key focus point of my research here in Thailand. My laboratory started with studying plants response to salinity using a unicellular green alga, Chlamydomonas reinhardtii, and rice as plant models. The research approaches were separated into two major directions. In the first direction, so called bottom-up, key epigenetic components regulating gene expression under salt stress are individually investigated. In another approach, so called top-down, overall changes in protein expression profile during plant exposure to salinity stress are examined. Knowledge gained from these two approaches can be merged to provide better understanding how plants successfully cope with excess salinity. Recently, the work on differentially-expressed proteome profiles of C. reinhardtii under salinity stress was published (Yokthongwattana et al. 2012). By learning how this single cell alga responds to salinity stresses might pave ways for a better understanding of the similar response in higher plants to the same stress and ultimately to improve the plants tolerance toward soil salinity.

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Attachments for the Young Scientist Award for 13th FAOBMB Application
List of Publications in International Journals (a) Full list of publications 1. C. Yokthongwattana, B. Mahong, S. Roytrakul, N. Phaonaklop, J. Narangajavana and K. Yokthongwattana. Proteomic analysis of salinitystressed Chlamydomonas reinhardtii revealed differential expression and induction of a large number of important housekeeping proteins. Planta. 235(3), 649-659 (2012) (IF = 3.098) 2. C. Yokthongwattana, E. Bucher, M. Caikovski, I. Vaillant, J. Nicolet, O. Mittelsten Scheid and J. Paszkowski. MOM1 and Pol IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J. 29(2), 340-351 (2010) (IF = 10.124) 3. M. Caikovski, C. Yokthongwattana, Y. Habu, T. Nishimura, O. Mathieu and J. Paszkowski. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet. 4(8), e1000165 (2008) (IF = 9.543) 4. O. Mathieu, J. Reinders, M. Caikovski, C. Smathajitt and J. Paszkowski. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell. 130(5), 851-862 (2007) (IF = 32.406) 5. Y. Habu, O. Mathieu, M. Tariq, A.V. Probst, C. Smathajitt, T. Zhu and J. Paszkowski. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. 7(12), 1279-1284 (2006) (IF = 7.822)

(b) Highlighted list of top five publications 1. C. Yokthongwattana, B. Mahong, S. Roytrakul, N. Phaonaklop, J. Narangajavana and K. Yokthongwattana. Proteomic analysis of salinity-stressed Chlamydomonas reinhardtii revealed differential expression and induction of a large number of important housekeeping proteins. Planta. 235(3), 649-659 (2012) (IF = 3.098) The article describes the study of differential protein profiles observed in Chlamydomonas reinhardtii exposed to salinity stress. By using proteomic approach, we have identified exclusively expressed proteins in control or 300 mM NaCl treated cells. Two dimensional gel electrophoresis has revealed unique 18 protein spots in the control and 99 spots in the salt-treated cells. The proteins specific to salt treatment can be grouped according to its function into general metabolic proteins, energy productions, translation and stress-related proteins. Interestingly, we have identified several housekeeping proteins exclusive detected in the salt-treatment culture. This is particular striking since these proteins are required regularly for the cell functions. Speculations have been toward the post-translational modifications of these proteins in order to regulate their functions under salinity stress. CY, BM, and NP contributed to experimental data. CY, KY with the help of SR analyzed the data. CY together with KY designed and supervised the work.

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2. C. Yokthongwattana, E. Bucher, M. Caikovski, I. Vaillant, J. Nicolet, O. Mittelsten Scheid and J. Paszkowski. MOM1 and Pol IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J. 29(2), 340-351 (2010) (IF = 10.124) This work described the isolation of enhancer mutation of mom1 mutant. mom1 mutants unlike other epigenetic mutants shows no change in global DNA methylation as well as histone modifications. Therefore, we attempted to dissect MOM1 mediated gene silencing by screening its genetic interactor via modifier screen. We have successfully identified mom1 enhancer 1 (moe1) which showed that enhanced previously silent luciferase expression. The strong luciferase signal was observed only in mom1 and moe1 double mutant. Later we have identified that moe1 was another allele of nrpe1, a plant-specific RNA polymerase V. In plant, RNA pol V is involved in gene silencing through RNA-mediated DNA methylation. Therefore, this work was the first report demonstrates the link between transcriptional gene silencing, RNAmediated gene silencing and DNA methylation. CY, EB, MC, IV, JN, and OMS contributed to experimental data. JP supervised the work and wrote the paper together with CY and EB. 3. M. Caikovski, C. Yokthongwattana, Y. Habu, T. Nishimura, O. Mathieu and J. Paszkowski. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet. 4(8), e1000165 (2008) (IF = 9.543) This article reported on functional characterization of an epigenetic component, MOM1. The MOM1 protein is a plant specific protein. Based on bioinformatics analysis, MOM1 homologs have been found in vascular plants such as moss, poplar and rice. MOM1 show no overall sequence homology to any known epigenetic factors reported to date. But it share homology to many proteins including ATP-dependent chromatin remodeling. This work has also shown that even though MOM1 is a large nuclear protein of about 2001 amino acid, only 13% of the protein is indispensable for its function. Conserved domain of poplar homolog of MOM1 could complement mom1 mutant suggesting functional conservation of MOM1 in controlling gene silencing in plants. Conceived and designed the experiments: MC, CY, YH, TN, OM, and JP Performed the experiments: MC, CY, YH, TN, and OM Analyzed the data: MC, CY, YH, TN, OM, and JP Wrote the paper: MC, TN, OM, and JP 4. O. Mathieu, J. Reinders, M. Caikovski, C. Smathajitt and J. Paszkowski. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell. 130(5), 851-862 (2007) (IF = 32.406) This article demonstrates the importance of DNA methylation in epigenetic regulation. The methyltransferase 1 mutant showed abnormal plant phenotypes, changes in chromatin structure, alteration of gene expression. Global decreased in DNA methylation together with changes in histone marks was observed. These alterations were severed in successive generations of met1 mutant. Interestingly we observed remethylation at some loci in successive generations of met1 mutant as a result of RNAPage 4 of 9

directed DNA methylation, inhibitions of DNA demethylase and re-localization of histone silent marks. These lead to a conclusion that other epigenetic mechanisms have been triggered in successive generations of met1 mutant which might function as rescue mechanisms for plant to coordinate and maintained epigenetic inheritance. Conceived and designed the experiments: CS (for CY), MC, JR, OM, and JP Performed the experiments: CS (for CY), MC, JR, and OM Analyzed the data: CS (for CY), MC, JR, OM and JP Wrote the paper: OM, and JP with the help of CS (for CY), MC and JR

5. Y. Habu, O. Mathieu, M. Tariq, A.V. Probst, C. Smathajitt, T. Zhu and J. Paszkowski. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. 7(12), 1279-1284 (2006) (IF = 7.822) This article demonstrated epigenetic regulation of intermediate heterochromatin. Generally in Arabidopsis constitutive heterochromatic regions are marked by DNA hypermethylation, high level of histone H3K9 di-methylation and low level of histone H3K4 di-methylation. In contrast the actively transcribed genic region carried high level of H3K4 di-methylation and low level of H3K9 di-methylation. Intermediate heterochromatin contains two opposing histone marks. We showed that MOM1 function is required to regulate expression of these intermediate heterochromatic regions. These genes are aberrantly expressed in mom1 mutant. Conceived and designed the experiments: CS (for CY), YH, OM and JP Performed the experiments: CS (for CY), YH, OM, MT, AVP and TZ Analyzed the data: CS (for CY), YH, OM and JP Wrote the paper: YH, and JP with the help of CS (for CY) and OM

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Abstract Phosphoproteome profile of a unicellular green alga, Chlamydomonas reinhardtii under salinity stress
Chotika Yokthongwattana1, Sayamon Sithisan1, Atchara Paemanee2, Sittiruk Roytrakul2
1 Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Phahonyothin Rd., Bangkok 10900, Thailand 2 Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathumthani 12120, Thailand

Soil salinity is a major problem for agriculture in Thailand and worldwide. About 20% of agricultural area faces soil salinity problem. At the cellular level, adaptation to salinity stress requires substantial changes in gene and protein expression. The rapid alterations of plant protein profile in response to salinity stress have been commonly observed. Proteins important for stress tolerance and adaptation are increased and the dispensable ones are decreased. Moreover, not only the level of protein is regulated but protein activity is also controlled. One of various possible ways for regulating protein activity is through phosphorylation. Phosphoproteins have been identified from various plants under different stimuli such as hormonal treatment, drought and salinity. In this work, we successfully identified phosphoproteins differentially expressed in a model unicellular green alga, Chlamydomoans reinhardtii, under salinity stress using proteomic approach. The differentially-expressed proteins span various functional categories. Possible roles of these proteins will be discussed.

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Curriculum Vitae

CHOTIKA YOKTHONGWATTANA
Address : E-mail : Nationality: Deparment of Biochemistry, Faculty of Science, Kasetsart University, 50 Phahonyothin Rd., Ladyao, Chatuchak, Bangkok 10900 THAILAND fscicks@ku.ac.th Thai

EDUCATIONAL BACKGROUND

2003 - 2007 1999 - 2004 1995- 1999

Dr. Sc. (Biology) Department of Plant Biology, Faculty of Science, Univesity of Geneva M. Sc. (Biotechnology) Department of Biotechnology, Faculty of Science, Mahidol University B. Sc. (Biotechnology) Department of Biotechnology, Faculty of Science, Mahidol University

PROFESSIONAL EXPERIENCE

Jan 2008 - current Sep 2007 Dec 2007 Sep 2003 and Sep 2004 Jan 2002- Sep 2003

Lecturer at Department of Biochemistry, Faculty of Science, Kasetsart University Post-doctoral researcher at Department of Biochemistry, Faculty of Science, Mahidol University Teaching Assistant in Plant Biology Practical Course, Department of Plant biology, Faculty of Science, University of Geneva, Geneva Switzerland Visiting scientist, Friedrich Miescher Institute, Basel, Switzerland

RESEARCH PUBLICATIONS

Yokthongwattana C , Mahong B, Roytrakul S, Phaonaklop N, Narangajavana J, Yokthongwattana K. Proteomic analysis of salinity-stressed Chlamydomonas reinhardtii revealed differential expression and induction of a large number of important housekeeping proteins. 2012. Planta. 235(3): 649-659. (Journal Citation Reports IF 2010 = 3.098) Yokthongwattana C, Bucher E, Caikovski M, Vaillant I, Nicolet J, Mittelsten Scheid O, Paszkowski J. MOM1 and Pol IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. 2010. EMBO J. 29(2):340-351. (Journal Citation Reports 2010 = 10.124) Caikovski M, Yokthongwattana C, Habu Y, Nishimura T, Mathieu O, Paszkowski J. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic Page 7 of 9

control in vascular plants. 2008. PLoS Genet. 4(8): e1000165. (Journal Citation Reports 2010 = 9.543) Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. 2007. Cell. 130(5): 851-862. (Journal Citation Reports 2010 = 32.406) Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, Zhu T, Paszkowski J. Epigenetic regulation of transcription in intermediate heterochromatin. 2006. EMBO Rep. 7(12): 1279-1284. (Journal Citation Reports 2010 = 7.822)

REVIEW ARTICLES

- Thai Journals of Genetics (Thai Journal IF 2010 = 0.125, Thai-Journal Citation index Center)

TEXTBOOK TRANSLATION

. . : , . -. . (Biochemistry). () M.K. Campbell S.O. Farrell 6th edition ISBN ---- . . : , . -. . (Biochemistry). () M.K. Campbell S.O. Farrell 6th edition ISBN ---- . . : , . -. . (Biochemistry). () M.K. Campbell S.O. Farrell 6th edition ISBN ----

PROCEEDINGS

Chaiyong N and Yokthongwattana C. 2011. Characterization and Expression Analysis of Histone Acetyltransferases in Chlamydomonas reinhardtii under Salinity Stress. Proceeding of The 3rd International Conference on Biochemistry and Molecular Biology. Page 104-107. Ruangsit W and Yokthongwattana C. 2011. Characterization and Expression Analysis of DNA Methyltransferases in Chlamydomonas reinhardtii. Proceeding of The 3rd International Conference on Biochemistry and Molecular Biology. Page 128-132.

AWARDS

Best poster presentation award Yokthongwattana C and Narangajavana J. Screening and Characterization of Components Required for Epigenetic Regulation in Chlamydomonas reinhardtii . 10, 14th- 16th October 2010, Petchburi, Thailand

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ORAL PRESENTATIONS

Functional dissection of MOM1 ; its possible involvement in a chromatin remodelling complex The 15th Swiss Plant Molecular and Cell Biology conference, 15th -17th March 2006, Bad Ragaz, Switzerland Tackle MOM1 function(s) : its possible involvement in a chromatin remodelling complex Epigenome workshop on Nuclear assembly and nuclear organisation, 26th Sep. 2005, La Grande Motte, France

POSTER PRESENTATIONS

Chaiyong N and Yokthongwattana C. 2011. Characterization and Expression Analysis of Histone Acetyltransferases in Chlamydomonas reinhardtii under Salinity Stress. Proceeding of The 3rd International Conference on Biochemistry and Molecular Biology. 6th-8th April 2011. Chiang Mai, Thailand Ruangsit W and Yokthongwattana C. 2011. Characterization and Expression Analysis of DNA Methyltransferases in Chlamydomonas reinhardtii. Proceeding of The 3rd International Conference on Biochemistry and Molecular Biology. 6th-8th April 2011. Chiang Mai, Thailand. Yokthongwattana C and Narangajavana J. Screening and Characterization of Components Required for Epigenetic Regulation in Chlamydomonas reinhardtii. . 10, 14th- 16th October 2010, Petchburi, Thailand Pathanraj D, Boontem W, and Yokthongwattana C. Expression Analysis of DNA methyltransferases in Thai rice varieties under salt stress. The 1st National Rice Research Conference: Moving rice research Towards Innovation, 14th- 16th December 2010, Kasetsart University, Bangkok, Thailand Smathajitt C and Paszkowski J. Enhancer of mom1 mutation. EMBO Conference on Chromatin and Epigenetics, 3rd-7th May 2007, Heidelberg, Germany Mathieu O, Reinders J, Caikovski M, Smathajitt C and Pazskowski J. CG methylation orchestrates epigenetic stability in Arabidopsis 24th Symposium in Plant Biology: Gene silencing: the biology of small RNAs and the epigenome, 18th - 20th January 2007, Riverside, California, USA Caikovski M, Smathajitt C, Habu Y, and Paszkowski J. Arabidopsis MOM1 protein is a severely degenerated CHD3 homolog. 71st CSHL symposium: Regulatory RNAs, 31st May- 5th June 2006, Cold Spring Habor Laboratory, USA Smathajitt C, Habu Y, Caikovski M, and Paszkowski J. Functional dissection of MOM1: its possibly involvement in chromatin remodeling complex. EMBO/FEBS conference on Nuclear Structure and Dynamics, 24th- 28th September 2005, La Grande Motte, France Smathajitt C, Teerawanichpan P, and Narangajavana J. DNA de-methylation in germinating rice seeds under anoxic stress the 12th Annual meeting of Thai Society for Biotechnolog, 1st -3rd November 2000, Kanchanaburi, Thailand

OTHER WORK EXPERIENCE

Translator at the Expertnet books Co. Ltd.

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MAHIDOL UNIVERSITY
Professor Piamsook Pongsawasdi Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand e-mail: piamsook.p@chula.ac.th; piamsook.p@gmail.com July 29, 2012 Dear Professor Piamsook Pongsawasdi, Chair of the FAOBMB Fellowship Committee It gives me an immense pleasure to recommend Dr. Chotika Yokthongwattana for your kind consideration. Dr. Yokthongwattana would like to apply for the YSP-Travel Fellowships for 13th FAOBMB Congress which will be held in Bangkok during 23-29 November, 2012. I have known Dr. Yokthongwattana for about 16 years, since she entered the Bachelor Degree Program in Biotechnology at Department of Biotechnology, Faculty of Science, Mahidol University in year 1996. She got her B.Sc. in 1999 and continue for her M.Sc. at the same place under my supervision. Later in year 2003, she joined Prof. Paszkowski J. at Friedrich Miescher Institute, Basel, Switzerland and got her Ph.D. in year 2007 in Biology from Department of Plant Biology, Faculty of Science, Univesity of Geneva, Switzerland. Dr. Yokthongwattana has long been interested in plant epigenetic regulation, as seen in her publications in high level scientific journals during her advanced study. After finished her Ph.D. and came back to work for Kasetsart University, she got research support from Thailand Research Funds for young researcher, in which I have been her research mentor. Her research focus mainly on the epigenetic regulation during plant exposure to environmental stresses. Her first publication from her own laboratory here at Kasetsart University has just been accepted for publication in high standard journal. During her study at Department of Biotechnology and working under my supervision, she had proven herself to be a very hard working girl. She is an active person with high responsibility and enthusiasm. Dr. Yokthongwattana performs her research meticulously, and is accurate and careful in her experiments as well as her record keeping. With these great qualifications of Dr. Yokthongwattana, she is clearly an exceptional researcher, and I wish her all a bright and prosperous career ahead. The opportunity to get the YSP-Travel Fellowships for 13th FAOBMB Congress will encourage her to go further and I trust that this young lady will contribute to this research field, I am thus highly recommend her for your kind consideration. If you require more specific information, please do not hesitate to contact me, as I will be delighted to provide such assistance for Dr. Yokthongwattana as I can. Sincerely Yours,

Since 1888

Jarunya Narangajavana, Ph.D., Associate Professor Plant Biochemistry and Molecular Genetics Laboratory Department of Biotechnology, Faculty of Science, Mahidol University Rama 6 Road, Bangkok 10400, Thailand Tel: 66-2-2015319 Fax: 66-2-3547160 e-mail: scjnr@mahidol.ac.th http://www.sc.mahidol.ac.th/scbt/