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Research Interests

In complex organisms, identical genome is packaged in cell type specific manner during embryonic development - one genome gives rise to multiple epigenomes - that determine the cell type specific expression pattern of genes and cellular identity. Once this packaging is achieved by an intricate developmental program, the chromatin structure is maintained during subsequent cell divisions by epigenetic cellular memory mechanisms. Using Drosophila as our major model organism, we are investigating molecular mechanisms of these processes. We use genetic, cell biology, biochemical and bioinformatics approaches to investigate evolutionarily conserved features of genome organization, chromatin structure and epigenetic regulation of genes during embryonic development. We also investigate functional relevance of non-coding sequences of complex genomes, in particular the repetitive part, in nuclear architecture, chromatin organization and gene regulation. Taking comparative genomics approach we study molecular basis of the functional features of chromatin level regulatory elements like chromatin domain boundary and cellular memory elements.

Selected Publications

Repeat performance: how do genome packaging and regulation depend on simple sequence repeats Ram P Kumar, Ramamoorthy Senthilkumar, Vipin Singh and Rakesh K Mishra BioEssays 32, 165-174, 2010.


Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit Ramamoorthy Senthilkumar and Rakesh K Mishra BMC Genomics 10, 459, 2009.

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3 Vivek S Chopra, Arumugam Srinivasan, Ram P Kumar, Krishnaveni Mishra, Denis Basquin, Mylène Docquier, Carole Seum, Daniel Pauli, Rakesh K Mishra Dev. Biol. 317, 660-670, 2008.

Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix Rashmi U. Pathak, Nandini Rangaraj, Satish Kallappagoudar, Krishnaveni Mishra, and Rakesh K. Mishra Mol. Cell. Biol. 27, 4796-4806, 2007.

Extreme conservation of noncoding DNA near HoxD complex of vertebrates Ch Sabarinadh, S Subramanian, A Tripathi and Rakesh K Mishra BMC Genomics, 5, 75, 2004

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Publications

TitleJournalYear
Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid G3 (Bethesda). 10(5):1485-1494. 2020
Sperm methylome alterations following yoga-based lifestyle intervention in patients of primary male infertility: A pilot study Andrologia. 2020 May;52(4):e13551. 2020
Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair J Biosci. 2020; 45:38. 2020
Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects J Biosci. 2020; 45:12. 2020
MSDB: a comprehensive, annotated database of microsatellites Nucleic Acids Res. 2020 Jan 8;48(D1):D155-D159. 2020
SETDB1 modulates the differentiation of both the crystal cells and the lamellocytes in Drosophila Dev Biol. 2019 Dec 1;456(1):74-85. 2019
Heterochromatic hues of transcription-the diverse roles of noncoding transcripts from constitutive heterochromatin FEBS J. 2019 Dec; 286(23):4626-4641. 2019
Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 2019
Drosophila Choline transporter non-canonically regulates pupal eclosion and NMJ integrity through a neuronal subset of mushroom body. Dev Biol. 2019
Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes. Genomics. 2018
Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis. Methods Mol Biol. 2018
Epigenetic factors Polycomb (Pc) and Suppressor of zeste (Su(z)2) negatively regulate longevity in Drosophila melanogaster. Biogerontology. 2018
Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos Journal of Bioscience. 2018
Damage-responsive elements in Drosophila regeneration Genome Res 2018
Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells-Transmission of hallmarks of nuclear organization through mitosis Mol Cell Proteomics 2018
PERF: An Exhaustive Algorithm for Ultra-Fast and Efficient Identification of Microsatellites from Large DNA Sequences. Bioinformatics 2017
The placental gateway of maternal transgenerational epigenetic inheritance. J Genet. 2017 Jul;96(3):465-482. 2017
Long Noncoding RNAs in Mammalian Development and Diseases. Adv Exp Med Biol. 2017;1008:155-198. doi: 10.1007/978-981-10-5203-3_6. 2017
Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation. Cell Mol Life Sci. 2017 Aug 30. 2017
C-State: An interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search BMC Bioinformatics 2017
O-GlcNAcylation of Boundary melanogaster correlates with active histone marks at the promoters of its target genes Nucleus 2017
Ultraconserved sequences associated with HoxD cluster have strong repression activity. Genome Biol Evol 2017
Simple Sequence repeats showing "length preference have regulatory functions in humans." Gene 2017
MSDB:A Comperhensive Database of Simple Sequence Repeats Genome Biol Evol 2017
Finding clues to the riddle of sex determination in zebrafish. JOURNAL OF BIOSCIENCES, 41: 145-155. 2016
DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila. SCIENTIFIC REPORTS, 6: 19572. 2016
MoD Special issue on "Upstream and Downstream of Hox Genes". MECHANISMS OF DEVELOPMENT, 138: 63-63. 2015
Drosophila Rif1 is an essential gene and controls late developmental events by Sci Rep. 2015 May 29;5:10679 2015
A fine balance: epigenetic control of cellular quiescence by the tumor suppressor Nucleic Acids Res. 2015 Jun 3. pii: gkv567. 2015
Code in the Non-Coding Proc Indian Natn Sci Acad 2015
Design and synthesis of pyrazole-oxindole conjugates targeting tubulin polymerization as new anticancer agents. European Journal of Medicinal Chemistry 2015
A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene. Nucleic Acids Res 2015 Jul 27;43(13):6236-56 2015
The functional diversity of Drosophila Ino80 in development Mech Dev. 2015 Nov;138 Pt 2:113-21 2015
Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev. 2015 Nov;138 Pt 2:160-9 2015
Specific combinations of boundary element and Polycomb response element are required for the regulation of the Hox genes in Drosophila melanogaster. Mech Dev.2015 Nov; 138 Pt 2:141-50 2015
Expansion of the polycomb system and evolution of complexity. Mech Dev. 2015 Nov;138 Pt 2:97-112 2015
Transposable element `roo` attaches to nuclear matrix of the Drosophila J Insect Sci. 2013;13:111. 2014
Mining the cis-regulatory elements of Hox clusters. Methods Mol Biol. 2014;1196:121-31. 2014
Length and sequence dependent accumulation of simple sequence repeats in Gene. 2014 Nov 10;551(2):167-75. 2014
Role of abd-A and Abd-B in development of abdominal epithelia breaks posterior PLoS Genet. 2014 Oct 23;10(10):e1004717. 2014
CARM1 regulates astroglial lineage through transcriptional regulation of Nanog Mol Biol Cell. 2015 Jan 15;26(2):316-26. 2014
Genome-wide mapping of matrix attachment regions in Drosophila melanogaster. BMC Genomics. 2014 Nov 25;15:1022. 2014
Restraining the enhancers from straying. J Biosci. 2014 Dec;39(5):739-40. 2014
High-wire act: the poised genome and cellular memory. FEBS J. 2014 Dec 1 2014
Functional sub-division of the Drosophila genome via chromatin looping: the Nucleus. 2013 Mar-Apr;4(2):115-22. 2013
AAGAG repeat RNA is an essential component of nuclear matrix in Drosophila. RNA Biol. 2013 Apr;10(4):564-71. 2013
Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in Epigenetics Chromatin. 2013 Apr 22;6(1):8. 2013
GATA simple sequence repeats function as enhancer blocker boundaries. Nat Commun. 2013;4:1844 2013
A functionally conserved Polycomb response element from mouse HoxD complex Sci Rep. 2013 Oct 22;3:3011. 2013
Emerging trends of long non-coding RNAs in gene activation. FEBS J. 2014 Jan;281(1):34-45. 2013
Chromatin domain boundary element search tool for Drosophila. Nucleic Acids Res. 40 (10), 4385-4395, 2012 2012
Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes. BMC Genomics. 2012 Jun 19; 13(1):255. 2012
Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development. Subcellular Biochemistry, Volume 61, 177-207, 2013 2012
Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae. Nucleic Acids Res. 2012 Dec 4. [Epub ahead of print] 2012
Dynamics of Nuclear Matrix Proteome during Embryonic Development in Drosophila melanogaster J. Biosci. 36 (3), 439-459, 2011 2011
Tone up your chromatin and stay young J. Biosci. 36(1), 5-11, 2011 2011
Epigenetic profile of the euchromatic region of human Y chromosome Nucleic Acids Res. 39, 3594-606, 2011 2011
A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster Nucleic Acids Res. 39, 3543-57, 2011 2011
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes BMC Bioinformatics. 26, 609, 2010 2010
A functionally conserved boundary element from the mouse HoxD locus requires GAGA factor in Drosophila Development 137, 4239-47, 2010 2010
Nuclear matrix proteome analysis of Drosophila melanogaster. Mol. & Cell. Proteomics 9, 2005-2018, 2010 2010
Vertebrate homologue of Drosophila GAGA factor. J. Mol. Biol. 400, 437-447, 2010. 2010
The paternal hidden agenda: Epigenetic inheritance through sperm chromatin. Epigenetics 5, 1-6, 2010. 2010
Chromatin remodeling protein INO80 influences expression of homeotic genes in Drosophila. Genes Cells 15, 725-735, 2010. 2010
Regulation of cellular chromatin state: insight from quiescence and differentiation Organogenesis 6, 37-47, 2010. 2010
Repeat performance: how do genome packaging and regulation depend on simple sequence repeats? BioEssays 32, 165-174, 2010. 2010
Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit BMC Genomics 10, 549, 2009. 2009
Cytogenetic characterization and fluorescence in situ hybridization of (GATA)10 repeats on established primary cell cultures from Indian water snake (Natrix piscator) and Indian mugger (Crocodylus palustris) embryos. Cytogenet Genome Res. 127, 287-96, 2009. 2009
SnS-Align: A graphic tool for alignment of distantly related proteins. International Journal of Bioinformatics Research & Applications (IJBRA) 5, 663-673, 2009. 2009
Chromatin and Disease (Book Review) Current Science 97, 261-262, 2009. 2009
Chromatin and Disease (Book Review) Current Science 97, 261-262, 2009. 2009
Divide and (epigenetic) rule: Chromatin Domains as Functional and Structural Units of Genomes (book chapter). Current Trends in Science. INSA Platinum Jubilee Special Publication (ISBN: 978-81-85324-16-6), pp. 211-224, 2009 2009
Differentiation to Dedifferentiation: Induced pluripotent stem cells (book chapter). Recent Trends in Biotechnology, M P Singh (ed.), Nova Science Publishers), New York (ISBN: 978-1-60876-148-7, 2009 2009
Polycomb Group of Genes and the Epigenetics of Aging (book chapter). Epigenetics of Aging, Tollefsbol, Trygve O. (Ed.) Springer (ISBN: 978-1-4419-0638-0), pp. 135-150, 2009. 2009
Genome to Epigenome (book chapter). In Chromosomes to Genome, Rakesh K. Mishra (Editor), I.K. International Publishing House, New Delhi (ISBN: 978-93-80026-21-3), pp. 31-39, 2009. 2009
Chromosomes to Genome (book). I.K. International Publishing House, New Delhi (ISBN: 978-93-80026-21-3), 2009, 222 pages. 2009
A double-edged sword to force posterior dominance of Hox genes BioEssays 30, 1058-1061, 2008. 2008
An intronic DNA sequence within the mouse Neuronatin gene exhibits biochemical characteristics of an ICR and acts as a transcriptional activator in Drosophila Mechanisms of Development 125, 963-973, 2008. 2008
Epigenetic regulation of genes during development: A conserved theme from flies to mammals J. Genet. Genomics 35, 413-429, 2008. 2008
Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3 Dev. Biol. 317, 660-670, 2008. 2008
Reptin and Pontin antagonistically function with PcG and TrxG complexes to mediate Hox gene control EMBO Reports 9, 260-266, 2008. 2008
Chromatin Domain Boundaries: Defining the functional domains in genome Proc. Ind. Natl. Sci. Acad. 73, 239-253, 2007. 2007
Involvement of Polycomb-Group Genes in Establishing HoxD Temporal Colinearity Genesis 45, 570-576, 2007. 2007
Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix Mol. Cell. Biol. 27, 4796-4806, 2007. 2007
MiRacles in Hox gene regulation BioEssays 28, 445-448, 2006. 2006
Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between grainyhead and pleohomeotic Mol. Cell. Biol. 26, 1434-1444, 2006. 2006
Synergistic recognition of an epigenetic DNA element by Pleiohomeotic and a Polycomb core complex Genes & Development 19, 1755-1760, 2005. 2005
To SIR with Polycomb: linking silencing mechanisms BioEssays 27, 119-121, 2005 2005
Extreme conservation of noncoding DNA near HoxD complex of vertebrates BMC Genomics, 5, 75, 2004 2004
Bridging the gap but breaking the rule: a tunicate twists the hox puzzle (Research News) Current Science 87, 1038-1040, 2004 2004
Edward B Lewis (1918-2004) (Commentary) J. Biosciences 29, 231-233, 2004 2004
The enhancer blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA factor binding sites Genetics 168, 1371-1384, 2004. 2004
Bioinformatics and the Art of Sequence Analysis Recent Advances in Biotechnology (N C Gautam and M P Singh, eds), Shree Publishers, New Delhi, PP. 21-41, 2004 2004
Trl-GAGA Directly Interacts with lola like and Both are Part of the Repressive Complex of Polycomb Group of Genes Mechanisms of Development 120, 681-689, 2003. 2003
Genome-Wide Analysis of Bkm Sequences (GATA repeats): Predominant Association with Sex Chromosomes and Potential Role in Higher Order Chromatin Organization and Function Bioinformatics 19, 681-685, 2003. 2003
Extreme Conservation of Non-Repetitive Non-Coding Regions Near HoxD Complex of Vertebrates (Deposited research article) Genome Biology 4, P2, 2003. 2003
Genome-Wide Analysis of Microsatellite Repeats in Humans: Their Abundance and Density in Specific Genomic Regions Genome Biology 4, R13, 2003. 2003
Triplet repeats in human genome: distribution and their association with genes and other genomic regions (Discovery Note) Bioinformatics 19, 549-552, 2003 2003
MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes (Deposited research article) Genome Biology 2002, 3(12):preprint0011.1-0011.13 2002
The iab-7 Polycomb Response Element Maps to a Nucleosome-Free Region of Chromatin and Requires Both GAGA and Pleiohomeotic for Silencing Activity Mol. Cell. Biol. 21, 1311-1318, 2001. 2001
Boundaries that demarcate structural and functional domains of chromatin. J. Biosciences 24, 377-399, 1999. 1999
Getting at the core of the colinearity of Hox genes. Current Science 77, 213-216, 1999. 1999
A conserved sequence motif in Polycomb-Response Elements. Molecular Cell 1, 1065-1066, 1998. 1998
Selective inhibition of cell-free translation by oligonucleotides targeted to an mRNA hairpin structure. Nucleic Acids Research 26, 2273-2278, 1998 1998
Chromatin domain boundaries in the Bithorax complex Cell. Mol. Life Sci. 54, 60-70, 1998. 1998
Synthesis of a novel polynucleotide : potential R-L model. Current Science 57, 574-577, 1988. 1998
Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element. Antisense Nucleic Acid Drug Development 7, 369-380, 1997. 1997
Three small nucleolar RNAs that are involved in ribosomal RNA precursor processing. Proc. Natl. Acad. Sci. (USA) 94, 4972-4977, 1997. 1997
Targeting nucleic acid secondary structure by antisense oligonucleotides designed through in vitro selection. Proc. Natl. Acad. Sci. (USA) 93, 10679-10684, 1996. 1996
Improved leishmanicidal effect of phosphorothioate antisense oligonucleotides by LDL-mediated delivery. Biochim. Biophys. Acta 1264, 229-237, 1995. 1995
Synthetic nucleases crafted from L-lysine. Proc. Indian Acad. Sci., Chem. Sci. 106, 1071-1088, 1994. 1994
In vitro selection of antisense oligonucleotides targeted to a hairpin structure. C. R. Acad. Sci.(Paris) 317, 977-982, 1994. 1994
Design of simple and flexible dimeric peptide model for DNA recognition and scission. J. Chem. Soc. (Chemical Communications) 5, 107-109, 1994. 1994
Antisense phosphorothioate oligonucleotides : selective killing of the intracellular parasite Leishmania amazonensis. Proc. Natl. Acad. Sci. (USA) 91, 7859-7863, 1994. 1994
DNA intercalation and photoinduced cleavage by 4-nitro- (N hexylamine)1,8-Naphthalimide. Nucleotides & Nucleotides 13, 963-978, 1994. 1994
Differential influence of DNA supercoiling on in vivo strength of promoters varying in structure and organisation in E. coli. FEBS Letters 340, 189-192, 1994. 1994
Self-association properties of naphthalimide derived fluorescent DNA intercalators. Indian J. Chemistry 32B, 540-545, 1993. 1993
Mechanism of initiation of transcription by E. coli RNA polymerase on supercoiled template. Molecular Microbiology 8, 507-515, 1993. 1993
Design of a chemical nuclease model with (lys)2 Cu as the core motif. J Chem. Soc. (Chemical Communications) 4, 337-339, 1993. 1993
Promoter search and strength of a promoter: two important means for global regulation of gene expression in E. coli. J. Biosciences 18, 1-11, 1993. 1993
Inheritance of chromatin structure: DNA methylation and other means. (Research news) Current Science 64, 212-214, 1993. 1993
Yeast budding forages through redundancy. (Scientific correspondence) Current Science 63, 111-112, 1992. 1992
Photoinduced strand scission of double helical DNA by 1,8-Naphthalimide derived intercalators. Current Science 62, 693-695, 1992. 1992
Promoter recognition and transcription efficiency in E. coli: influence of DNA conformation and topology. Proceedings of DAE Symposium on Molecular Biology of Microorganisms, p. 120-125, 1992. 1992
Sequence specific chemical recognition of DNA. Nucleotides & Nucleotides 10, 609-612, 1991. 1991
Mechanism of initiation of transcription in Escherichia coli. Nucleotides & Nucleotides 10, 607-608, 1991. 1991
Screening of clones containing altered DNA conformations by plasmid topoprofile shift. J. Biochem. Biophys. Meth. 22, 171-175, 1991. 1991
Unusual DNA structures: sequence requirements and role in transcriptional control. Structure & Methods Vol. 2: DNA Protein Complexes & Proteins (Sharma, R H & Sharma, M H, Eds.), Adenine Press, N.Y., p. 33-49, 1990. 1990
DNA duplex with the potential to change handedness after every half a turn. Nucleic Acids Research 17, 7273-7281, 1989. 1989
Sequence criteria for Z-DNA formation: studies on poly d(ACGT). Nucleic Acids Research 17, 450, 1989. 1989
Sequence specificity of Z-DNA formation in oligonucleotides. Biochemistry International 17, 121-13, 1988. 1988
Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution. Nucleic Acids Research 16, 4651-4665, 1988. 1988
Use of protecting groups as purification tool in large scale synthesis of small deoxyoligonucleotides. Indian J. Chemistry 27B, 817-820, 1988. 1988
Improved synthesis of oligodeoxynucleotides using 3-methoxy-4 phenoxy benzoyl group for amino protection. Nucleic Acids Research 14, 6197-6112, 1986. 1986

Rakesh Kumar Mishra

Director

2658

mishra@ccmb.res.in

Rashmi Upadhyay Pathak

Senior Principal Scientist

2656

rashmi@ccmb.res.in

A Srinivasan

Sr. Technical Officer(2)

2652

asrini@ccmb.res.in

Runa Hamid

Project Investigator

2783

runahamid@ccmb.res.in

Shreekant Verma

CSIR-PDF

2660

shreekant@ccmb.res.in

Shagufta Khan

Senior Research Fellow

2656

shagufta@ccmb.res.in

K. Phanindhar

Senior Research Fellow

2660

kundurthiphanindhar@ccmb.res.in

Nikhil Hajirnis

Senior Research Fellow

2652

nikhil.hajirnis@ccmb.res.in

Ashish Bihani

Senior Research Fellow

2652

ashish@ccmb.res.in

Ravina Saini

Junior Research Fellow

2783

ravina@ccmb.res.in

Avvaru Akshay Kumar

Junior Research Fellow

2960

avvaru@ccmb.res.in

Soujanya M. S

DBT-JRF

2783

msoujanya@ccmb.res.in

Sonu Yadav

CSIR-JRF

2656

sonu@ccmb.res.in