The plant-specific DOF transcription factors have important biological role in plant morphogenesis growth and development. In this study sequences of ten Ocimum bacilicum Dof gene promoters were analyzed. Identification of biologically significant CREs (Cis-acting regulatory elements) was performed and CREs corresponding to light response, abiotic and biotic stress response, phytohormone response, and tissue-specific elements were found. Genes promoter analysis also revealed the presence of AP2, C2H2, bZIP, bHLH, GATA, Dof, GATA, HSF, NF-Y, and Homedomain. Transcription factor binding site in the promoter region of ObDof genes. These findings not only contribute to the understanding of the gene function of candidate ObDof genes for further analysis, but the information also contributes to the understanding of the gene regulatory network.

1. COMPUTATIONAL ANALYSIS OF CIS-REGULATORY ELEMENTS AND
ASSOCIATED TRANSCRIPTION FACTOR OF DOF GENES OF Ocimum basilicum
Presented by
Vartika Rai
rvartika37@gmail.com
M.Sc. Biotechnology [IInd sem.]
Siddharth university, kapilvastu
A Project Report On

2. Acknowledgement
First of all, I would like to Offer my sincere
gratitude.
To My Mentor Dr. Kapil Gupta who was
constantly checking up on the progress of
the study and putting inputs effortlessely.

3. Brief Overview of the Project(Abstract)
• In this study sequences of ten Ocimum
basilicum Dof gene promoters were analyzed.
• Identification of biologically significantCREs
(Cis acting regulatory elements) were
performed.
• CREs corresponding to
Light response, abiotic and biotic stress response,
phytohormone response and tissue-specific
elements

4. Continued…
• Genes promoter analysis revealed
The presence AP2, C2H2, bZIP, bHLH,
GATA,Dof,GATA, HSF, NF-Y, and Homedomain.
These findings not only contribute to the
understanding of gene function of candidate
ObDof genes for further analysis, the information
also contributes to the understanding of the gene
regulatory network.

5. Introduction
Basil (Ocimum basilicum),
also called sweet basil,
annual herb of the
mint family
(Lamiaceae), grown for
its aromatic leaves.
Basil is likely native to
India and is widely
grown as a kitchen
herb.

6. Objectives
Retrieval of promoter sequences of
Dof TF genes from O. basilicum.
Prediction of CREs (Cis Regulatory
Elements) from the
promotersequences of Dof TF genes
from O. basilicum.
Prediction of TF binding sites in the
promoter sequences of Dof TF
genesfrom O. basilicum.

7. Review of Literature
REGULATION OF GENE EXPRESSION
Cis-acting regulatory elements (CREs) are DNA sequences
that reside in the upstream region of structural genes
that are necessary to regulate differential gene
expression.
Transcription factors (TFs) bind TFBSs in the promoter
sequence, to switch on and off or adjust the rate of
transcription of their target genes. This results in
change in gene expression temporarily and spatially in
response to developmental or environmental signals.

8. Continued....
TRANSCRIPTION FACTORS
The proteins that govern transcription can be
classified into RNA polymerases and general factors
that form the basal transcription apparatus,
sequence specific DNA-binding transcription factors
(TFs), large multi-subunit co-activators and co-
factors, and chromatin related proteins such as
histone acetyltransferases. The basal apparatus is
required for the initiation of RNA synthesis at all
promoters.

9. PLANTS- SPECIFIC TRANSCRIPTION FACTORS
In plants, many DNA sequence-specific
transcription factors involved in gene
expression have been identified (Meshi and
Iwabuchi, 1995). These transcription factors
often form families of structurally related
proteins with similar DNA-binding specificities.

10. Transcription factors
are classified on the
basis of their structural
features.
Some of the important
classes of transcription
factors are listed
below-
o Helix-Turn-Helix
(HTH)-This type of
transcription factor
binds DNA as dimer.
o Leucine Zipper-Also
binds DNA as dimer,
variation in bZIP.
o Zinc Finger-binds to
DNA either as
monomer or dimer.
o Helix-Loop-Helix-
binds to DNA as dimer.
o High Mobility Group
(HMG) box motif.

11. DOF FAMILY OF TRANSCRIPTION FACTOR
The Dof family is one of the well-known
characterized plant specific transcription factor
having diverse roles. Multiple Dof genes have
been identified in numerous plants. Dof
transcription factors play role in a variety of
biological processes like photosynthetic carbon
assimilation, light regulated gene expression,
accumulation of seed storage proteins,
germination, dormancy, response to
phytohormones, flowering time and guard
specific gene expression etc that are unique to
plants.

12. Biotic and Abiotic Stress
The role of Dof transcription factors in biotic stress
tolerance has been investigated in barley seeds based on
its interaction with cystatin gene (Martinez and
Diaz,2005). Two Dof proteins, SAD and BPBF, interact
specifically in vitro with oligonucleotides containing Dof
binding-sites derived from the cystatin gene promoters.
Another Dof protein, OBP1 from Arabidopsis that
interacts with an ocs element binding factor OBF4 is
related with biotic stress (Singh, 2002andZhang,1995).

13. Methods Used in the Study
• Sequence Retrieval of ObDof gene promoters
• Cis-element analysis of the ObDof gene
promoters using PLANT CARE
• Transcription Factor binding site analysis of
the ObDof gene promoters using Plant PAN
3.0

14. Results
Sequence Retrieval of Ocimum basilicum Dof
promoters For finding O basilicum DOF Promoter,
Arabidopsis gene nucleotide sequences comprising
only to CDS were downloaded from PTFDB database.
Analysis of Cis-regulatory element in ObDof promoters
Search for the cis-acting regulatory components in the
1500-bp sequence, upstream to start codon of ObDOF
genes was carried out using PlantCare to understand
theirfunctions in growth, stress and hormone
responses (Lescot et al., 2002).

15. Analysis of TFs binding motifs in ObDof
promoters Identification of transcription factor
binding sites (TFBs) are important for
understanding the function of TFs and their
interactions with TF-TFBs pairs.

16. Thank-you!