Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition

PloS One
Arindam Deb, Sudip Kundu

Abstract

Combinations of cis-regulatory elements (CREs) present at the promoters facilitate the binding of several transcription factors (TFs), thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe) infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experiment...Continue Reading

References

Apr 1, 1991·Computer Applications in the Biosciences : CABIOS·D S Prestridge
Oct 1, 1996·The Plant Journal : for Cell and Molecular Biology·N BateD Twell
Dec 10, 1998·Nucleic Acids Research·K HigoT Korenaga
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P BermanMichael B Eisen
Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Aug 16, 2002·Current Opinion in Plant Biology·Barbara N Kunkel, David M Brooks
Oct 5, 2002·Nucleic Acids Research·Sridhar Hannenhalli, Samuel Levy
Nov 22, 2002·Physical Review Letters·M E J Newman
Jan 10, 2003·Nucleic Acids Research·Guoying LiuMichael A Siani-Rose
Mar 15, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman
Jun 14, 2003·Plant Physiology·Rebecca L BrownJohn M Manners
Jul 11, 2003·Nature·Michael Levine, Robert Tjian
Oct 4, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman, Juyong Park
Oct 7, 2003·Annual Review of Microbiology·Nicholas J Talbot
Nov 25, 2003·Nucleic Acids Research·Nilanjana Banerjee, Michael Q Zhang
Dec 19, 2003·Nucleic Acids Research·M A HarrisUNKNOWN Gene Ontology Consortium
Aug 4, 2004·Genome Biology·Mamoru KatoMichael Q Zhang
Aug 28, 2004·Nature Structural & Molecular Biology·Attila ReményiMatthias Wilmanns
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Nov 18, 2005·Science's STKE : Signal Transduction Knowledge Environment·Sarah M Assmann
Feb 14, 2006·Bioinformatics·Balázs AdamcsekTamás Vicsek
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Zhen XieQingxi J Shen
Apr 25, 2006·BMC Bioinformatics·Amrita PatiT M Murali
Jul 11, 2006·Nature Medicine·Stefan Kins, Konrad Beyreuther
Aug 22, 2006·Journal of Plant Physiology·Xiaoqiang LiuChengcai Chu
Dec 6, 2006·Nucleic Acids Research·Shu OuyangC Robin Buell
Dec 19, 2006·Biophysical Journal·Md Aftabuddin, S Kundu

❮ Previous
Next ❯

Citations

Sep 29, 2019·International Journal of Molecular Sciences·Changmi WangJing Yang

❮ Previous
Next ❯

Methods Mentioned

BETA
in vivo transcription

Software Mentioned

PERL scripts
Signal Scan
R
GT1CONSENSUS
CFinder
GATABOX
Bioconductor
RepeatMasker
Cytoscape

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.