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Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes

N. A. Kolchanov, T. I. Merkulova, E. V. Ignatieva, E. A. Ananko, D. Yu. Oshchepkov, V. G. Levitsky, G. V. Vasiliev, N. V. Klimova, V. M. Merkulov, T. Charles Hodgman
2007 Briefings in Bioinformatics  
We also present a case study of the interplay between experimental and theoretical approaches to the successful prediction of Steroidogenic Factor 1 (SF1).  ...  This article provides short review of approaches to computational recognition of TFBS in genomic sequences and methods of experimental verification of predicted sites.  ...  Acknowledgements The authors are grateful to Galina B. Chirikova for her assistance in translation.  ... 
doi:10.1093/bib/bbm027 pmid:17627963 fatcat:ip5nd7m6vfanzcb5vtc66l7mdi

Recent Computational Approaches to Understand Gene Regulation: Mining Gene Regulation In Silico

I. Abnizova, T. Subhankulova, W. Gilks
2007 Current Genomics  
This paper reviews recent computational approaches to the understanding of gene regulation in eukaryotes.  ...  We will consider the following computational areas: o gene regulatory network construction; o evolution of regulatory DNA; o studies of its structural and statistical informational properties; o and finally  ...  ACKNOWLEDGEMENTS We are thankful to Graham Ellis for support and to Rene te Boekhorst for hard work with references.  ... 
doi:10.2174/138920207780368150 pmid:18660846 pmcid:PMC2435357 fatcat:ztr3u3c42zazzdp6ug4pwy5l54

Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution

Martha L Bulyk, Michael Levine
2009 Current Opinion in Genetics and Development  
Her lab uses experimental and computational approaches to study transcription factor-DNA interactions and transcriptional regulatory networks, both in model organisms and in the human genome.  ...  Her group is also developing computational methods, including those that examine evolutionary conservation, to understand transcriptional regulatory codes in genomes.  ...  Her lab uses experimental and computational approaches to study transcription factor-DNA interactions and transcriptional regulatory networks, both in model organisms and in the human genome.  ... 
doi:10.1016/j.gde.2009.11.003 pmid:19932611 pmcid:PMC2799937 fatcat:txrd2qyprrdhnk6zl3jgyy73te

Computational analyses of eukaryotic promoters

Michael Q Zhang
2007 BMC Bioinformatics  
Here I give a basic introduction of the problem and recent update on both experimental and computational approaches. More details may be found in the extended references.  ...  Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverseengineering gene regulation  ...  computational studies in cis-regulatory motif discovery.  ... 
doi:10.1186/1471-2105-8-s6-s3 pmid:17903284 pmcid:PMC1995544 fatcat:o4vszyvcxzhzhjmc5uwhzbj6j4

Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues

Hiroki Yokota
2002 Frontiers in Bioscience  
A linear model was built in order to estimate the mRNA levels of a group of genes from their regulatory DNA sequences.  ...  The availability of human genome sequences provides life scientists and biomedical engineers with a challenging opportunity to develop computational and experimental tools for quantitatively analyzing  ...  ACKNOWLEDGEMENTS The authors would like to thank Y.T. Konttinen and T.D. Bunker for use of the expression data, J. Chen, Z. Ben Miled, and O.  ... 
doi:10.2741/a747 fatcat:brqeeb47kzewtiybnjrn65tm5e

Genomes, phylogeny, and evolutionary systems biology

M. Medina
2005 Proceedings of the National Academy of Sciences of the United States of America  
More sophisticated comparative approaches are starting to combine computational prediction and laboratory validation of regulatory networks.  ...  It has become apparent, however, that sequence conservation alone will not help identify all cis-regulatory elements by phylogenetic footprinting, and additional data and experimental approaches have to  ...  A pioneer example is the ENCODE initiative which aims to identify all functional elements in the human genome by using coordinated computational and experimental efforts in a multispecies framework (52  ... 
doi:10.1073/pnas.0501984102 pmid:15851668 pmcid:PMC1131869 fatcat:3yyrren45ve6lkfwktx7zyom6i

Combinatorial gene regulation in Plasmodium falciparum

2006 Trends in Genetics  
To elucidate this paradox, we identified regulatory sequences, using an approach that integrates the sequence conservation among species and the correlation in mRNA expression within a species.  ...  We propose that Plasmodium uses the few regulatory proteins it has in a combinatorial approach for gene regulation, explaining the relative paucity in regulatory proteins.  ...  This work was supported in part by a grant from the Netherlands Organization for Scientific Research (NWO).  ... 
doi:10.1016/j.tig.2005.12.002 pmid:16380193 fatcat:sn2fuilo2vgnnhn5hqbhscqtda

Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets

Harold D. Kim, Tal Shay, Erin K. O'Shea, Aviv Regev
2009 Science  
Small-Scale Approaches to Eukaryotic Gene-Regulation Functions Eukaryotic systems have regulatory circuits that are more complex than those of prokaryotes.  ...  We discuss the potential of combining small-and large-scale approaches to understand the working and wiring of transcriptional regulatory circuits.  ... 
doi:10.1126/science.1171347 pmid:19628860 pmcid:PMC2745280 fatcat:fvbgduakwjh63n6phwul24gl7e

Chapter 10 Genomic Identification of Regulatory Elements by Evolutionary Sequence Comparison and Functional Analysis [chapter]

Gabriela G. Loots
2008 Advances in Genetics  
In Section IV.A we will review several experimental approaches employed to validate and characterize predicted transcriptional regulatory elements. A.  ...  By subjecting eukaryotic genomic sequences to computational comparisons and subsequent experimentation, we are inching our way toward a more comprehensive catalog of common regulatory motifs that lie behind  ... 
doi:10.1016/s0065-2660(07)00010-7 pmid:18282510 pmcid:PMC2882178 fatcat:ikp33rs4qvanpkjf2cp4ze7lny

The Use of Functional Genomics in Synthetic Promoter Design [chapter]

Michael L.
2011 Computational Biology and Applied Bioinformatics  
Nowadays it is difficult to imagine an area of knowledge that can continue developing without the use of computers and informatics.  ...  On the other hand, the growth of the computational power for processing and storage has also increased the necessity for deeper knowledge in the field.  ...  At present these tools are mainly applied in the study of lower eukaryotes where the genome is less complex and regulatory elements are easier to identify, extending these algorithms to the human genome  ... 
doi:10.5772/20653 fatcat:cuvqdjmlojbntaepfwmnyq4sci

Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues

Lei Qian
2002 Frontiers in Bioscience  
ACKNOWLEDGEMENTS The authors would like to thank Y.T. Konttinen and T.D. Bunker for use of the expression data, J. Chen, Z. Ben Miled, and O.  ...  Bukhrus for their valuable advice, and Heather Ramsey for proofreading. This study was in part supported by Twenty-First Century Research and Technology Funds.  ...  In response to a growing need to integrate experimental mRNA data with human genome sequences, we developed a unique computational approach named "PROmoter-Based Estimation (PROBE)" analysis and conducted  ... 
doi:10.2741/qian pmid:12045007 fatcat:fmgpfcmvhfa4thdmqqodouetma

Recent advances in computational promoter analysis in understanding the transcriptional regulatory network

Ping Qiu
2003 Biochemical and Biophysical Research Communications - BBRC  
The computational approach to the study of transcriptional regulation networks has become more attractive and feasible with the rapid accumulation of complete genome sequences and the advance of high-throughput  ...  regulatory elements prediction, and transcription factor target gene identification, are discussed.  ...  Richard Paul Sorrentino for his critical editing and comments on the manuscript. I apologize for those wonderful works that have not been cited by the review due to the limit of space.  ... 
doi:10.1016/j.bbrc.2003.08.052 pmid:12963016 fatcat:ssdhqwzrh5hb5cz67euj23l7i4

Identifying regulatory elements in eukaryotic genomes

L. Narlikar, I. Ovcharenko
2009 Briefings in Functional Genomics & Proteomics  
In this review, we survey experimental and computational approaches geared towards the identification of proximal and distal gene regulatory elements in the genomes of complex eukaryotes.  ...  Transcriptional regulation is mediated by proteins binding to regulatory elements on the DNA in a combinatorial manner, where particular combinations of transcription factor binding sites establish specific  ...  Acknowledgements We are grateful to Leila Taher and Valer Gotea for critical comments and assistance with manuscript preparation.  ... 
doi:10.1093/bfgp/elp014 pmid:19498043 pmcid:PMC2764519 fatcat:svvheq5juze73opazulwr6w3ma

Eukaryotic gene regulation in three dimensions and its impact on genome evolution

M Madan Babu, Sarath Chandra Janga, Ines de Santiago, Ana Pombo
2008 Current Opinion in Genetics and Development  
In this review, we discuss recent studies that highlight the role of spatial components in gene regulation and their impact on genome evolution.  ...  Recent advances in molecular techniques and high-resolution imaging are beginning to provide exciting insights into the higher order chromatin organization within the cell nucleus and its influence on  ...  Acknowledgements MMB and SCJ acknowledge MRC-LMB. SCJ acknowledges support from CCT and MMB thanks Darwin College and Schlumberger Ltd for generous support. AP and IS thank the MRC-CSC for support.  ... 
doi:10.1016/j.gde.2008.10.002 pmid:19007886 fatcat:vhl5n6yuzrdonjcmrxvogisq5y

Exploring genetic regulatory networks in metazoan development: methods and models

Marc S. Halfon, Alan M. Michelson
2002 Physiological Genomics  
In this article we review some of the main methodological issues surrounding genome annotation, transcriptional profiling, and computational prediction of cis-regulatory elements and discuss how the power  ...  of model genetic organisms can be used to experimentally verify and extend the results of genomic research.  ...  By combining genetic analysis, microarray and other transcriptional profiling methods, and computational approaches to identifying and characterizing cis-regulatory sequences, we can begin not just to  ... 
doi:10.1152/physiolgenomics.00072.2002 pmid:12209016 fatcat:tboelmvydvg4tggx4gytbfuk5i
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