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ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Santi González, Bàrbara Montserrat-Sentís, Friman Sánchez, Montserrat Puiggròs, Enrique Blanco, Alex Ramirez, David Torrents
2012 Computer applications in the biosciences : CABIOS  
Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith-Waterman algorithm that allows local searches of conserved TFBS clusters and the detection  ...  Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding  ...  ACKNOWLEDGEMENTS We thank Mar Albà, Steven Laurie and our entire group for constructive feedback during the development of this work and during the writing of the manuscript.  ... 
doi:10.1093/bioinformatics/bts024 pmid:22253291 pmcid:PMC3307110 fatcat:6gcxqupm5bcprhnt32e5rmmzlu

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal, Pierre de Langen, Aurélie Bergon, Fabrice Lopez, Benoit Ballester
2021 Nucleic Acids Research  
, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators.  ...  ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse  ...  ACKNOWLEDGEMENTS We would like to thank Nathalie Arquier and Laurent Perrin for their expertises and scientific discussions regarding the curation and annotation of Drosophila melanogaster ChIP-seq data  ... 
doi:10.1093/nar/gkab996 pmid:34751401 pmcid:PMC8728178 fatcat:k2zuwebeizfk5khhm5funirbfi

Plant Cis-regulatory elements: methods of identification and applications

Usman Ijaz
2020 Asian Journal of Agriculture and Biology  
Two aspects of cis-elements are targeted; one is properties and examples of condition-specific cis-elements while the other is techniques used for their identification.  ...  Biotic and abiotic factors badly affect the productivity and growth of plants and found the major yield-limiting factor in agriculture.  ...  ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. Bioinformatics. 28:763-770.  ... 
doi:10.35495/ajab.2019.08.352 fatcat:yuwwmxinvfe4paxkljmfmypj54

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos
2007 Genome Biology  
Comparison of promoter conservation in 513 protein coding genes and related transcription factor binding sites (TFBSs) showed that 41% of the known human TFBSs are located in the 6.7% of promoter regions  ...  of promoter conservation and transcription factor binding site turnover among mam-mals Abstract Background: Being the first noneutherian mammal sequenced, Monodelphis domestica (opossum) offers great potential  ...  This work was supported by NIH grants RR014214 and NO1 AI-50018, NSF grant MCB0316255 and a grant with the Pennsylvania Department of Health.  ... 
doi:10.1186/gb-2007-8-5-r84 pmid:17506886 pmcid:PMC1929153 fatcat:odbdkbxpirfuzi5jw2vhw4ehsu

Predicting transcription factor binding sites using local over-representation and comparative genomics

Matthieu Defrance, Hélène Touzet
2006 BMC Bioinformatics  
Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs  ...  Results: We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position  ...  Background The computational identification of functional transcription factor (TF) binding sites (TFBSs) from a nucleotide sequence alone is difficult.  ... 
doi:10.1186/1471-2105-7-396 pmid:16945132 pmcid:PMC1570149 fatcat:f7n4cgucrbfo5op66qjrydj6b4

Transcriptional Induction of ADAMTS5 Protein by Nuclear Factor-κB (NF-κB) Family Member RelA/p65 in Chondrocytes during Osteoarthritis Development

Hiroshi Kobayashi, Makoto Hirata, Taku Saito, Shozo Itoh, Ung-il Chung, Hiroshi Kawaguchi
2013 Journal of Biological Chemistry  
Exhaustive comparison of the genomic sequences of human, macaque, and mouse ADAMTS5 genes revealed that the proximal 1.4 kb of the 5-end-flanking regions containing several consensus motifs was highly  ...  In the ADAMTS5 gene, there were three NF-B binding motifs, in which deletion, mutagenesis, and tandem repeat analyses of the luciferase assay identified the core responsive elements of RelA/ p65 to be  ...  We initially compared the genomic sequences of proximal promoter regions among mouse, macaque, and human ADAMTS5 genes and identified highly conserved regions containing putative transcription factor binding  ... 
doi:10.1074/jbc.m113.452169 pmid:23963448 pmcid:PMC3789961 fatcat:po33d7dmbfbihmbbjrvcjoaoxy

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach

Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P Fairfax, Kenneth Chan, Katharine Plant, Julian C Knight
2014 Genome Biology  
We confirm recruitment to proximal promoter sequences in MHC class II genes and more distally involving the canonical CIITA enhanceosome.  ...  We analyse CIITA recruitment for pathophysiologically relevant primary human B cells and monocytes, resting and treated with interferon-gamma, in the context of the epigenomic regulatory landscape and  ...  Acknowledgements We are grateful to all the volunteers who participated in this study and to members of the Knight laboratory for their advice and input.  ... 
doi:10.1186/preaccept-3072014071278914 pmid:25366989 pmcid:PMC4243378 fatcat:kjcmrwrgczdfffvcodgpoj42wq

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach

Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P Fairfax, Kenneth Chan, Katharine Plant, Julian C Knight
2014 Genome Biology  
We confirm recruitment to proximal promoter sequences in MHC class II genes and more distally involving the canonical CIITA enhanceosome.  ...  We analyse CIITA recruitment for pathophysiologically relevant primary human B cells and monocytes, resting and treated with interferon-gamma, in the context of the epigenomic regulatory landscape and  ...  Acknowledgements We are grateful to all the volunteers who participated in this study and to members of the Knight laboratory for their advice and input.  ... 
doi:10.1186/s13059-014-0494-z pmid:25366989 pmcid:PMC4243378 fatcat:bjvbfdqztnhx7boqz5uubb3zwa

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif

Amar Drawid, Nupur Gupta, Vijayalakshmi H Nagaraj, Céline Gélinas, Anirvan M Sengupta
2009 BMC Bioinformatics  
Results: We have developed a tool based on a Hidden Markov Model (HMM) that identifies binding location of transcription factors with preference for self-overlapping DNA motifs by combining the effects  ...  Many of the current regulatory site identification methods do not explicitly take into account the overlapping sites.  ...  We thank Jeff Delrow for analyzing and providing the chicken microarray data.  ... 
doi:10.1186/1471-2105-10-208 pmid:19583839 pmcid:PMC2718928 fatcat:kbehcjo4njgm7d3vkyhosbj2ja

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

P. J. Balwierz, M. Pachkov, P. Arnold, A. J. Gruber, M. Zavolan, E. van Nimwegen
2014 Genome Research  
Although gene expression and chromatin state dynamics are ultimately encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our  ...  We developed a methodology that models gene expression or chromatin modifications in terms of genome-wide predictions of regulatory sites and completely automated it into a web-based tool called ISMARA  ...  Acknowledgments We would like to thank Jean Hausser for help in the probewise processing of microarray data and members of the van Nimwegen research group for helpful discussions.  ... 
doi:10.1101/gr.169508.113 pmid:24515121 pmcid:PMC4009616 fatcat:szjua3fcnvgxlgihzblncwohk4

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

Ron Schwessinger, Maria C. Suciu, Simon J. McGowan, Jelena Telenius, Stephen Taylor, Doug R. Higgs, Jim R. Hughes
2017 Genome Research  
The alpha-globin promoters interact with five distal regulatory elements with the signatures of enhancers and bind many of the known erythroid master transcription factors, of which two (called R1 and  ...  Regulation of gene expression occurs via the binding of tissue-specific and general transcription factors (TFs) to regulatory sequences (promoters, enhancers, and boundary elements).  ... 
doi:10.1101/gr.220202.117 pmid:28904015 pmcid:PMC5630036 fatcat:faa32yoyfbebvhr7i6kbiiqmye

The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink, Stefanie Scheu
2021 BMC Genomic Data  
Background Transcription factors (TFs) control gene expression by direct binding to regulatory regions of target genes but also by impacting chromatin landscapes and modulating DNA accessibility for other  ...  AP-1 family members exhibit (1) increased gene expression, (2) enhanced chromatin accessibility in their promoter region, and (3) a TF DNA binding motif that is globally enriched in genomic regions that  ...  We thank Johannes Ptok and Heiner Schaal (Institute of Virology, University of Düsseldorf) for critical reading of the manuscript.  ... 
doi:10.1186/s12863-021-00991-2 pmid:34544361 pmcid:PMC8454182 fatcat:jc3qrxqi25czfl7abrgtj7d2bm

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Seyed Yahya Anvar, Guy Allard, Elizabeth Tseng, Gloria M. Sheynkman, Eleonora de Klerk, Martijn Vermaat, Raymund H. Yin, Hans E. Johansson, Yavuz Ariyurek, Johan T. den Dunnen, Stephen W. Turner, Peter A. C. 't Hoen
2018 Genome Biology  
Henk Buermans for technical assistance, and Pacific Biosciences for making the full-length mRNA sequencing data available for this study.  ...  Hagen Tilgner for constructive discussions on the manuscript, Dr.  ...  We locally ran DREME [70] (v. 4.11.4) for each region separately and performed a motif search using a negative background (R1, R2, and R3 regions from exons that were not significantly coupled).  ... 
doi:10.1186/s13059-018-1418-0 pmid:29598823 pmcid:PMC5877393 fatcat:pbjlhmoij5apzpciwczyl4ih6e

The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity

Matthew R J Mason, Susan Erp, Kim Wolzak, Axel Behrens, Gennadij Raivich, Joost Verhaagen
2021 Human Molecular Genetics  
The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites.  ...  In particular the transcriptional targets and specific functions of the various transcription factors are unclear.  ...  for proof-reading and editing of the manuscript.  ... 
doi:10.1093/hmg/ddab315 pmid:34718572 pmcid:PMC9029231 fatcat:7r6pt5es4fevzglx7w37sdnquy

Direct Inhibition of IRF-Dependent Transcriptional Regulatory Mechanisms Associated With Disease

Aleksandra Antonczyk, Bart Krist, Malgorzata Sajek, Agata Michalska, Anna Piaszyk-Borychowska, Martyna Plens-Galaska, Joanna Wesoly, Hans A. R. Bluyssen
2019 Frontiers in Immunology  
Interferon regulatory factors (IRFs) are a family of homologous proteins that regulate the transcription of interferons (IFNs) and IFN-induced gene expression.  ...  This complex formation is crucial for DNA binding and the commencing of target-gene expression. IRFs bind DNA and exert their activating potential as homo or heterodimers with other IRFs.  ...  ACKNOWLEDGMENTS We would like to thank members of the Department of Human Molecular Genetics for their critical discussion and input.  ... 
doi:10.3389/fimmu.2019.01176 pmid:31178872 pmcid:PMC6543449 fatcat:ux4mpybrx5bclov3pqt2xtzt7y
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