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RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera (+1 others)
2018 Nucleic Acids Research  
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences.  ...  ) analysis of regulatory variations, (v) comparative genomics.  ...  ACKNOWLEDGEMENTS We are particularly thankful to the colleagues who help us installing and maintaining RSAT servers: Victor del Moral Chavez, Romualdo Zayas-Lagunas, Alfredo José Hernández Alvarez (Centro  ... 
doi:10.1093/nar/gky317 pmid:29722874 pmcid:PMC6030903 fatcat:hau274l2trgfhhtpxtwsqftyna

Editorial: The 16th annual Nucleic Acids Research web server issue 2018

2018 Nucleic Acids Research  
HMMer website for homology search using profile hidden Markov models, and a 20th anniversary paper on RSAT, which detects DNA regulatory motifs.  ...  Tools for RNA analysis include Freiburg RNA tools, a broad collection of RNA analysis tools, pirScan, for predicting targets of PIWI interacting RNA (piRNA) and psRNATarget, for plant small RNA target  ...  Numerical, textual, and graphical output should be mixed and visualization tools that add information or increase the user's understanding should be utilized.  ... 
doi:10.1093/nar/gky518 pmid:29982807 pmcid:PMC6030837 fatcat:x7lzti7w2nhp5elvqmg5at77rq

ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins [article]

Amanda Demeter, Mari Carmen Romero-Mulero, Luca Csabai, Márton Ölbei, Padhmanand Sudhakar, Wilfried Haerty, Tamás Korcsmáros
2020 bioRxiv   pre-print
We identified three ULK1-specific and one ULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes.  ...  Nucleic Acids 493 Res. 46, D428-D434 (2018). 494 35. Nguyen, N. T. T. et al. RSAT 2018: regulatory sequence analysis tools 20th 495 anniversary. Nucleic Acids Res. 46, W209-W214 (2018). 496 36.  ...  The EMBL-EBI search and sequence analysis tools APIs in 2019. 491 Nucleic Acids Res. 47, W636-W641 (2019). 492 34. Gouw, M. et al. The eukaryotic linear motif resource -2018 update.  ... 
doi:10.1101/2020.02.27.967901 fatcat:gd4onv2q7jb6lkidorry23jju4

Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

Maria Angeles Decena, Sergio Gálvez-Rojas, Federico Agostini, Ruben Sancho, Bruno Contreras-Moreira, David L. Des Marais, Pilar Hernandez, Pilar Catalán
2021 Plants  
Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species.  ...  Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes.  ...  RSAT 2018: Regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 2018, 46, W209–W214. [CrossRef] [PubMed] 66.  ... 
doi:10.3390/plants10122664 pmid:34961135 pmcid:PMC8709310 fatcat:m76jpbgsznbthm3vswd7smx55q

FANCD2 tunes the UPR preventing mitochondrial stress-induced common fragile site instability [article]

Philippe Fernandes, Benoit Miotto, Claude Saint-Ruf, Viola Nahse, Silvia Ravera, Enrico Cappelli, Valeria Naim
2019 bioRxiv   pre-print
Furthermore, a genomic analysis of FANCD2 binding sites identified an enrichment for mitochondrial UPR transcriptional response elements in FANCD2 bound regions.  ...  RSAT 2018: regulatory sequence analysis tools 20th 838 anniversary. Nucleic Acids Res 46, W209-W214 (2018). 839 840 author/funder. All rights reserved.  ...  FANCD2 ChIP seq data were 608 scanned with RSAT (Regulatory Sequence Analysis Tools)-matrix-scan 66, 67 to 609 identify instances of MURE1, MURE2 (mitochondrial UPR response elements) and 610 CHOP motifs  ... 
doi:10.1101/808915 fatcat:6s4a5l7werhexdnvaanxc6m52y

A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox Clusters [article]

Havva Ortabozkoyun Kara, Pin-Yao Huang, Hyunwoo Cho, Varun Narendra, Gary LeRoy, Jane A. Skok, Aristotelis Tsirigos, Esteban O. Mazzoni, Danny Reinberg
2020 bioRxiv   pre-print
Upon loss of MAZ, local contacts within topologically associated domains (TADs) were disrupted, as evidenced by HiC analysis.  ...  Nguyen et al., RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res 46, W209-W214 (2018). L. Bailey, C.  ...  ChIPseq "bed" file coordinates were converted into "fasta" by using fetch sequences tool within Regulatory Sequence Analysis Tools (RSAT) (58) , and MEME was used for motif analysis of MAZ in ESCs and  ... 
doi:10.1101/2020.08.25.267237 fatcat:tvhgdnmqlrbxde3jgu6cfoia4a

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency

Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro
2021 Development  
By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA.  ...  RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res 46, W209-W214.  Niwa, H., Miyazaki, J., and Smith, A.G. (2000).  ...  De-novo motif discovery on Esrrb/Nr5a2 bound regions in FCS/L used the Regulatory Sequence Analysis Tools (RSAT) with standard parameters ( (Nguyen et al., 2018) .  ... 
doi:10.1242/dev.199604 pmid:34397088 pmcid:PMC8451941 fatcat:wlvilejwbrc5xamui6lkwa2v3i

Postnatal Arx transcriptional activity regulates functional properties of PV interneurons

Donald J. Joseph, Markus Von Deimling, Yuiko Hasegawa, Ana G. Cristancho, Rebecca C. Ahrens-Nicklas, Stephanie L. Rogers, Rashmi Risbud, Almedia J. McCoy, Eric D. Marsh
2020 iScience  
Behavioral analysis uncovered an increase in anxiety.  ...  Genome-wide sequencing of fluorescence activated cell sorted (FACS) PVIs revealed that Arx impinged on network excitability via genes primarily associated with synaptic and extracellular matrix pathways  ...  RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 46, W209-W214. Nordli, D.R., Jr. (2012). Epileptic encephalopathies in infants and children. J. Clin.  ... 
doi:10.1016/j.isci.2020.101999 pmid:33490907 pmcid:PMC7807163 fatcat:d3aalnnry5dtbhpvatkunhl3qy

Evolution and control of the DUO1 regulatory network in land plants

Siti Nur Aishah Mohd Kamal
Phylogenetic analysis showed that DAZ3 and DAZ3L are restricted to the eudicots superrosid-superasterid clade and most likely evolved from ancestral DAZ1 sequences.  ...  These factors are dependent upon a key regulatory module formed by the MYB transcription factor DUO1 POLLEN 1 (DUO1), and DUO1-ACTIVATED ZINC FINGER 1 / DUO1-ACTIVATED ZINC FINGER 2 (DAZ1/DAZ2), C2H2 zinc  ...  : regulatory sequence analysis tools 20th anniversary.  ... 
doi:10.25392/ fatcat:fqq5gqgpebbf5e3nvnmzxswlgm