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Deciphering cis-regulatory elements using REgulamentary

Riva SG, Georgiades E, Herrmann JC, Gür ER, Sanders E, Sergeant M, Baxter M, Hughes JR.   +7 more
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Mammalian evolution of human cis-regulatory elements and transcription factor binding sites

Science, 2023
Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 ...
Gregory Andrews, K. Fan, H. Pratt, Nishigandha Phalke, E. Karlsson, K. Lindblad-Toh, S. Gazal, Jill E. Moore, Z. Weng, Gregory Andrews, Joel C. Armstrong, M. Bianchi, B. Birren, K. Bredemeyer, Ana M. Breit, M. Christmas, H. Clawson, Joana Damas, F. Di Palma, M. Diekhans, Michael X. Dong, E. Eizirik, K. Fan, Cornelia Fanter, Nicole M. Foley, K. Forsberg-Nilsson, Carlos J. Garcia, J. Gatesy, S. Gazal, D. Genereux, Linda Goodman, Jenna R. Grimshaw, Michaela K. Halsey, Andrew J. Harris, G. Hickey, Michael Hiller, Allyson Hindle, R. Hubley, Graham M. Hughes, Jeremy Johnson, David Juan, Irene M. Kaplow, E. Karlsson, Kathleen C. Keough, B. Kirilenko, Klaus‐Peter Koepfli, Jennifer M. Korstian, Amanda Kowalczyk, S. Kozyrev, Alyssa J. Lawler, C. Lawless, T. Lehmann, D. Levesque, H. Lewin, Xue Li, Abigail L. Lind, K. Lindblad-Toh, Ava Mackay-Smith, Voichita D. Marinescu, Tomàs Marquès-Bonet, Victor C. Mason, J. Meadows, Wynn K. Meyer, Jill E. Moore, L. R. Moreira, Diana D. Moreno-Santillán, Kathleen Morrill, G. Muntané, W. Murphy, A. Navarro, M. Nweeia, S. Ortmann, Austin B. Osmanski, B. Paten, Nicole S. Paulat, Andreas R. Pfenning, BaDoi N. Phan, K. Pollard, H. Pratt, D. Ray, Steven K. Reilly, Jeb Rosen, I. Ruf, Louise Ryan, Oliver A. Ryder, Pardis C Sabeti, Daniel E. Schäffer, Aitor Serres, B. Shapiro, Arian F. A. Smit, M. Springer, Chaitanya Srinivasan, C. Steiner, Jessica M. Storer, Kevin A. M. Sullivan, P. Sullivan, E. Sundström, Megan A. Supple, Ross Swofford, Joy-El R B Talbot, E. Teeling, Jason Turner-Maier, A. Valenzuela, Franziska Wagner, O. Wallerman, Chao Wang, Juehan Wang, Z. Weng, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Xiaomeng Zhang   +111 more
semanticscholar   +1 more source

Mapping regulatory elements

Nature Biotechnology, 2016
Regulatory genomic elements can now be studied in their native context using two CRISPR-based high-throughput approaches.
Yuexin Zhou, Wensheng Wei
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Erythroid regulatory elements

STEM CELLS, 1993
Erythroid differentiation leads to the production of red blood cells that contain a high level of hemoglobin. This level is mainly regulated by globin gene transcription during development and differentiation. Although numerous cis-acting sequences are involved in transcriptional activity of globin genes, combinations of three motifs, CCACC, SP1 and ...
Paul-Henri Romeo, N Raich
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Regulatory elements in the KlHEM1 promoter

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2008
In Kluyveromyces lactis the gene encoding 5-aminolevulinate synthase, KlHEM1, is regulated at the transcriptional level by carbon source and oxygen availability. The KlHEM1 promoter, fused to the reporter lacZ gene, has been analysed by deletion and direct mutagenesis techniques in order to find regulatory elements functionally relevant in this ...
Laura Núñez, María Esperanza Cerdán, Ana María Rodríguez-Torres   +2 more
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Conserved regulatory elements in AMPK

Nature, 2013
arising from B. Xiao et al. , 230–233 (2011)10.1038/nature09932 The AMP-activated protein kinase (AMPK), an αβγ heterotrimeric enzyme, has a central role in regulating cellular metabolism and energy homeostasis1.
Chen, Lei, Xin, Feng-Jiao, Wang, Jue, Hu, Jicheng, Zhang, Yuan-Yuan, Wan, Shuo, Cao, Lu-Sha, Lu, Chang, Li, Peng, Yan, S. Frank, Neumann, Dietbert, Schlattner, Uwe, Xia, Bin, Wang, Zhi-Xin, Wu, Jia-Wei   +14 more
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Regulatory elements in aflatoxin biosynthesis

Mycotoxin Research, 2006
This review provides a synopsis of factors involved in the regulation of aflatoxin inAspergillus species at the molecular level. Much of the knowledge available today on the regulation of secondary metabolite production in fungi has been gleaned from studies of the aflatoxin gene cluster inA. flavus andA.
Kenneth C. Ehrlich, Jeffrey W. Cary, Shubha P. Kale, Thomas E. Cleveland, Deepak Bhatnagar, Ana M. Calvo   +5 more
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REGULATORY ELEMENTS OF MARINE CYANOBACTERIA

Genome Informatics 2007, 2007
The free-living, oxyphototroph bacteria of the group of Prochlorococcus populate widely the oceans. Genomic information of nine marine cyanobacteria was used to predict signals essential for regulation. We implemented a pipeline that automatically calculates BLASTp alignments of query genomes, selects a representative subset of orthologs and predicts ...
Szymon M. Kielbasa, Hanspeter Herzel, Ilka M. Axmann   +2 more
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Prediction of Regulatory Elements

2008
Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene.
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Structures of regulatory elements in mRNAs

Current Opinion in Structural Biology, 2006
Messenger RNAs often contain structures in their 5'-untranslated region that serve to regulate or promote expression of their gene product. Recent structural studies have revealed that riboswitches, which bind a variety of small molecule metabolites, including purine bases, S-adenosylmethionine, amino acids and cofactors, can contain sophisticated ...
openaire   +3 more sources