ZFIN Lab: Vertebrate Development and Regeneration Lab

ZFIN ID: ZDB-LAB-210514-1

Vertebrate Development and Regeneration Lab

PI/Director:	Bessa, Jose
Contact Person:	Bessa, Jose
Email:	jose.bessa@ibmc.up.pt
URL:
Address:
Country:
Phone:	+351 226 074 900
Fax:
Line Designation:	iis

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show all 6 genomic features

STATEMENT OF RESEARCH INTERESTS

The Vertebrate Development and Regeneration group studies the mechanisms of cis-transcriptional regulation of genes and how mutations on non-coding cis-transcriptional regulatory sequences might impact in the development of some human diseases, in particular diabetes and pancreatic cancer. To achieve this, the VDR lab uses genomic strategies to identify non-coding cis-transcriptional regulatory sequences and perform genetic functional assays in zebrafish to evaluate the function of these sequences.

LAB MEMBERS

Cabezas-Sainz, Pablo Post-Doc	Galhardo, Mafalda Post-Doc	perrod, chiara Post-Doc
Amorim, João Graduate Student	Duque, Marta Graduate Student	Eufrásio, Ana Graduate Student
Ferreira, Fábio Graduate Student	Silva, Victor Graduate Student	Teixeira, Joana Graduate Student
Marques, Joana Research Staff

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Lenis-Rojas, O.A., Roma-Rodrigues, C., Carvalho, B., Cabezas-Sainz, P., Fernández Vila, S., Sánchez, L., Baptista, P.V., Fernandes, A.R., Royo, B. (2022) In Vitro and In Vivo Biological Activity of Ruthenium 1,10-Phenanthroline-5,6-dione Arene Complexes. International Journal of Molecular Sciences. 23(21):

Moral-Sanz, J., Fernandez-Rojo, M.A., Colmenarejo, G., Kurdyukov, S., Brust, A., Ragnarsson, L., Andersson, Å., Vila, S.F., Cabezas-Sainz, P., Wilhelm, P., Vela-Sebastian, A., Fernández-Carrasco, I., Chin, Y.K.Y., López-Mancheño, Y., Smallwood, T.B., Clark, R.J., Fry, B.G., King, G.F., Ramm, G.A., Alewood, P.F., Lewis, R.J., Mulvenna, J.P., Boyle, G.M., Sanchez, L.E., Neely, G.G., Miles, J.J., Ikonomopoulou, M.P. (2022) The structural conformation of the tachykinin domain drives the anti-tumoral activity of an octopus peptide in melanoma BRAF^V600E. British journal of pharmacology. 179(20):4878-4896

Matinha-Cardoso, J., Coutinho, F., Lima, S., Eufrásio, A., Carvalho, A.P., Oliva-Teles, A., Bessa, J., Tamagnini, P., Serra, C.R., Oliveira, P. (2022) Novel protein carrier system based on cyanobacterial nano-sized extracellular vesicles for application in fish. Microbial biotechnology. 15(8):2191-2207

Bordeira-Carriço, R., Teixeira, J., Duque, M., Galhardo, M., Ribeiro, D., Acemel, R.D., Firbas, P.N., Tena, J.J., Eufrásio, A., Marques, J., Ferreira, F.J., Freitas, T., Carneiro, F., Goméz-Skarmeta, J.L., Bessa, J. (2022) Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers. Nature communications. 13:1945

Lenis-Rojas, O.A., Cordeiro, S., Horta-Meireles, M., Fernández, J.A.A., Fernández Vila, S., Rubiolo, J.A., Cabezas-Sainz, P., Sanchez, L., Fernandes, A.R., Royo, B. (2021) N-Heterocyclic Carbene Iron Complexes as Anticancer Agents: In Vitro and In Vivo Biological Studies. Molecules. 26(18):

Ferreira, F.J., Carvalho, L., Logarinho, E., Bessa, J. (2021) foxm1 Modulates Cell Non-Autonomous Response in Zebrafish Skeletal Muscle Homeostasis. Cells. 10(5)

Eufrásio, A., Perrod, C., Ferreira, F.J., Duque, M., Galhardo, M., Bessa, J. (2020) In vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes Associated SNPs. Diabetes. 69(12):2794-2805

Amorim, J.P., Gali-Macedo, A., Marcelino, H., Bordeira-Carriço, R., Naranjo, S., Rivero-Gil, S., Teixeira, J., Galhardo, M., Marques, J., Bessa, J. (2020) A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. Cell Reports. 32:107862

Seixas, A.I., Loureiro, J.R., Costa, C., Ordóñez-Ugalde, A., Marcelino, H., Oliveira, C.L., Loureiro, J.L., Dhingra, A., Brandão, E., Cruz, V.T., Timóteo, A., Quintáns, B., Rouleau, G.A., Rizzu, P., Carracedo, Á., Bessa, J., Heutink, P., Sequeiros, J., Sobrido, M.J., Coutinho, P., Silveira, I. (2017) A Pentanucleotide ATTTC Repeat Insertion in the Non-coding Region of DAB1, Mapping to SCA37, Causes Spinocerebellar Ataxia. American journal of human genetics. 101:87-103

Fernández-Miñán, A., Bessa, J., Tena, J.J., Gómez-Skarmeta, J.L. (2016) Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish. Methods in cell biology. 135:413-30

Cebola, I., Rodríguez-Seguí, S.A., Cho, C.H., Bessa, J., Rovira, M., Luengo, M., Chhatriwala, M., Berry, A., Ponsa-Cobas, J., Maestro, M.A., Jennings, R.E., Pasquali, L., Morán, I., Castro, N., Hanley, N.A., Gomez-Skarmeta, J.L., Vallier, L., Ferrer, J. (2015) TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors. Nature cell biology. 17:615-26

Ariza-Cosano, A., Bensimon-Brito, A., Gómez-Skarmeta, J.L., Bessa, J. (2015) sox21a directs lateral line patterning by modulating FGF signaling. Developmental Neurobiology. 75(1):80-92

Spieler, D., Kaffe, M., Knauf, F., Bessa, J., Tena, J.J., Giesert, F., Schormair, B., Tilch, E., Lee, H., Horsch, M., Czamara, D., Karbalai, N., von Toerne, C., Waldenberger, M., Gieger, C., Lichtner, P., Claussnitzer, M., Naumann, R., Müller-Myhsok, B., Torres, M., Garrett, L., Rozman, J., Klingenspor, M., Gailus-Durner, V., Fuchs, H., Hrabě de Angelis, M., Beckers, J., Holter, S.M., Meitinger, T., Hauck, S.M., Laumen, H., Wurst, W., Casares, F., Gómez-Skarmeta, J.L., Winkelmann, J. (2014) Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon. Genome research. 24:592-603

Bessa, J., Luengo, M., Rivero-Gil, S., Ariza-Cosano, A., Maia, A.H., Ruiz-Ruano, F.J., Caballero, P., Naranjo, S., Carvajal, J.J., and Gómez-Skarmeta, J.L. (2014) A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates. Genome research. 24(3):487-95

Regadas, I., Matos, M.R., Monteiro, F.A., Gomez-Skarmeta, J.L., Lima, D., Bessa, J., Casares, F., and Reguenga, C. (2013) Several Cis-regulatory Elements Control mRNA Stability, Translation Efficiency, and Expression Pattern of Prrxl1 (Paired Related Homeobox Protein-like 1). The Journal of biological chemistry. 288(51):36285-301

Ariza-Cosano, A., Visel, A., Pennacchio, L.A., Fraser, H.B., Gómez-Skarmeta, J.L., Irimia, M., and Bessa, J. (2012) Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics. 13(1):713

Royo, J.L., Bessa, J., Hidalgo, C., Fernández-Miñán, A., Tena, J.J., Roncero, Y., Gómez-Skarmeta, J.L., and Casares, F. (2012) Identification and Analysis of Conserved cis-Regulatory Regions of the MEIS1 Gene. PLoS One. 7(3):e33617

Bessa, J., Tena, J.J., de la Calle-Mustienes, E., Fernández-Miñán, A., Naranjo, S., Fernández, A., Montoliu, L., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2009) Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(9):2409-2417

Bessa, J., Tavares, M.J., Santos, J., Kikuta, H., Laplante, M., Becker, T.S., Gómez-Skarmeta, J.L., and Casares, F. (2008) meis1 regulates cyclin D1 and c-myc expression, and controls the proliferation of the multipotent cells in the early developing zebrafish eye. Development (Cambridge, England). 135(5):799-803