Imperial College London


Faculty of MedicineInstitute of Clinical Sciences

Professor of Computational Biology



+44 (0)20 3313 8353b.lenhard Website




Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318




230ICTEM buildingHammersmith Campus






BibTex format

author = {Marletaz, F and Firbas, PN and Maeso, I and Tena, JJ and Bogdanovic, O and Perry, M and Wyatt, CDR and de, la Calle-Mustienes E and Bertrand, S and Burguera, D and Acemel, RD and van, Heeringen SJ and Naranjo, S and Herrera-Ubeda, C and Skvortsova, K and Jimenez-Gancedo, S and Aldea, D and Marquez, Y and Buono, L and Kozmikova, I and Permanyer, J and Louis, A and Albuixech-Crespo, B and Le, Petillon Y and Leon, A and Subirana, L and Balwierz, PJ and Duckett, PE and Farahani, E and Aury, J-M and Mangenot, S and Wincker, P and Albalat, R and Benito-Gutierrez, E and Canestro, C and Castro, F and D'Aniello, S and Ferrier, DEK and Huang, S and Laudet, V and Marais, GAB and Pontarotti, P and Schubert, M and Seitz, H and Somorjai, I and Takahashi, T and Mirabeau, O and Xu, A and Yu, J-K and Carninci, P and Ramon, Martinez-Morales J and Crollius, HR and Kozmik, Z and Weirauch, MT and Garcia-Fernandez, J and Lister, R and Lenhard, B and Holland, PWH and Escriva, H and Luis, Gomez-Skarmeta J and},
doi = {10.1038/s41586-018-0734-6},
journal = {Nature},
pages = {64--70},
title = {Amphioxus functional genomics and the origins of vertebrate gene regulation},
url = {},
volume = {564},
year = {2018}

RIS format (EndNote, RefMan)

AB - Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.
AU - Marletaz,F
AU - Firbas,PN
AU - Maeso,I
AU - Tena,JJ
AU - Bogdanovic,O
AU - Perry,M
AU - Wyatt,CDR
AU - de,la Calle-Mustienes E
AU - Bertrand,S
AU - Burguera,D
AU - Acemel,RD
AU - van,Heeringen SJ
AU - Naranjo,S
AU - Herrera-Ubeda,C
AU - Skvortsova,K
AU - Jimenez-Gancedo,S
AU - Aldea,D
AU - Marquez,Y
AU - Buono,L
AU - Kozmikova,I
AU - Permanyer,J
AU - Louis,A
AU - Albuixech-Crespo,B
AU - Le,Petillon Y
AU - Leon,A
AU - Subirana,L
AU - Balwierz,PJ
AU - Duckett,PE
AU - Farahani,E
AU - Aury,J-M
AU - Mangenot,S
AU - Wincker,P
AU - Albalat,R
AU - Benito-Gutierrez,E
AU - Canestro,C
AU - Castro,F
AU - D'Aniello,S
AU - Ferrier,DEK
AU - Huang,S
AU - Laudet,V
AU - Marais,GAB
AU - Pontarotti,P
AU - Schubert,M
AU - Seitz,H
AU - Somorjai,I
AU - Takahashi,T
AU - Mirabeau,O
AU - Xu,A
AU - Yu,J-K
AU - Carninci,P
AU - Ramon,Martinez-Morales J
AU - Crollius,HR
AU - Kozmik,Z
AU - Weirauch,MT
AU - Garcia-Fernandez,J
AU - Lister,R
AU - Lenhard,B
AU - Holland,PWH
AU - Escriva,H
AU - Luis,Gomez-Skarmeta J
AU - Irimia,M
DO - 10.1038/s41586-018-0734-6
EP - 70
PY - 2018///
SN - 0028-0836
SP - 64
TI - Amphioxus functional genomics and the origins of vertebrate gene regulation
T2 - Nature
UR -
UR -
UR -
VL - 564
ER -