Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Evolution of anterior Hox regulatory elements among chordates

(2011) Alfonso Natale et al.   BMC EVOLUTIONARY BIOLOGY

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Transphyletic conservation of developmental regulatory state in animal evolution

(2011) J. L. Royo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

(2010) Danilo Licastro et al.   BMC GENOMICS

Limited functions of Hox genes in the larval development of the ascidian Ciona intestinalis

(2010) T. Ikuta et al.   DEVELOPMENT

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

(2010) O. Tassy et al.   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

(2010) F. Denoeud et al.   SCIENCE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Conserved noncoding elements and the evolution of animal body plans

(2009) Tanya Vavouri et al.   BIOESSAYS

Highly Divergent Gene Expression Programs Can Lead to Similar Chordate Larval Body Plans

(2009) Daniel Sobral et al.   CURRENT BIOLOGY

Flexibility of transcription factor target site position in conserved cis-regulatory modules

(2009) R. Andrew Cameron et al.   DEVELOPMENTAL BIOLOGY

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

(2009) A. L. Hufton et al.   GENOME RESEARCH

Functional autonomy of distant-acting human enhancers

(2009) Axel Visel et al.   GENOMICS

Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

(2009) Jochen Gehrig et al.   NATURE METHODS

The evolution of Fox genes and their role in development and disease

(2009) Sridhar Hannenhalli et al.   NATURE REVIEWS GENETICS

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

(2009) Xianjun Dong et al.   NUCLEIC ACIDS RESEARCH

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

Ascidians and the Plasticity of the Chordate Developmental Program

(2008) Patrick Lemaire et al.   CURRENT BIOLOGY

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

(2008) L. Z. Holland et al.   GENOME RESEARCH

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

(2008) A. L. Hufton et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION