Conserved non-coding elements: developmental gene regulation meets genome organization

D Polychronopoulos, JWD King, AJ Nash… - Nucleic acids …, 2017 - academic.oup.com
Comparative genomics has revealed a class of non-protein-coding genomic sequences that
display an extraordinary degree of conservation between two or more organisms, regularly …

Chromatin and epigenetic features of long-range gene regulation

N Harmston, B Lenhard - Nucleic acids research, 2013 - academic.oup.com
The precise regulation of gene transcription during metazoan development is controlled by a
complex system of interactions between transcription factors, histone modifications and …

A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

JR Mandel, RB Dikow, VA Funk… - Applications in plant …, 2014 - Wiley Online Library
• Premise of the study: The Compositae (Asteraceae) are a large and diverse family of
plants, and the most comprehensive phylogeny to date is a meta‐tree based on 10 …

The mystery of extreme non-coding conservation

N Harmston, A Barešić… - … Transactions of the …, 2013 - royalsocietypublishing.org
Regions of several dozen to several hundred base pairs of extreme conservation have been
found in non-coding regions in all metazoan genomes. The distribution of these elements …

Conserved nonexonic elements: a novel class of marker for phylogenomics

SV Edwards, A Cloutier, AJ Baker - Systematic Biology, 2017 - academic.oup.com
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at
least in vertebrates, they appear less subject to strong variation in GC content among …

Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution

B Song, D Morse, Y Song, Y Fu, X Lin… - Genome biology and …, 2017 - academic.oup.com
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and
Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the …

The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates

D Burgess, M Freeling - The Plant Cell, 2014 - academic.oup.com
In vertebrates, conserved noncoding elements (CNEs) are functionally constrained
sequences that can show striking conservation over> 400 million years of evolutionary …

Conservation and functional element discovery in 20 angiosperm plant genomes

D Hupalo, AD Kern - Molecular biology and evolution, 2013 - academic.oup.com
Here, we describe the construction of a phylogenetically deep, whole-genome alignment of
20 flowering plants, along with an analysis of plant genome conservation. Each included …

Ancient cis-regulatory constraints and the evolution of genome architecture

M Irimia, I Maeso, SW Roy, HB Fraser - Trends in Genetics, 2013 - cell.com
The order of genes along metazoan chromosomes has generally been thought to be largely
random, with few implications for organismal function. However, two recent studies …

Ultraconserved elements occupy specific arenas of three-dimensional mammalian genome organization

RB McCole, J Erceg, W Saylor, C Wu - Cell reports, 2018 - cell.com
This study explores the relationship between three-dimensional genome organization and
ultraconserved elements (UCEs), an enigmatic set of DNA elements that are perfectly …