Genomic approaches towards finding cis-regulatory modules in animals

RC Hardison, J Taylor - Nature Reviews Genetics, 2012 - nature.com
Differential gene expression is the fundamental mechanism underlying animal development
and cell differentiation. However, it is a challenge to identify comprehensively and accurately …

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

DN Cooper, JM Chen, EV Ball, K Howells… - Human …, 2010 - Wiley Online Library
The number of reported germline mutations in human nuclear genes, either underlying or
associated with inherited disease, has now exceeded 100,000 in more than 3,700 different …

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

C Schmidl, M Klug, TJ Boeld, R Andreesen… - Genome …, 2009 - genome.cshlp.org
DNA methylation participates in establishing and maintaining chromatin structures and
regulates gene transcription during mammalian development and cellular differentiation …

What does our genome encode?

JA Stamatoyannopoulos - Genome research, 2012 - genome.cshlp.org
In its first production phase, The ENCODE Project Consortium (ENCODE) has generated
thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses …

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

N Dogan, W Wu, CS Morrissey, KB Chen… - Epigenetics & …, 2015 - Springer
Background Regulated gene expression controls organismal development, and variation in
regulatory patterns has been implicated in complex traits. Thus accurate prediction of …

Identifying transcriptional cis‐regulatory modules in animal genomes

K Suryamohan, MS Halfon - Wiley Interdisciplinary Reviews …, 2015 - Wiley Online Library
Gene expression is regulated through the activity of transcription factors (TF s) and
chromatin‐modifying proteins acting on specific DNA sequences, referred to as cis …

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for …

B D'haene, C Attanasio, D Beysen, J Dostie… - PLoS …, 2009 - journals.plos.org
To date, the contribution of disrupted potentially cis-regulatory conserved non-coding
sequences (CNCs) to human disease is most likely underestimated, as no systematic …

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 …

Balanced translocations in mental retardation

G Vandeweyer, RF Kooy - Human genetics, 2009 - Springer
Over the past few decades, the knowledge on genetic defects causing mental retardation
has dramatically increased. In this review, we discuss the importance of balanced …

Extent of differential allelic expression of candidate breast cancer genes is similar in blood and breast

AT Maia, I Spiteri, AJX Lee, M O'Reilly, L Jones… - Breast cancer …, 2009 - Springer
Introduction Normal gene expression variation is thought to play a central role in inter-
individual variation and susceptibility to disease. Regulatory polymorphisms in cis-acting …