Hearing silence: non-neutral evolution at synonymous sites in mammals

JV Chamary, JL Parmley, LD Hurst - Nature Reviews Genetics, 2006 - nature.com
Although the assumption of the neutral theory of molecular evolution—that some classes of
mutation have too small an effect on fitness to be affected by natural selection—seems …

Gene coexpression networks in human brain identify epigenetic modifications in alcohol dependence

I Ponomarev, S Wang, L Zhang, RA Harris… - Journal of …, 2012 - Soc Neuroscience
Alcohol abuse causes widespread changes in gene expression in human brain, some of
which contribute to alcohol dependence. Previous microarray studies identified individual …

A novel regulatory player in the innate immune system: long non-coding RNAs

Y Xie, Y Wei - International journal of molecular sciences, 2021 - mdpi.com
Long non-coding RNAs (lncRNAs) represent crucial transcriptional and post-transcriptional
gene regulators during antimicrobial responses in the host innate immune system. Studies …

DNA methylation and structural and functional bimodality of vertebrate promoters

N Elango, SV Yi - Molecular biology and evolution, 2008 - academic.oup.com
Human promoters divide into 2 classes, the low CpG (LCG) and the high CpG (HCG), based
on their CpG dinucleotide content. The LCG class of promoters is hypermethylated and is …

Housekeeping genes tend to show reduced upstream sequence conservation

D Farré, N Bellora, L Mularoni, X Messeguer, MM Albà - Genome biology, 2007 - Springer
Background Understanding the constraints that operate in mammalian gene promoter
sequences is of key importance to understand the evolution of gene regulatory networks …

Both selective and neutral processes drive GC content evolution in the human genome

U Pozzoli, G Menozzi, M Fumagalli, M Cereda… - BMC evolutionary …, 2008 - Springer
Background Mammalian genomes consist of regions differing in GC content, referred to as
isochores or GC-content domains. The scientific debate is still open as to whether such …

Phylogenomic analysis of the emergence of GC-rich transcription elements

P Khuu, M Sandor, J DeYoung… - Proceedings of the …, 2007 - National Acad Sciences
We have applied a comparative phylogenomic analysis to study the evolutionary
relationships between GC content, CpG-dinucleotide content (CpGs), potential nuclear …

Impact of GC content on gene expression pattern in chicken

YS Rao, XW Chai, ZF Wang, QH Nie… - Genetics Selection …, 2013 - Springer
Background GC content varies greatly between different genomic regions in many
eukaryotes. In order to determine whether this organization named isochore organization …

DNA methylation rebalances gene dosage after mammalian gene duplications

AYF Chang, BY Liao - Molecular biology and evolution, 2012 - academic.oup.com
Although gene duplication plays a major role in organismal evolution, it may also lead to
gene dosage imbalance, thereby having an immediate adverse effect on an organism's …

A New chromosome-assigned mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome

TD Brekke, AST Papadopulos, E Julià… - Molecular Biology …, 2023 - academic.oup.com
Chromosome-scale genome assemblies based on ultralong-read sequencing technologies
are able to illuminate previously intractable aspects of genome biology such as fine-scale …