Enhancer-gene specificity in development and disease

T Pachano, E Haro, A Rada-Iglesias - Development, 2022 - journals.biologists.com
Enhancers control the establishment of spatiotemporal gene expression patterns throughout
development. Over the past decade, the development of new technologies has improved our …

The origin of animal body plans: a view from fossil evidence and the regulatory genome

DH Erwin - Development, 2020 - journals.biologists.com
The origins and the early evolution of multicellular animals required the exploitation of
holozoan genomic regulatory elements and the acquisition of new regulatory tools …

Gene expression variability across cells and species shapes innate immunity

T Hagai, X Chen, RJ Miragaia, R Rostom, T Gomes… - Nature, 2018 - nature.com
As the first line of defence against pathogens, cells mount an innate immune response,
which varies widely from cell to cell. The response must be potent but carefully controlled to …

iProEP: a computational predictor for predicting promoter

HY Lai, ZY Zhang, ZD Su, W Su, H Ding… - … Therapy-Nucleic Acids, 2019 - cell.com
Promoter is a fundamental DNA element located around the transcription start site (TSS) and
could regulate gene transcription. Promoter recognition is of great significance in …

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

M Brozovic, C Dantec, J Dardaillon… - Nucleic acids …, 2018 - academic.oup.com
Abstract ANISEED (www. aniseed. cnrs. fr) is the main model organism database for
tunicates, the sister-group of vertebrates. This release gives access to annotated genomes …

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

E Oberbeckmann, N Krietenstein, V Niebauer… - Nature …, 2021 - nature.com
The fundamental molecular determinants by which ATP-dependent chromatin remodelers
organize nucleosomes across eukaryotic genomes remain largely elusive. Here, chromatin …

[HTML][HTML] refTSS: a reference data set for human and mouse transcription start sites

I Abugessaisa, S Noguchi, A Hasegawa… - Journal of molecular …, 2019 - Elsevier
Transcription starts at genomic positions called transcription start sites (TSSs), producing
RNAs, and is mainly regulated by genomic elements and transcription factors binding …

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

SH Lewis, L Ross, SA Bain, E Pahita, SA Smith… - PLoS …, 2020 - journals.plos.org
Cytosine methylation is an ancient epigenetic modification yet its function and extent within
genomes is highly variable across eukaryotes. In mammals, methylation controls …

Identification of DNA-methylated CpG islands associated with gene silencing in the adult body tissues of the Ogye chicken using RNA-Seq and reduced …

WJ Lim, KH Kim, JY Kim, S Jeong, N Kim - Frontiers in genetics, 2019 - frontiersin.org
DNA methylation is an epigenetic mark that plays an essential role in regulating gene
expression. CpG islands are DNA methylations regions in promoters known to regulate …

Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions

P Sarkies - Biochemical Society Transactions, 2022 - portlandpress.com
DNA methylation is an epigenetic modification with a very long evolutionary history.
However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome …