Enhancer grammar in development, evolution, and disease: dependencies and interplay

GA Jindal, EK Farley - Developmental cell, 2021 - cell.com
Each language has standard books describing that language's grammatical rules. Biologists
have searched for similar, albeit more complex, principles relating enhancer sequence to …

From Notochord Formation to Hereditary Chordoma: The Many Roles of Brachyury

Y Nibu, DS José-Edwards… - BioMed research …, 2013 - Wiley Online Library
Chordoma is a rare, but often malignant, bone cancer that preferentially affects the axial
skeleton and the skull base. These tumors are both sporadic and hereditary and appear to …

Diverse logics and grammar encode notochord enhancers

BP Song, MF Ragsac, K Tellez, GA Jindal, JL Grudzien… - Cell reports, 2023 - cell.com
The notochord is a defining feature of all chordates. The transcription factors Zic and ETS
regulate enhancer activity within the notochord. We conduct high-throughput screens of …

Conserved enhancers control notochord expression of vertebrate Brachyury

CL Kemmler, J Smolikova, HR Moran… - Nature …, 2023 - nature.com
The cell type-specific expression of key transcription factors is central to development and
disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning …

Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells

AL Evans, T Faial, MJ Gilchrist, T Down, L Vallier… - PloS one, 2012 - journals.plos.org
Background The T-box transcription factor Brachyury (T) is essential for formation of the
posterior mesoderm and the notochord in vertebrate embryos. Work in the frog and the …

Evolution of the bilaterian mouth and anus

C Nielsen, T Brunet, D Arendt - Nature ecology & evolution, 2018 - nature.com
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut
with one major gastric opening. However, there is no consensus on how this happened. Did …

Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona

LJ Negrón-Piñeiro, Y Wu, S Popsuj… - Nature …, 2024 - nature.com
Tissue-specific gene expression is fundamental in development and evolution, and is
mediated by transcription factors and by the cis-regulatory regions (enhancers) that they …

Functional and evolutionary insights from the Ciona notochord transcriptome

WM Reeves, Y Wu, MJ Harder, MT Veeman - Development, 2017 - journals.biologists.com
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model
for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow …

The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates

A Di Gregorio - Current Topics in Developmental Biology, 2020 - Elsevier
The notochord is a structure required for support and patterning of all chordate embryos,
from sea squirts to humans. An increasing amount of information on notochord development …

[HTML][HTML] Integrated microarray and ChIP analysis identifies multiple Foxa2 dependent target genes in the notochord

OJ Tamplin, BJ Cox, J Rossant - Developmental biology, 2011 - Elsevier
The node and notochord are key tissues required for patterning of the vertebrate body plan.
Understanding the gene regulatory network that drives their formation and function is …