[HTML][HTML] Cell fate decisions, transcription factors and signaling during early retinal development

R Diacou, P Nandigrami, A Fiser, W Liu… - Progress in retinal and …, 2022 - Elsevier
The development of the vertebrate eyes is a complex process starting from anterior-posterior
and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye …

[HTML][HTML] Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation

S Baek, I Lee - Computational and structural biotechnology journal, 2020 - Elsevier
Most genetic variations associated with human complex traits are located in non-coding
genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a …

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

A Farmer, S Thibivilliers, KH Ryu, J Schiefelbein… - Molecular Plant, 2021 - cell.com
Similar to other complex organisms, plants consist of diverse and specialized cell types. The
gain of unique biological functions of these different cell types is the consequence of the …

Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina

P Lyu, T Hoang, CP Santiago, ED Thomas, AE Timms… - Cell reports, 2021 - cell.com
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites,
control neurogenesis and cell-fate specification in the developing central nervous system. In …

High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci

C Marchal, N Singh, Z Batz, J Advani, C Jaeger… - Nature …, 2022 - nature.com
Chromatin organization and enhancer-promoter contacts establish unique spatiotemporal
gene expression patterns in distinct cell types. Non-coding genetic variants can influence …

Stress induced aging in mouse eye

Q Xu, C Rydz, VA Nguyen Huu, L Rocha… - Aging …, 2022 - Wiley Online Library
Aging, a universal process that affects all cells in an organism, is a major risk factor for a
group of neuropathies called glaucoma, where elevated intraocular pressure is one of the …

Aging of the retina: molecular and metabolic turbulences and potential interventions

L Campello, N Singh, J Advani… - Annual Review of …, 2021 - annualreviews.org
Multifaceted and divergent manifestations across tissues and cell types have curtailed
advances in deciphering the cellular events that accompany advanced age and contribute to …

Self-organization of the retina during eye development, retinal regeneration in vivo, and in retinal 3D organoids in vitro

EN Grigoryan - Biomedicines, 2022 - mdpi.com
Self-organization is a process that ensures histogenesis of the eye retina. This highly
intricate phenomenon is not sufficiently studied due to its biological complexity and genetic …

CHARGE syndrome protein CHD7 regulates epigenomic activation of enhancers in granule cell precursors and gyrification of the cerebellum

NC Reddy, SP Majidi, L Kong, M Nemera… - Nature …, 2021 - nature.com
Regulation of chromatin plays fundamental roles in the development of the brain.
Haploinsufficiency of the chromatin remodeling enzyme CHD7 causes CHARGE syndrome …

Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids

JH Kim, SJ Mun, JH Kim, MJ Son, SY Kim - Iscience, 2023 - cell.com
To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids
from two states (expandable and more differentiated) were subjected to single-cell RNA-seq …