[PDF][PDF] RNA interactions are essential for CTCF-mediated genome organization

R Saldaña-Meyer, J Rodriguez-Hernaez, T Escobar… - Molecular cell, 2019 - cell.com
The function of the CCCTC-binding factor (CTCF) in the organization of the genome has
become an important area of investigation, but the mechanisms by which CTCF dynamically …

[PDF][PDF] Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion

…, DE Comstock, CK Collings, X Chen, JR Hernaez… - Molecular cell, 2023 - cell.com
Highly coordinated changes in gene expression underlie T cell activation and exhaustion.
However, the mechanisms by which such programs are regulated and how these may be …

[HTML][HTML] Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

J Tan, N Shenker-Tauris, J Rodriguez-Hernaez… - Nature …, 2023 - nature.com
Investigating how chromatin organization determines cell-type-specific gene expression
remains challenging. Experimental methods for measuring three-dimensional chromatin …

3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages

…, DC Di Giammartino, J Rodriguez-Hernaez… - Nature Structural & …, 2024 - nature.com
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that
give rise to three essential lineages: the trophectoderm, the epiblast and the primitive …

[HTML][HTML] NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

P Lhoumaud, S Badri, J Rodriguez-Hernaez… - Nature …, 2019 - nature.com
CTCF and cohesin play a key role in organizing chromatin into topologically associating
domain (TAD) structures. Disruption of a single CTCF binding site is sufficient to change …

[HTML][HTML] Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

M Nishana, C Ha, J Rodriguez-Hernaez, A Ranjbaran… - Genome biology, 2020 - Springer
Background Ubiquitously expressed CTCF is involved in numerous cellular functions, such
as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only …

The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid

J Rodríguez Hernáez, ME Cerón Cucchi… - Microbial …, 2018 - microbiologyresearch.org
Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other
mammals, including humans. Indeed, it is one of the most common bacteria found in the …

[PDF][PDF] Cell type-specific prediction of 3D chromatin architecture

J Tan, J Rodriguez-Hernaez, T Sakellaropoulos… - bioRxiv, 2022 - scholar.archive.org
The mammalian genome is spatially organized in the nucleus to enable cell type-specific
gene 17 expression. Investigating how chromatin architecture determines this specificity …

RNA interactions with CTCF are essential for its proper function

R Saldaña-Meyer, J Rodriguez-Hernaez, M Nishana… - biorxiv, 2019 - biorxiv.org
The function of the CCCTC-binding factor (CTCF) in the organization of the genome has
become an important area of investigation, but the mechanisms of how CTCF dynamically …

[HTML][HTML] Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the …

…, E Salataj, DC Di Giammartino, J Rodriguez-Hernaez… - Biorxiv, 2023 - ncbi.nlm.nih.gov
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that
give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the …