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Chemical inhibitors destabilize HuR binding to the AU-rich element of TNF-α mRNA

Min-Ju Chae
Hye Youn Sung
Woong-Yang Park
ResearchOpen Access30 Nov 2009
Experimental & Molecular Medicine

Volume: 41, P: 824-831
Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

Chromatin run-on and sequencing (ChRO-seq) is a new method that maps the location of RNA polymerase using virtually any input sample. Here, ChRO-seq is used to study nascent transcription in human glioblastoma, and to identify regulators of tumor subtype.

Tinyi Chu
Edward J. Rice
Charles G. Danko
Research22 Oct 2018
Nature Genetics

Volume: 50, P: 1553-1564
Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

Enhancer RNAs are transcribed bidirectionally from core transcription initiation regions. Here, by employing nascent RNA sequencing, the authors identify quantitative trait loci (QTLs) associated with enhancer RNA level and directionality, revealing the bipartite architecture of enhancers.

Katla Kristjánsdóttir
Alexis Dziubek
Hojoong Kwak
ResearchOpen Access24 Nov 2020
Nature Communications

Volume: 11, P: 1-12
Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size

In a ferret model, the microcephaly-associated gene Aspm regulates cortical expansion by controlling the transition of ventricular radial glial cells to more differentiated cell types.

Matthew B. Johnson
Xingshen Sun
Byoung-Il Bae
Research11 Apr 2018
Nature

Volume: 556, P: 370-375
Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

Mahat et al. describe how to map the genome-wide positions of active RNA polymerases using a modified nuclear run-on approach called PRO-seq. Details for PRO-cap, a modification that identifies transcription start sites, are also included.

Dig Bijay Mahat
Hojoong Kwak
John T Lis
Protocols21 Jul 2016
Nature Protocols

Volume: 11, P: 1455-1476
m⁶A enhances the phase separation potential of mRNA

The cytosolic N⁶-methyladenosine (m⁶A)-binding proteins YTHDF1, YTHDF2 and YTHDF3 undergo liquid–liquid phase separation in vitro and in cells; this is enhanced by polymethylated mRNAs to form complexes that partition into different cellular phase-separated compartments.

Ryan J. Ries
Sara Zaccara
Samie R. Jaffrey
Research10 Jul 2019
Nature

Volume: 571, P: 424-428
eRNA co-expression network uncovers TF dependency and convergent cooperativity

Seungha Alisa Lee
Katla Kristjánsdóttir
Hojoong Kwak
ResearchOpen Access04 Nov 2023
Scientific Reports

Volume: 13, P: 1-13
RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts

Seyeon Bae
Kibyeong Kim
Kyung-Hyun Park-Min
Research14 Dec 2022
Cellular & Molecular Immunology

Volume: 20, P: 94-109

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Chemical inhibitors destabilize HuR binding to the AU-rich element of TNF-α mRNA

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

m⁶A enhances the phase separation potential of mRNA

eRNA co-expression network uncovers TF dependency and convergent cooperativity

RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts

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