[HTML][HTML] Enhancer RNAs are an important regulatory layer of the epigenome

V Sartorelli, SM Lauberth - Nature structural & molecular biology, 2020 - nature.com
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development
and disease through their regulation of transcription, RNA processing and translation …

[HTML][HTML] Transcriptional regulation and its misregulation in disease

TI Lee, RA Young - Cell, 2013 - cell.com
The gene expression programs that establish and maintain specific cell states in humans
are controlled by thousands of transcription factors, cofactors, and chromatin regulators …

[HTML][HTML] Modification of enhancer chromatin: what, how, and why?

E Calo, J Wysocka - Molecular cell, 2013 - cell.com
Emergence of form and function during embryogenesis arises in large part through cell-type-
and cell-state-specific variation in gene expression patterns, mediated by specialized cis …

[HTML][HTML] Targeted Perturb-seq enables genome-scale genetic screens in single cells

D Schraivogel, AR Gschwind, JH Milbank, DR Leonce… - Nature …, 2020 - nature.com
The transcriptome contains rich information on molecular, cellular and organismal
phenotypes. However, experimental and statistical limitations constrain sensitivity and …

Genome-wide mapping and analysis of chromosome architecture

AD Schmitt, M Hu, B Ren - Nature reviews Molecular cell biology, 2016 - nature.com
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …

[HTML][HTML] Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

J Dekker, MA Marti-Renom, LA Mirny - Nature Reviews Genetics, 2013 - nature.com
How DNA is organized in three dimensions inside the cell nucleus and how this affects the
ways in which cells access, read and interpret genetic information are among the longest …

[HTML][HTML] Enhancers: five essential questions

LA Pennacchio, W Bickmore, A Dean… - Nature Reviews …, 2013 - nature.com
Although enhancers are crucial and widespread gene-regulatory elements, we are far from
a complete understanding of how they function or their importance in areas such as disease …

The Hitchhiker's guide to Hi-C analysis: practical guidelines

BR Lajoie, J Dekker, N Kaplan - Methods, 2015 - Elsevier
Over the last decade, development and application of a set of molecular genomic
approaches based on the chromosome conformation capture method (3C), combined with …

Efficient generation of knock-in transgenic zebrafish carrying reporter/driver genes by CRISPR/Cas9-mediated genome engineering

Y Kimura, Y Hisano, A Kawahara, S Higashijima - Scientific reports, 2014 - nature.com
The type II bacterial CRISPR/Cas9 system is rapidly becoming popular for genome-
engineering due to its simplicity, flexibility and high efficiency. Recently, targeted knock-in of …

[HTML][HTML] Unlinking an lncRNA from its associated cis element

VR Paralkar, CC Taborda, P Huang, Y Yao… - Molecular cell, 2016 - cell.com
Long non-coding (lnc) RNAs can regulate gene expression and protein functions. However,
the proportion of lncRNAs with biological activities among the thousands expressed in …