Disentangling the many layers of eukaryotic transcriptional regulation

KM Lelli, M Slattery, RS Mann - Annual review of genetics, 2012 - annualreviews.org
Regulation of gene expression in eukaryotes is an extremely complex process. In this
review, we break down several critical steps, emphasizing new data and techniques that …

The transcriptional regulatory code of eukaryotic cells–insights from genome-wide analysis of chromatin organization and transcription factor binding

LO Barrera, B Ren - Current opinion in cell biology, 2006 - Elsevier
Control of eukaryotic gene expression involves combinatorial interactions between
transcription factors and regulatory sequences in the genome. In addition, chromatin …

Coupling and coordination in gene expression processes: a systems biology view

S Komili, PA Silver - Nature Reviews Genetics, 2008 - nature.com
Genome-scale analyses have allowed us to progress beyond studying gene expression at
the level of individual components of a given process by providing global information about …

[PDF][PDF] Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation

AJ Keung, CJ Bashor, S Kiriakov, JJ Collins, AS Khalil - Cell, 2014 - cell.com
The transcription of genomic information in eukaryotes is regulated in large part by
chromatin. How a diverse array of chromatin regulator (CR) proteins with different functions …

[PDF][PDF] Deciphering the multi-scale, quantitative cis-regulatory code

S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome

ND Heintzman, B Ren - Cellular and Molecular Life Sciences, 2007 - Springer
Eukaryotic transcriptional regulation requires the integration of complex signals by the
transcriptional promoter. Distinct sequence elements, characteristic chromatin modifications …

Histone variants: dynamic punctuation in transcription

CM Weber, S Henikoff - Genes & development, 2014 - genesdev.cshlp.org
Eukaryotic gene regulation involves a balance between packaging of the genome into
nucleosomes and enabling access to regulatory proteins and RNA polymerase …

Generating specificity in genome regulation through transcription factor sensitivity to chromatin

L Isbel, RS Grand, D Schübeler - Nature Reviews Genetics, 2022 - nature.com
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

How eukaryotic genes are transcribed

BJ Venters, BF Pugh - Critical reviews in biochemistry and …, 2009 - Taylor & Francis
Regulation of eukaryotic gene expression is far more complex than one might have
imagined 30 years ago. However, progress towards understanding gene regulatory …

[PDF][PDF] Molecular co-occupancy identifies transcription factor binding cooperativity in vivo

C Sönmezer, R Kleinendorst, D Imanci, G Barzaghi… - Molecular cell, 2021 - cell.com
Gene activation requires the cooperative activity of multiple transcription factors at cis-
regulatory elements (CREs). Yet, most transcription factors have short residence time …