Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain.

Toward a mechanistic understanding of variable chromatin modules

Gerard Llimos Aubach

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is almost identical between organisms of the same species (>99.9% in humans), however it varies in a small percentage due to some nucleotides being different at specific positions of the genome. This variation in the DNA will therefore influence our traits and affect our susceptibility to a certain condition. Thus, their study is highly relevant in genetics and biomedicine since they allow not only to predict the predisposition to a disease, such as cancer, but also to understand the molecular and cellular mechanism behind a certain phenotype. The effect of a genetic variant on a phenotype is given by their capacity to modulate the expression of a gene, either by directly impacting its sequence and thus changing the protein, or by regulating its expression levels. Interestingly, more than 88% of the disease-associated genetic variants present in humans are located outside genes, on the so-called non-coding part of the genome. This poses a challenge to identify what gene the genetic variant affects and to understand how it does so. Genetic variants do not only influence gene expression but they also affect the epigenetics state of the DNA (i.e. DNA methylation, histone marks, transcription factor (TF) binding...) and its 3D conformation, consequently modifying the activity of gene regulatory elements like promoters and enhancers. Previously, it has been shown that some of these regulatory regions located in the same locus exhibit a high level of molecular coordination and interindividual variation, mostly affected by genetic variation or environmental effects. These regions were termed variable chromatin modules (VCMs) or cis-regulatory domains (CRDs) and are thought to be the manifestation of fine-grained regulatory units of the genome. Understanding how a VCM is formed and the molecular basis behind the cooperativity between regulatory elements is an outstanding question in the field. In this work, we aim at resolving part of this puzzle by mechanistically dissecting one VCM that is influenced by a non-coding germline variant in B cells. Using a set of tools such as genetic engineering, TF binding assays and chromosome conformation studies, we demonstrate that this variant creates a de novo binding site for the TF MEF2, which acts as a pioneering factor for dozens of other collaborating TFs. In turn, this actuates a cluster of enhancers spanning a region over 150 kilobases (kb) that regulates AXIN2 gene expression, and is associated with a global compaction of the chromatin. In addition, in line with the known tumor-suppressor properties of AXIN2, we found that this variant influences chronic lymphocytic leukemia (CLL) progression and predisposition. Together, the characterization of the AXIN2 VCM provides an unique example to the community of how a germline variant is able to switch on an entire genomic locus with high degree of cooperativity between regulatory elements, since it captures both the formation and transition behavior of a VCM. Furthermore, given the link with CLL, this focal variant could have translational potential by serving as a patient-stratifying or treatment diagnostic.

EPFL2021

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous production of mRNA. The diversity in bursting patterns displayed by different genes suggests the existence of a connection between bursting and gene regulation. Experimental strategies such as single-molecule RNA FISH, MS2-GFP or short-lived protein reporters allow the quantification of transcriptional bursting and the comparison of bursting kinetics between conditions, allowing therefore the identification of molecular mechanisms modulating transcriptional bursting. In this review we recapitulate the impact on transcriptional bursting of different molecular aspects of transcription such as the chromatin environment, nucleosome occupancy, histone modifications, the number and affinity of regulatory elements, DNA looping and transcription factor availability. More specifically, we examine their role in tuning the burst size or the burst frequency. While some molecular mechanisms involved in transcription such as histone marks can affect every aspect of bursting, others predominantly influence the burst size (e.g. the number and affinity of cis-regulatory elements) or frequency (e.g. transcription factor availability).

Royal Society of Chemistry2017

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Julien Bryois, Bart Deplancke, David Hacker, Nouria Hernandez, Sunil Kumar Raghav, Sarah Thurnheer, Gilles Udin, Sebastian Martin Waszak, Alisa Yurovsky

DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation, we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-range, and long-range allelic coordination among the studied molecular phenotypes. We observed genetic influence on most of these phenotypes, with histone modifications exhibiting strong context-dependent behavior. Our results implicate transcription factors as primary mediators of sequence-specific regulation of gene expression programs, with histone modifications frequently reflecting the primary regulatory event.

American Association for the Advancement of Science2013

Toward a mechanistic understanding of variable chromatin modules

Gerard Llimos Aubach

EPFL2021