Biology subjects

Williams, B. A.

Publications and source records attributed to Williams, B. A..

4 recordsLinked to original sources

bioRxiv2018

Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by PU.1

PU.1 is a dominant but transient regulator in early T-cell precursors and a potent transcriptional controller of developmentally important pro-T cell genes. Before T-lineage commitment, open chromatin is frequently occupied by PU.1, and many PU.1 sites lose accessibility when PU.1 is later downregulated. Pioneering activity of PU.1 was tested in in this developmentally dynamic context, by quantitating the relationships between PU.1 occupancy and site quality and accessibility as PU.1 levels naturally declined in pro-T cell development, and by using stage-specific gain and loss of function perturbations to relate binding to effects on target genes. PU.1 could bind closed genomic sites, but rapidly opened many of them, despite the absence of its frequent collaborators, C/EBP factors. The dynamic properties of PU.1 engagements implied that PU.1 binding affinity and concentration determine its occupancy choices, but with quantitative tradeoffs for occupancy between site sequence quality and stage-dependent site accessibility in chromatin. At non-promoter sites PU.1 binding criteria were more stringent than at promoters, and PU.1 was also much more effective as a transcriptional regulator at non-promoter sites where local chromatin accessibility depended on the presence of PU.1. Runx motifs and Runx1 binding were often linked to PU.1 at open sites, but highly expressed PU.1 could bind its sites without Runx1. Notably, closed chromatin presented a qualitative barrier to occupancy by the PU.1 DNA binding domain alone. Thus, effective pioneering at closed chromatin sites also depends on requirements beyond site recognition served by non-DNA binding domains of PU.1.

immunology↗

bioRxiv2017

Systematic mapping of chromatin state landscapes during mouse development

Embryogenesis requires epigenetic information that allows each cell to respond appropriately to developmental cues. Histone modifications are core components of a cells epigenome, giving rise to chromatin states that modulate genome function. Here, we systematically profile histone modifications in a diverse panel of mouse tissues at 8 developmental stages from 10.5 days post conception until birth, performing a total of 1,128 ChIP-seq assays across 72 distinct tissue-stages. We combine these histone modification profiles into a unified set of chromatin state annotations, and track their activity across developmental time and space. Through integrative analysis we identify dynamic enhancers, reveal key transcriptional regulators, and characterize the role of chromatin-based repression in developmental gene regulation. We also leverage these data to link enhancers to putative target genes, revealing connections between coding and non-coding sequence variation in disease etiology. Our study provides a compendium of resources for biomedical researchers, and achieves the most comprehensive view of embryonic chromatin states to date.

genomics↗

bioRxiv2017

Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus

Genetic studies have revealed an essential role for cytosine DNA methylation in mammalian development. However, its spatiotemporal distribution in the developing embryo remains obscure. Here, we profiled the methylome landscapes of 12 mouse tissues/organs at 8 developmental stages spanning from early embryogenesis to birth. Indepth analysis of these spatiotemporal epigenome maps systematically delineated ~2 million methylation variant regions and uncovered widespread methylation dynamics at nearly one-half million tissue-specific enhancers, whose human counterparts were enriched for variants involved in genetic diseases. Strikingly, these predicted regulatory elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. Accumulation of non-CG methylation within gene bodies of key developmental transcription factors coincided with their transcriptional repression during later stages of fetal development. These spatiotemporal epigenomic maps provide a valuable resource for studying gene regulation during mammalian tissue/organ progression and for pinpointing regulatory elements involved in human developmental diseases.

genomics↗

bioRxiv2017

Genetic Analysis of a Metazoan Pathway using Transcriptomic Phenotypes

RNA-seq is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Linear models can quantify expression effects of individual mutants and identify epistatic effects in double mutants. To make interpretation of these high-dimensional measurements intuitive, we developed a single coefficient to quantify transcriptome-wide epistasis that accurately reflects the underlying interactions. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes that have opposing changes in expression in egl-9(lf) compared to vhl-1(lf) but the egl-9(lf); vhl-1(lf) mutant has the same phenotype as egl-9(lf). This class violates the classical model of HIF-1 regulation, but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.\n\nSignificance StatementTranscriptome profiling is a way to quickly and quantitatively measure gene expression level. Because of their quantitative nature, there is widespread interest in using transcriptomic profiles as a phenotype for genetic analysis. However, a source of major concern is that whole-animal transcriptomic profiles mix the expression signatures of multiple cellular states, making it hard to accurately reconstruct genetic interactions. Additionally, it has been difficult to quantify epistasis, the signature of genetic interaction between two genes, in these molecular phenotypes. Here, we show that it is possible to accurately reconstruct genetic interactions between genes using whole-animal RNA sequencing, and we demonstrate a powerful new way to measure and understand epistasis arising from these measurements. This suggests that whole-organism RNA-seq can be a powerful tool with which to understand genetic interactions in entire organisms and not only in isolated cells. With the advent of genome engineering tools, generating mutants has become easier and faster for many organisms. As mutants become easier to create, phenotyping them has become a major bottleneck in understanding the biological functions of the genes in question. Our work presents a possible solution to this problem, because transcriptome profiling is fast and sensitive to genetic perturbations regardless of the context they operate in.

genetics↗