David Gokhman

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

Methylating the Family Tree DNA sequences show a high level of similarities between humans and ancient hominids but the degree to which there are differences between methylated regions in their genomes that may explain phenotypic differences is unclear. Gokhman et al. (p. 523, published online 17 April) demonstrate that naturally degraded methylated cytosines in ancient DNA are converted to thymines and can be used to reconstruct ancient methylomes. The results suggest differences in methylation in bone tissues between modern humans and ancient hominids in a set of genes important for limb development. Estimates of differentially methylated nucleotides illuminate differences between modern human and ancient hominid bones. Ancient DNA sequencing has recently provided high-coverage archaic human genomes. However, the evolution of epigenetic regulation along the human lineage remains largely unexplored. We reconstructed the full DNA methylation maps of the Neandertal and the Denisovan by harnessing the natural degradation processes of methylated and unmethylated cytosines. Comparing these ancient methylation maps to those of present-day humans, we identified ~2000 differentially methylated regions (DMRs). Particularly, we found substantial methylation changes in the HOXD cluster that may explain anatomical differences between archaic and present-day humans. Additionally, we found that DMRs are significantly more likely to be associated with diseases. This study provides insight into the epigenetic landscape of our closest evolutionary relatives and opens a window to explore the epigenomes of extinct species.

Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones

Histones, the building blocks of eukaryotic chromatin, are essential for genome packaging, function and regulation. However, little is known about their transcriptional regulation. Here we conducted a comprehensive computational analysis, based on chromatin immunoprecipitation–sequencing and −microarray analysis (ChIP-seq and ChIP-chip) data of over 50 transcription factors and histone modifications in mouse embryonic stem cells. Enrichment scores supported by gene expression data from gene knockout studies identified E2f1 and E2f4 as master regulators of histone genes, CTCF and Zfx as repressors of core and linker histones, respectively, and Smad1, Smad2, YY1 and Ep300 as restricted or cell type–specific regulators. We propose that histone gene regulation is substantially more complex than previously thought, and that a combination of factors orchestrate histone gene regulation, from strict synchronization with S phase to targeted regulation of specific histone subtypes.

Archaic Adaptive Introgression in TBX15/WARS2

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.

Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics

Recent years have witnessed the rise of ancient DNA (aDNA) technology, allowing comparative genomics to be carried out at unprecedented time resolution. While it is relatively straightforward to use aDNA to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. Here we review recent works demonstrating that highly degraded aDNA still contains sufficient information to allow reconstruction of epigenetic signals, including DNA methylation and nucleosome positioning maps. We discuss challenges arising from the tissue specificity of epigenetics, and show how some of them might in fact turn into advantages. Finally, we introduce a method to infer methylation states in tissues that do not tend to be preserved over time.

BindDB: An Integrated Database and Webtool Platform for "Reverse-ChIP" Epigenomic Analysis.

The high-throughput revolution has brought an unprecedented amount of epigenomic data for embryonic stem cells (ESCs), including genome-wide profiles of chromatin-bound proteins and histone modifications generated by chromatin immunoprecipitation assays (ChIP-seq). As dataset after dataset of ChIP-seq data is added to the pool, the time is ripe to reverse the viewpoint from being factor-oriented to the perspective of genomic locations in order to offer a comprehensive view of chromatin characteristics and regulatory elements that govern coherent gene groups or chromosomal regions.

Systematic identification of gene family regulators in mouse and human embryonic stem cells.

Pluripotent self-renewing embryonic stem cells (ESCs) have been the focus of a growing number of high-throughput experiments, revealing the genome-wide locations of hundreds of transcription factors and histone modifications. While most of these datasets were used in a specific context, all datasets combined offer a comprehensive view of chromatin characteristics and regulatory elements that govern cell states. Here, using hundreds of datasets in ESCs, we generated colocalization maps of chromatin proteins and modifications, and built a discovery pipeline for regulatory proteins of gene families. By comparing genome-wide binding data with over-expression and knockdown analysis of hundreds of genes, we discovered that the pluripotency-related factor NR5A2 separates mitochondrial from cytosolic ribosomal genes, regulating their expression. We further show that genes with a common chromatin profile are enriched for distinct Gene Ontology (GO) categories. Our approach can be generalized to reveal common regulators of any gene group; discover novel gene families, and identify common genomic elements based on shared chromatin features.

Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans

Changes in gene regulation are broadly accepted as key drivers of phenotypic differences between closely related species. However, identifying regulatory changes that shaped human-specific traits is a very challenging task. Here, we use >60 DNA methylation maps of ancient and present-day human groups, as well as six chimpanzee maps, to detect regulatory changes that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting vocalization and facial features went through particularly extensive methylation changes. Specifically, we identify silencing patterns in a network of genes (SOX9, ACAN, COL2A1 and NFIX), and propose that they might have played a role in the reshaping of the human face, and in forming the 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that may have shaped the modern human face and voice, and suggest that they arose after the split from Neanderthals and Denisovans.Summary Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.Identifying changes in gene regulation that shaped human-specific traits is critical to understanding human adaptation. Here, we use dozens of ancient and present-day DNA methylation maps to detect regulatory changes that emerged in modern humans. We show that genes affecting vocalization and facial features went through particularly extensive changes in methylation. Especially, we identify expansive changes in a network of genes regulating skeletal development (SOX9, ACAN and COL2A1), and in NFIX, which controls facial projection and voice box (larynx) development. We propose that these changes played a key role in shaping the human face, and in forming the human 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that shaped the modern human face and voice, and suggest that they arose after the split from Neanderthals and Denisovans.

Gene ORGANizer: linking genes to the organs they affect

Abstract One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il), a phenotype-based tool that directly links human genes to the body parts they affect. It is built upon an exhaustive curated database that links >7000 genes to ∼150 anatomical parts using >150 000 gene-organ associations. The tool offers user-friendly platforms to analyze the anatomical effects of individual genes, and identify trends within groups of genes. We demonstrate how Gene ORGANizer can be used to make new discoveries, showing that chromosome X is enriched with genes affecting facial features, that positive selection targets genes with more constrained phenotypic effects, and more. We expect Gene ORGANizer to be useful in a variety of evolutionary, medical and molecular studies aimed at understanding the phenotypic effects of genes.

Inferring Past Environments from Ancient Epigenomes

Abstract Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals.

Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern Humans from Neanderthals and Denisovans

Changes in gene regulation are broadly accepted as key drivers of phenotypic differences between closely related species. However, identifying regulatory changes that shaped human-specific traits is a very challenging task. Here, we use >60 DNA methylation maps of ancient and present-day human groups, as well as six chimpanzee maps, to detect regulatory changes that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting vocalization and facial features went through particularly extensive methylation changes. Specifically, we identify silencing patterns in a network of genes (SOX9, ACAN, COL2A1 and NFIX), and propose that they might have played a role in the reshaping of the human face, and in forming the 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that may have shaped the modern human face and voice, and suggest that they arose after the split from Neanderthals and Denisovans.Summary Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.Identifying changes in gene regulation that shaped human-specific traits is critical to understanding human adaptation. Here, we use dozens of ancient and present-day DNA methylation maps to detect regulatory changes that emerged in modern humans. We show that genes affecting vocalization and facial features went through particularly extensive changes in methylation. Especially, we identify expansive changes in a network of genes regulating skeletal development (SOX9, ACAN and COL2A1), and in NFIX, which controls facial projection and voice box (larynx) development. We propose that these changes played a key role in shaping the human face, and in forming the human 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that shaped the modern human face and voice, and suggest that they arose after the split from Neanderthals and Denisovans.