David Ruau

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the databases cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.

DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias

DNMT3A, the gene encoding the de novo DNA methyltransferase 3A, is among the most frequently mutated genes in hematologic malignancies. However, the mechanisms through which DNMT3A normally suppresses malignancy development are unknown. Here, we show that DNMT3A loss synergizes with the FLT3 internal tandem duplication in a dose-influenced fashion to generate rapid lethal lymphoid or myeloid leukemias similar to their human counterparts. Loss of DNMT3A leads to reduced DNA methylation, predominantly at hematopoietic enhancer regions in both mouse and human samples. Myeloid and lymphoid diseases arise from transformed murine hematopoietic stem cells. Broadly, our findings support a role for DNMT3A as a guardian of the epigenetic state at enhancer regions, critical for inhibition of leukemic transformation.

Update of NUREBASE: nuclear hormone receptor functional genomics

Nuclear hormone receptors are an abundant class of ligand-activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. New developments in NUREBASE include explicit declaration of alternative transcripts of each gene, and expression data for human and mouse nuclear receptors. The core of NUREBASE is reviewed, and it is completed by NUREBASE_DAILY, automatically updated every 24 h. All information on accessing and installing NUREBASE may be found at http://www. ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html.

The epigenetic regulators CBP and p300 facilitate leukemogenesis and represent therapeutic targets in acute myeloid leukemia

Growing evidence links abnormal epigenetic control to the development of hematological malignancies. Accordingly, inhibition of epigenetic regulators is emerging as a promising therapeutic strategy. The acetylation status of lysine residues in histone tails is one of a number of epigenetic post-translational modifications that alter DNA-templated processes, such as transcription, to facilitate malignant transformation. Although histone deacetylases are already being clinically targeted, the role of histone lysine acetyltransferases (KAT) in malignancy is less well characterized. We chose to study this question in the context of acute myeloid leukemia (AML), where, using in vitro and in vivo genetic ablation and knockdown experiments in murine models, we demonstrate a role for the epigenetic regulators CBP and p300 in the induction and maintenance of AML. Furthermore, using selective small molecule inhibitors of their lysine acetyltransferase activity, we validate CBP/p300 as therapeutic targets in vitro across a wide range of human AML subtypes. We proceed to show that growth retardation occurs through the induction of transcriptional changes that induce apoptosis and cell-cycle arrest in leukemia cells and finally demonstrate the efficacy of the KAT inhibitors in decreasing clonogenic growth of primary AML patient samples. Taken together, these data suggest that CBP/p300 are promising therapeutic targets across multiple subtypes in AML.

Erratum: DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias (Cancer Cell (2016) 29(6) (922–934) (S1535610816302082) (10.1016/j.ccell.2016.05.003))

1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA 2 Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA 3 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai 20092, China. 4 Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA 5 Department of Pathology and Immunology, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas 77030, USA 6 Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 7 Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA 8 Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA 9 Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK 10 Greehey Childrens Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 11 Rice University, Houston, Texas 77030

Building an ENCODE-style data compendium on a shoestring

One perhaps unintended consequence of the unquestionable success of the human genome project has been a shift in the biomedical research funding landscape towards large scale programs, commonly involving several hundred scientists and budgets of hundreds of millions of dollars. This emphasis on large-scale projects however is sometimes questioned, as illustrated by recent debates following last year’s publications from the ENCODE project 1,2. Here we have explored an alternative approach. Rather than making advanced decisions about the datasets that should be generated for a given research community, as large scale projects have to do, we have instead compiled all datasets produced by that community, as soon as they are deposited in public databases. We demonstrate that such real-time curation can exceed large consortia efforts, which constitutes a highly topical contribution to the ongoing ‘small vs big science’ debate. We created HAEMCODE, a repository for transcription factor (TF) binding maps in mouse blood cells, generated by chromatin immunoprecipitation sequencing (ChIP-seq) . Using a standardized analysis pipeline we manually curated more than 300 TF ChIP-Seq studies from a wide range of primary mouse haematopoietic cells and major cell line models. As of September 2013, the HAEMCODE compendium covered 84 TFs across 24 major blood cell types. Haemopoiesis is also a major focus of ENCODE, yet the currently available mouse ENCODE data covers less than half of HAEMCODE (36 TFs, May 2013), with only 9 ENCODE TFs not available elsewhere. We next developed a web interface (http://haemcode.stemcells.cam.ac.uk) to provide data access as well as a range of online analysis tools, designed to be useful to both experimentalist and computational biologists. The classical use case consists of selecting experiments within HAEMCODE before being directed to a workspace, which offers pre-computed options to inspect and/or download selected ChIP-Seq datasets. Additional online tools can compute global similarity between selected experiments, investigate overrepresentation of a user-submitted gene list in any subset of ChIP-Seq experiments3, inspect pre-computed results from de-novo motif discovery, and output all ChIP-Seq experiments with binding peaks for a user-supplied gene locus. Integration of publicly available data represents a powerful approach to make novel discoveries across diseases, species and platforms that would be impossible to achieve from single projects4. Successful completion of the HAEMCODE project on a small budget highlights this approach as a potentially widely applicable complement to multi-million dollar research initiatives.

Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells

Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles

Abstract Integrated analysis of multiple genome-wide transcription factor (TF)-binding profiles will be vital to advance our understanding of the global impact of TF binding. However, existing methods for measuring similarity in large numbers of chromatin immunoprecipitation assays with sequencing (ChIP-seq), such as correlation, mutual information or enrichment analysis, are limited in their ability to display functionally relevant TF relationships. In this study, we propose the use of graphical models to determine conditional independence between TFs and showed that network visualization provides a promising alternative to distinguish ‘direct’ versus ‘indirect’ TF interactions. We applied four algorithms to measure ‘direct’ dependence to a compendium of 367 mouse haematopoietic TF ChIP-seq samples and obtained a consensus network known as a ‘TF association network’ where edges in the network corresponded to likely causal pairwise relationships between TFs. The ‘TF association network’ illustrates the role of TFs in developmental pathways, is reminiscent of combinatorial TF regulation, corresponds to known protein–protein interactions and indicates substantial TF-binding reorganization in leukemic cell types. With the rapid increase in TF ChIP-Seq data sets, the approach presented here will be a powerful tool to study transcriptional programmes across a wide range of biological systems.