Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data

Transcription factors are key regulators of both normal and malignant hematopoiesis. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) has become the method of choice to interrogate the genome-wide effect of transcription factors. We have collected and integrated 142 publicly available ChIP-Seq datasets for both normal and leukemic murine blood cell types. In addition, we introduce the new bioinformatic tool Gene Set Control Analysis (GSCA). GSCA predicts likely upstream regulators for lists of genes based on statistical significance of binding event enrichment within the gene loci of a user-supplied gene set. We show that GSCA analysis of lineage-restricted gene sets reveals expected and previously unrecognized candidate upstream regulators. Moreover, application of GSCA to leukemic gene sets allowed us to predict the reactivation of blood stem cell control mechanisms as a likely contributor to LMO2 driven leukemia. It also allowed us to clarify the recent debate on the role of Myc in leukemia stem cell transcriptional programs. As a result, GSCA provides a valuable new addition to analyzing gene sets of interest, complementary to Gene Ontology and Gene Set Enrichment analyses. To facilitate access to the wider research community, we have implemented GSCA as a freely accessible web tool (http://bioinformatics.cscr.cam.ac.uk/GSCA/GSCA.html)

Drosophila H1 Regulates the Genetic Activity of Heterochromatin by Recruitment of Su(var)3-9

Eukaryotic genomes harbor transposable elements and other repetitive sequences that must be silenced. Small RNA interference pathways play a major role in their repression. Here, we reveal another mechanism for silencing these sequences in Drosophila. Depleting the linker histone H1 in vivo leads to strong activation of these elements. H1-mediated silencing occurs in combination with the heterochromatin-specific histone H3 lysine 9 methyltransferase Su(var)3-9. H1 physically interacts with Su(var) 3-9 and recruits it to chromatin in vitro, which promotes H3 methylation. We propose that H1 plays a key role in silencing by tethering Su(var) 3-9 to heterochromatin. The tethering function of H1 adds to its established role as a regulator of chromatin compaction and accessibility

Deep RNA Sequencing Reveals Novel Cardiac Transcriptomic Signatures for Physiological and Pathological Hypertrophy

Although both physiological hypertrophy (PHH) and pathological hypertrophy (PAH) of the heart have similar morphological appearances, only PAH leads to fatal heart failure. In the present study, we used RNA sequencing (RNA-Seq) to determine the transcriptomic signatures for both PHH and PAH. Approximately 13–20 million reads were obtained for both models, among which PAH showed more differentially expressed genes (DEGs) (2,041) than PHH (245). The expression of 417 genes was barely detectable in the normal heart but was suddenly activated in PAH. Among them, Foxm1 and Plk1 are of particular interest, since Ingenuity Pathway Analysis (IPA) using DEGs and upstream motif analysis showed that they are essential hub proteins that regulate the expression of downstream proteins associated with PAH. Meanwhile, 52 genes related to collagen, chemokines, and actin showed opposite expression patterns between PHH and PAH. MAZ-binding motifs were enriched in the upstream region of the participating genes. Alternative splicing (AS) of exon variants was also examined using RNA-Seq data for PAH and PHH. We found 317 and 196 exon inclusions and exon exclusions, respectively, for PAH, and 242 and 172 exon inclusions and exclusions, respectively for PHH. The AS pattern was mostly related to gains or losses of domains, changes in activity, and localization of the encoded proteins. The splicing variants of 8 genes (i.e., Fhl1, Rcan1, Ndrg2, Synpo, Ttll1, Cxxc5, Egfl7, and Tmpo) were experimentally confirmed. Multilateral pathway analysis showed that the patterns of quantitative (DEG) and qualitative (AS) changes differ depending on the type of pathway in PAH and PHH. One of the most significant changes in PHH is the severe downregulation of autoimmune pathways accompanied by significant AS. These findings revealed the unique transcriptomic signatures of PAH and PHH and also provided a more comprehensive understanding at both the quantitative and qualitative levels

A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1

PU.1 is a hematopoietic transcription factor that is required for the development of myeloid and B cells. PU.1 is also expressed in erythroid progenitors, where it blocks erythroid differentiation by binding to and inhibiting the main erythroid promoting factor, GATA-1. However, other mechanisms by which PU.1 affects the fate of erythroid progenitors have not been thoroughly explored. Here, we used ChIP-Seq analysis for PU.1 and gene expression profiling in erythroid cells to show that PU.1 regulates an extensive network of genes that constitute major pathways for controlling growth and survival of immature erythroid cells. By analyzing fetal liver erythroid progenitors from mice with low PU.1 expression, we also show that the earliest erythroid committed cells are dramatically reduced in vivo. Furthermore, we find that PU.1 also regulates many of the same genes and pathways in other blood cells, leading us to propose that PU.1 is a multifaceted factor with overlapping, as well as distinct, functions in several hematopoietic lineages

The multidimensional nature of epigenetic information and its role in disease.

This year marks the 10th anniversary of the publications that reported the initial human genome sequence. In the historic press conference that announced this landmark accomplishment, it was proclaimed that the genome sequence would "revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases." However, subsequent work over the past decade has revealed that "complex diseases" are much more intricate than originally thought. Even with the advent of several new powerful technologies, our understanding of the underlying genetic etiologies of most complex and non-Mendelian diseases is far from complete. These results have raised the possibility that the DNA sequence, i.e., genetic information, may not be the only relevant source of information in order to understand the molecular basis of disease. In this review, we assemble evidence that information encoded beyond the DNA sequence, i.e., epigenetic information, may hold the key to a better understanding of various pathological conditions. Unlike the genetic information encoded within the DNA sequence, epigenetic information can be stored in multiple dimensions, such as in the form of DNA modifications, RNA, or protein. Ideas presented here support the view that to better understand the molecular etiology of diseases, we need to gain a better understanding of both the genetic and epigenetic components of biological information. We hence believe that the fast development of genome-wide technologies will facilitate a better understanding of both genetic and epigenetic dimensions of disease

Crosstalk between genetic and epigenetic information through cytosine deamination

Decades of work have elucidated the existence of two forms of heritable information, namely genetic and epigenetic, which are collectively referred to as the 'dual inheritance'. The underlying mechanisms behind these two modes of inheritance have so far remained distinct. Cytosine deaminases, such as activation-induced cytidine deaminase (AID) and other members of the APOBEC family, have been implicated both in genetic variation of somatic cells and in epigenetic remodeling of germ and pluripotent cells. We hereby synthesize these seemingly dissociated functions into one coherent model, and further suggest that cytosine deaminases, particularly AID, might have a broader influence by modulating epigenetic information in somatic or cancer cells, as well as by triggering genetic variation in germ and pluripotent cells through mutation followed by natural selection. We therefore propose that the AID/APOBEC family of deaminases are likely to have acted as drivers throughout vertebrate evolution