PUBLICATIONS

 
1.
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.
Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, Tiana G, Heard E
Cell. 2014 May 8; 157(4):950-63. doi: 10.1016/j.cell.2014.03.025.
A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model's predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.
2.
Developmental dynamics and disease potential of random monoallelic gene expression.
Gendrel AV, Attia M, Chen CJ, Diabangouaya P, Servant N, Barillot E, Heard E
Dev Cell. 2014 Feb 24; 28(4):366-80. doi: 10.1016/j.devcel.2014.01.016.
X chromosome inactivation (XCI) and allelic exclusion of olfactory receptors or immunoglobulin loci represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify several hundred RME genes in clonal neural progenitor cell lines derived from embryonic stem cells. RME occurs during differentiation, and, once established, the monoallelic state can be highly stable. We show that monoallelic expression also occurs in vivo, in the absence of DNA sequence polymorphism. Several of the RME genes identified play important roles in development and have been implicated in human autosomal-dominant disorders. We propose that monoallelic expression of such genes contributes to the fine-tuning of the developmental regulatory pathways they control, and, in the context of a mutation, RME can predispose to loss of function in a proportion of cells and thus contribute to disease.
3.
Changes in the organization of the genome during the mammalian cell cycle.
Giorgetti L, Servant N, Heard E
Genome Biol. 2013 Dec 24; 14(12):142. doi: 10.1186/gb4147.
By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle.
4.
Histone lysine methylation and chromatin replication.
Rivera C, Gurard-Levin ZA, Almouzni G, Loyola A
Biochim Biophys Acta. 2014 Dec; 1839(12):1433-9. doi:10.1016/j.bbagrm.2014.03.009. Epub 2014 Mar 28.
In eukaryotic organisms, the replication of the DNA sequence and its organization into chromatin are critical to maintain genome integrity. Chromatin components, such as histone variants and histone post-translational modifications, along with the higher-order chromatin structure, impact several DNA metabolic processes, including replication, transcription, and repair. In this review we focus on lysine methylation and the relationships between this histone mark and chromatin replication. We first describe studies implicating lysine methylation in regulating early steps in the replication process. We then discuss chromatin reassembly following replication fork passage, where the incorporation of a combination of newly synthesized histones and parental histones can impact the inheritance of lysine methylation marks on the daughter strands. Finally, we elaborate on how the inheritance of lysine methylation can impact maintenance of the chromatin landscape, using heterochromatin as a model chromatin domain, and we discuss the potential mechanisms involved in this process.
5.
Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX.
Lacoste N, et al. full author list
Mol Cell. 2014 Feb 20; 53(4):631-44. doi: 10.1016/j.molcel.2014.01.018. Epub 2014 Feb 13.
Centromeres are essential for ensuring proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover involving a heterotypic tetramer containing CenH3-H4 with H3.3-H4. Ectopic localization of this particle depends on the H3.3 chaperone DAXX rather than the dedicated CenH3 chaperone HJURP. This aberrant nucleosome occludes CTCF binding and has a minor effect on gene expression. Cells overexpressing CenH3 are more tolerant of DNA damage. Both the survival advantage and CTCF occlusion in these cells are dependent on DAXX. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments.
6.
A network of players in H3 histone variant deposition and maintenance at centromeres.
Muller S, Almouzni G
Biochim Biophys Acta. 2014 Mar; 1839(3):241-50. doi: 10.1016/j.bbagrm.2013.11.008. Epub 2013 Dec 6.
Centromeres are key chromosomal landmarks important for chromosome segregation and are characterized by distinct chromatin features. The centromeric histone H3 variant, referred to as CENP-A or CenH3(CENP-A) in mammals, has emerged as a key determinant for centromeric structure, function and epigenetic inheritance. To regulate the correct incorporation and maintenance of histones at this locus, the cell employs an intricate network of molecular players, among which histone chaperones and chromatin remodelling factors have been identified over the past years. The mammalian centromere-specific chaperone HJURP represents an interesting paradigm to understand the functioning of this network. This review highlights and discusses the latest findings on centromeric histone H3 variant deposition and regulation to delineate the current view on centromere establishment, maintenance and propagation throughout the cell cycle. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
7.
Developmental roles of histone H3 variants and their chaperones.
Filipescu D, Szenker E, Almouzni G
Trends Genet. 2013 Nov; 29(11):630-40. doi: 10.1016/j.tig.2013.06.002. Epub 2013Jul 2.
Animal development and lifetime potential exploit a balance between the stability and plasticity of cellular identity. Within the nucleus, this is controlled by an interplay involving lineage-specific transcription factors and chromatin dynamics. Histone H3 variants contribute to chromatin dynamics through the timing and sites of their incorporation, promoted by dedicated histone chaperones. Moreover, their individual modifications and binding partners provide distinct features at defined genomic loci. We highlight here the importance of the H3.3 replacement variant for the nuclear reprogramming that occurs during gametogenesis, fertilization, and germline establishment. Furthermore, we describe how the recently characterized H3.3 dynamics associated with gastrulation, myogenesis, or neurogenesis underline the role of chromatin changes in cell differentiation. Finally, we discuss the challenges of maintaining centromeric identity through propagation of the centromeric CenH3 variant in different cell types. Future challenges will be to gain a comprehensive picture of H3 variants and their chaperones during development and differentiation.
8.
Characterization of chromatin domains by 3D fluorescence microscopy: An automated methodology for quantitative analysis and nuclei screening.
Cantaloube S, Romeo K, Le Baccon P, Almouzni G, Quivy JP
Bioessays. 2012 Jun; 34(6):509-17. doi: 10.1002/bies.201100188. Epub 2012 Mar 27.
Fluorescence microscopy has provided a route to qualitatively analyze features of nuclear structures and chromatin domains with increasing resolution. However, it is becoming increasingly important to develop tools for quantitative analysis. Here, we present an automated method to quantitatively determine the enrichment of several endogenous factors, immunostained in pericentric heterochromatin domains in mouse cells. We show that this method permits an unbiased characterization of changes in the enrichment of several factors with statistical significance from a large number of nuclei. Furthermore, the nuclei can be sorted according to the enrichment value of these factors. This method should prove useful to monitor events related to changes in the amount, rather than the presence or absence, of any factor. By adapting a few parameters, it could be extended to other nuclear structures and the benefit of using available software will permit its use in many biological labs.
9.
Establishment of a replication fork barrier following induction of DNA binding in mammalian cells.
Beuzer P, Quivy JP, Almouzni G
Cell Cycle. 2014; 13(10):1607-16. doi: 10.4161/cc.28627. Epub 2014 Mar 25.
Understanding the mechanisms that lead to replication fork blocks (RFB) and the means to bypass them is important given the threat that they represent for genome stability if inappropriately handled. Here, to study this issue in mammals, we use integrated arrays of the LacO and/or TetO as a tractable system to follow in time a process in an individual cell and at a single locus. Importantly, we show that induction of the binding by LacI and TetR proteins, and not the presence of the repeats, is key to form the RFB. We find that the binding of the proteins to the arrays during replication causes a prolonged persistence of replication foci at the site. This, in turn, induces a local DNA damage repair (DDR) response, with the recruitment of proteins involved in double-strand break (DSB) repair such as TOPBP1 and 53BP1, and the phosphorylation of H2AX. Furthermore, the appearance of micronuclei and DNA bridges after mitosis is consistent with an incomplete replication. We discuss how the many DNA binding proteins encountered during replication can be dealt with and the consequences of incomplete replication. Future studies exploiting this type of system should help analyze how an RFB, along with bypass mechanisms, are controlled in order to maintain genome integrity.
10.
Transgenerational epigenetic inheritance: myths and mechanisms.
Heard E, Martienssen RA
Cell. 2014 Mar 27; 157(1):95-109. doi: 10.1016/j.cell.2014.02.045.
Since the human genome was sequenced, the term "epigenetics" is increasingly being associated with the hope that we are more than just the sum of our genes. Might what we eat, the air we breathe, or even the emotions we feel influence not only our genes but those of descendants? The environment can certainly influence gene expression and can lead to disease, but transgenerational consequences are another matter. Although the inheritance of epigenetic characters can certainly occur-particularly in plants-how much is due to the environment and the extent to which it happens in humans remain unclear.
11.
Differential network analysis for the identification of condition-specific pathway activity and regulation.
Gambardella G, Moretti MN, de Cegli R, Cardone L, Peron A, di Bernardo D
Bioinformatics. 2013 Jul 15; 29(14):1776-85. doi: 10.1093/bioinformatics/btt290. Epub 2013 Jun 6.
MOTIVATION: Identification of differential expressed genes has led to countless new discoveries. However, differentially expressed genes are only a proxy for finding dysregulated pathways. The problem is to identify how the network of regulatory and physical interactions rewires in different conditions or in disease. RESULTS: We developed a procedure named DINA (DIfferential Network Analysis), which is able to identify set of genes, whose co-regulation is condition-specific, starting from a collection of condition-specific gene expression profiles. DINA is also able to predict which transcription factors (TFs) may be responsible for the pathway condition-specific co-regulation. We derived 30 tissue-specific gene networks in human and identified several metabolic pathways as the most differentially regulated across the tissues. We correctly identified TFs such as Nuclear Receptors as their main regulators and demonstrated that a gene with unknown function (YEATS2) acts as a negative regulator of hepatocyte metabolism. Finally, we showed that DINA can be used to make hypotheses on dysregulated pathways during disease progression. By analyzing gene expression profiles across primary and transformed hepatocytes, DINA identified hepatocarcinoma-specific metabolic and transcriptional pathway dysregulation. AVAILABILITY: We implemented an on-line web-tool http://dina.tigem.it enabling the user to apply DINA to identify tissue-specific pathways or gene signatures. CONTACT: dibernardo@tigem.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
12.
A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient.
Pagliarini R, di Bernardo D
J Comput Biol. 2013 May; 20(5):383-97. doi: 10.1089/cmb.2012.0276. Epub 2013 Mar6.
Inborn errors of metabolism (IEM) are genetic diseases caused by mutations in enzymes or transporters affecting specific metabolic reactions that cause a block in the physiological metabolic fluxes. Therapeutic treatment can be achieved either by decreasing the metabolic flux upstream of the block or by increasing the flux downstream of the block. The identification of upstream and downstream fluxes however is not trivial, since metabolic reactions are intertwined in a complex network. To overcome this problem, we propose an innovative computational workflow to model the alteration of metabolism caused by IEM and predict the metabolites and reactions that are affected by the mutation. Our workflow exploits a recent genome-scale metabolic network model of hepatocyte metabolism to identify metabolites accumulating in hepatocytes due to single gene mutations in IEM via an innovative "differential flux analysis." We simulated 38 IEMs in the liver, and in about half of the cases, our workflow correctly identified the metabolites known to accumulate in the blood and urine of IEM patients.
13.
Genome recognition by MYC.
Sabo A, Amati B
Cold Spring Harb Perspect Med. 2014 Feb 1;4(2). pii: a014191. doi:10.1101/cshperspect.a014191.
MYC dimerizes with MAX to bind DNA, with a preference for the E-box consensus CACGTG and several variant motifs. In cells, MYC binds DNA preferentially within transcriptionally active promoter regions. Although several thousand promoters are bound under physiological (low MYC) conditions, these represent only a fraction of all accessible, active promoters. MYC overexpression-as commonly observed in cancer cells-leads to invasion of virtually all active promoters, as well as of distal enhancer elements. We summarize here what is currently known about the mechanisms that may guide this process. We propose that binding site recognition is determined by low-affinity protein-protein interactions between MYC/MAX dimers and components of the basal transcriptional machinery, other chromatin-associated protein complexes, and/or DNA-bound transcription factors. DNA binding occurs subsequently, without an obligate requirement for sequence recognition. Local DNA scanning then leads to preferential stabilization of the MYC/MAX dimer on high-affinity DNA elements. This model is consistent with the invasion of all active promoters that occurs at elevated MYC levels, but posits that important differences in affinity persist between physiological target sites and the newly invaded elements, which may not all be bound in a productive regulatory mode. The implications of this model for transcriptional control by MYC in normal and cancer cells are discussed in the light of the latest literature.
14.
Dual regulation of Myc by Abl.
Sanchez-Arevalo Lobo VJ, et al. full author list
Oncogene. 2013 Nov 7; 32(45):5261-71. doi: 10.1038/onc.2012.621. Epub 2013 Jan 14.
The tyrosine kinase c-Abl (or Abl) and the prolyl-isomerase Pin1 cooperatively activate the transcription factor p73 by enhancing recruitment of the acetyltransferase p300. As the transcription factor c-Myc (or Myc) is a known target of Pin1 and p300, we hypothesized that it might be regulated in a similar manner. Consistent with this hypothesis, overexpression of Pin1 augmented the interaction of Myc with p300 and transcriptional activity. The action of Abl, however, was more complex than predicted. On one hand, Abl indirectly enhanced phosphorylation of Myc on Ser 62 and Thr 58, its association with Pin1 and p300 and its acetylation by p300. These effects of Abl were exerted through phosphorylation of substrate(s) other than Myc itself. On the other hand, Abl interacted with the C-terminal domain of Myc and phosphorylated up to five tyrosine residues in its N-terminus, the principal of which was Y74. Indirect immunofluorescence or immunohistochemical staining suggested that the Y74-phosphorylated form of Myc (Myc-pY74) localized to the cytoplasm and coexisted either with active Abl in a subset of mammary carcinomas or with Bcr-Abl in chronic myeloid leukemia. In all instances, Myc-pY74 constituted a minor fraction of the cellular Myc protein. Thus, our data unravel two potential effects of Abl on Myc: first, Abl signaling can indirectly augment acetylation of Myc by p300, and most likely also its transcriptional activity in the nucleus; second, Abl can directly phosphorylate Myc on tyrosine: the resulting form of Myc appears to be cytoplasmic, and its presence correlates with Abl activation in cancer.
15.
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.
Sabo A, et al. full author list
Nature. 2014 Jul 24; 511(7510):488-92. doi: 10.1038/nature13537. Epub 2014 Jul 9.
The c-myc proto-oncogene product, Myc, is a transcription factor that binds thousands of genomic loci. Recent work suggested that rather than up- and downregulating selected groups of genes, Myc targets all active promoters and enhancers in the genome (a phenomenon termed 'invasion') and acts as a general amplifier of transcription. However, the available data did not readily discriminate between direct and indirect effects of Myc on RNA biogenesis. We addressed this issue with genome-wide chromatin immunoprecipitation and RNA expression profiles during B-cell lymphomagenesis in mice, in cultured B cells and fibroblasts. Consistent with long-standing observations, we detected general increases in total RNA or messenger RNA copies per cell (hereby termed 'amplification') when comparing actively proliferating cells with control quiescent cells: this was true whether cells were stimulated by mitogens (requiring endogenous Myc for a proliferative response) or by deregulated, oncogenic Myc activity. RNA amplification and promoter/enhancer invasion by Myc were separable phenomena that could occur without one another. Moreover, whether or not associated with RNA amplification, Myc drove the differential expression of distinct subsets of target genes. Hence, although having the potential to interact with all active or poised regulatory elements in the genome, Myc does not directly act as a global transcriptional amplifier. Instead, our results indicate that Myc activates and represses transcription of discrete gene sets, leading to changes in cellular state that can in turn feed back on global RNA production and turnover.
16.
Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency.
Iannelli F, et al. full author list
Nat Commun. 2014 May 13; 5:3850. doi: 10.1038/ncomms4850.
Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors.
17.
Topology of mammalian developmental enhancers and their regulatory landscapes.
de Laat W, Duboule D
Nature. 2013 Oct 24; 502(7472):499-506. doi: 10.1038/nature12753.
How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend on the precise expression of genes in space and time. The orchestration of transcription relies mostly on surrounding control sequences such as enhancers, millions of which form complex regulatory landscapes in the non-coding genome. Recent research shows that high-order chromosome structures make an important contribution to enhancer functionality by triggering their physical interactions with target genes.
18.
For genomes to stay in shape, insulators must be up to PAR.
Wijchers PJ, de Laat W
Cell. 2013 Sep 26; 155(1):15-6. doi: 10.1016/j.cell.2013.09.012.
Insulators drive nuclear organization by blocking or facilitating interactions between DNA regulatory elements. Ong et al. show that poly(ADP-ribosyl)ation of insulator binding proteins modulates their ability to physically interact with distant regulatory elements, implicating posttranslational modifications of nonhistone proteins in genome architecture.
19.
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.
Shukla R, et al. full author list
Cell. 2013 Mar 28; 153(1):101-11. doi: 10.1016/j.cell.2013.02.032.
LINE-1 (L1) retrotransposons are mobile genetic elements comprising ~17% of the human genome. New L1 insertions can profoundly alter gene function and cause disease, though their significance in cancer remains unclear. Here, we applied enhanced retrotransposon capture sequencing (RC-seq) to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic beta-catenin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2(-/-) mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC.
20.
Retrotransposon silencing during embryogenesis: dicer cuts in LINE.
Faulkner GJ
PLoS Genet. 2013 Nov; 9(11):e1003944. doi: 10.1371/journal.pgen.1003944. Epub 2013Nov 7.
21.
Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis.
Upton KR, Faulkner GJ
Mob DNA. 2014 May 9; 5:15. doi: 10.1186/1759-8753-5-15. eCollection 2014.
Transposable elements (TEs) are a prominent feature of most eukaryotic genomes. Despite rapidly accumulating evidence for the role of TE-driven insertional mutagenesis and structural variation in genome evolution, few clear examples of individual TEs impacting biology via perturbed gene regulation are available. A recent report describes the discovery of an alternative promoter for the murine erythroid transcription factor Pu.1. This promoter is located in an ORR1A0 long terminal repeat (LTR) retrotransposon intronic to Pu.1 and is regulated by the Kruppel-like factors KLF1 and KLF3. Expression of the resultant chimeric transcript, called Pu.2, spontaneously induces erythroid differentiation in vitro. These experiments illustrate how transcription factor binding sites spread by retrotransposition have the potential to impact networks encoding key biological processes in the host genome.
22.
Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population.
Richardson SR, Salvador-Palomeque C, Faulkner GJ
Bioessays. 2014 May; 36(5):475-81. doi: 10.1002/bies.201300181. Epub 2014 Feb 25.
Gene retrocopies are generated by reverse transcription and genomic integration of mRNA. As such, retrocopies present an important exception to the central dogma of molecular biology, and have substantially impacted the functional landscape of the metazoan genome. While an estimated 8,000-17,000 retrocopies exist in the human genome reference sequence, the extent of variation between individuals in terms of retrocopy content has remained largely unexplored. Three recent studies by Abyzov et al., Ewing et al. and Schrider et al. have exploited 1,000 Genomes Project Consortium data, as well as other sources of whole-genome sequencing data, to uncover novel gene retrocopies. Here, we compare the methods and results of these three studies, highlight the impact of retrocopies in human diversity and genome evolution, and speculate on the potential for somatic gene retrocopies to impact cancer etiology and genetic diversity among individual neurons in the mammalian brain.
23.
L1 retrotransposons, cancer stem cells and oncogenesis.
Carreira PE, Richardson SR, Faulkner GJ
FEBS J. 2014 Jan; 281(1):63-73. doi: 10.1111/febs.12601. Epub 2013 Nov 28.
Retrotransposons have played a central role in human genome evolution. The accumulation of heritable L1, Alu and SVA retrotransposon insertions continues to generate structural variation within and between populations, and can result in spontaneous genetic disease. Recent works have reported somatic L1 retrotransposition in tumours, which in some cases may contribute to oncogenesis. Intriguingly, L1 mobilization appears to occur almost exclusively in cancers of epithelial cell origin. In this review, we discuss how L1 retrotransposition could potentially trigger neoplastic transformation, based on the established correlation between L1 activity and cellular plasticity, and the proven capacity of L1-mediated insertional mutagenesis to decisively alter gene expression and functional output.
24.
Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress.
Tebbi A, et al. full author list
Carcinogenesis. 2016 Jan; 37(1):39-48. doi: 10.1093/carcin/bgv156. Epub 2015 Nov5.
Multidrug resistance 2 (Mdr2), also called adenosine triphosphate-binding cassette B4 (ABCB4), is the transporter of phosphatidylcholine (PC) at the canalicular membrane of mouse hepatocytes, which plays an essential role for bile formation. Mutations in human homologue MDR3 are associated with several liver diseases. Knockout of Mdr2 results in hepatic inflammation, liver fibrosis and hepatocellular carcinoma (HCC). Whereas the pathogenesis in Mdr2 (-/-) mice has been largely attributed to the toxicity of bile acids due to the absence of PC in the bile, the question of whether Mdr2 deficiency per se perturbs biological functions in the cell has been poorly addressed. As Mdr2 is expressed in many cell types, we used mouse embryonic fibroblasts (MEF) derived from Mdr2 (-/-) embryos to show that deficiency of Mdr2 increases reactive oxygen species accumulation, lipid peroxidation and DNA damage. We found that Mdr2 (-/-) MEFs undergo spontaneous transformation and that Mdr2 (-/-) mice are more susceptible to chemical carcinogen-induced intestinal tumorigenesis. Microarray analysis in Mdr2-/- MEFs and cap analysis of gene expression in Mdr2 (-/-) HCCs revealed extensively deregulated genes involved in oxidation reduction, fatty acid metabolism and lipid biosynthesis. Our findings imply a close link between Mdr2 (-/-) -associated tumorigenesis and perturbation of these biological processes and suggest potential extrahepatic functions of Mdr2/MDR3.
25.
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Fort A, et al. full author list
Nat Genet. 2014 Jun; 46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28.
The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis on nuclear and retrotransposon-derived transcripts. We have performed deep profiling of the nuclear and cytoplasmic transcriptomes of human and mouse stem cells, identifying a class of previously undetected stem cell-specific transcripts. We show that long terminal repeat (LTR)-derived transcripts contribute extensively to the complexity of the stem cell nuclear transcriptome. Some LTR-derived transcripts are associated with enhancer regions and are likely to be involved in the maintenance of pluripotency.
26.
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Nagano T, et al. full author list
Nature. 2013 Oct 3; 502(7469):59-64. doi: 10.1038/nature12593. Epub 2013 Sep 25.
Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture (3C) assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single-cell Hi-C, combined with genome-wide statistical analysis and structural modelling of single-copy X chromosomes, to show that individual chromosomes maintain domain organization at the megabase scale, but show variable cell-to-cell chromosome structures at larger scales. Despite this structural stochasticity, localization of active gene domains to boundaries of chromosome territories is a hallmark of chromosomal conformation. Single-cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organization underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns.
27.
Drosophila functional elements are embedded in structurally constrained sequences.
Kenigsberg E, Tanay A
PLoS Genet. 2013 May; 9(5):e1003512. doi: 10.1371/journal.pgen.1003512. Epub 2013 May 30.
Modern functional genomics uncovered numerous functional elements in metazoan genomes. Nevertheless, only a small fraction of the typical non-exonic genome contains elements that code for function directly. On the other hand, a much larger fraction of the genome is associated with significant evolutionary constraints, suggesting that much of the non-exonic genome is weakly functional. Here we show that in flies, local (30-70 bp) conserved sequence elements that are associated with multiple regulatory functions serve as focal points to a pattern of punctuated regional increase in G/C nucleotide frequencies. We show that this pattern, which covers a region tenfold larger than the conserved elements themselves, is an evolutionary consequence of a shift in the balance between gain and loss of G/C nucleotides and that it is correlated with nucleosome occupancy across multiple classes of epigenetic state. Evidence for compensatory evolution and analysis of SNP allele frequencies show that the evolutionary regime underlying this balance shift is likely to be non-neutral. These data suggest that current gaps in our understanding of genome function and evolutionary dynamics are explicable by a model of sparse sequence elements directly encoding for function, embedded into structural sequences that help to define the local and global epigenomic context of such functional elements.