Genome-wide lone strand adenine methylation in Deinococcus radiodurans R1: Regulation of gene expression through DR0643-dependent adenine methylation

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation- modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis- related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

Download Full-text

GFI1b As a Novel Oncosuppressor in AML

Blood ◽

10.1182/blood.v128.22.2717.2717 ◽

2016 ◽

Vol 128 (22) ◽

pp. 2717-2717 ◽

Cited By ~ 1

Author(s):

Aniththa Thivakaran ◽

Lacramioara Botezatu ◽

Judith Maria Hoenes ◽

Yahya Saleh Al-Matary ◽

Nadine Olberding ◽

...

Keyword(s):

Gene Expression ◽

Myeloid Leukemia ◽

Research Funding ◽

Molecular Level ◽

Regulation Of Gene Expression ◽

Leukemic Cells ◽

Hematopoietic Stem ◽

Genome Wide ◽

Blast Cells ◽

Leukemia Development

Abstract The proper differentiation of hematopoietic stem cells (HSCs) is regulated by a concert of different so called transcription factors (TFs). A disturbed function of these TFs can be the basis of malignant diseases such as acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). Growth Factor Independence 1b (Gfi1b) is a repressing transcription factor, with a key role in maintaining the quiescence of HSCs and the proper emergence and maturation of erythrocytes and platelets. Here we show that low expression of GFI1B in blast cells is associated with an inferior prognosis of AML and MDS patients. Using three different mice models of human AML (Nup98-HoxD13, MLL-AF9 and expression of a mutated K-Ras), we could show that reduced expression of Gfi1b accelerates AML development in mice and the latency is even more shortened when Gfi1b is conditionally deleted. Using a limiting dilution assay of transplantation of different number of Gfi1b-wildtype and Gfi1b-deficient cells, we could show that loss of Gfi1b significantly enhanced stemness of leukemic cells. Since Gfii1b is involved in epigenetic regulation of gene expression, we analyzed effect of loss of Gfi1b on an epigenetic level by analyzing the whole genome using Chip-Seq. We found that loss of Gfi1b leads to genome wide increased level of H3K9 acetylation of genes and hence expression of these genes involved in leukemia development. On a molecular level, we found that loss of Gfi1b not only increases the levels of reactive oxygen species (ROS), but also induces gene expression changes of key AML-pathways such as the p38/ AKT pathways. These results demonstrate that Gfi1b functions as an oncosuppressor in MDS/AML development. Disclosures Dührsen: Roche: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Alexion Pharmaceuticals: Honoraria, Research Funding. Khandanpour:Max-Eder: Research Funding; Hospital of Essen university: Research Funding.

Download Full-text

The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans

BMC Genomics ◽

10.1186/s12864-016-2837-5 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 66

Author(s):

Jessica Brunquell ◽

Stephanie Morris ◽

Yin Lu ◽

Feng Cheng ◽

Sandy D. Westerheide

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Regulation Of Gene Expression ◽

Genome Wide

Download Full-text

Multivariable regulation of gene expression plasticity in metazoans

10.1101/692863 ◽

2019 ◽

Author(s):

Long Xiao ◽

Zhiguang Zhao ◽

Fei He ◽

Zhuo Du

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Regulation Of Gene Expression ◽

Rapid Change ◽

High Plasticity ◽

Expression Levels ◽

Genome Wide ◽

Expression Potential ◽

Highly Correlated

ABSTRACTAn important capacity of genes is the rapid change of expression levels to cope with environment, known as expression plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness, and adaptation. In this study, we systematically quantified genome-wide gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression potential and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter cis-elements, trans-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2, and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications, and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.

Download Full-text

Promoter Proximal Pausing Limits Tumorous Growth Induced by the Yki Transcription Factor in Drosophila

Genetics ◽

10.1534/genetics.120.303419 ◽

2020 ◽

Vol 216 (1) ◽

pp. 67-77 ◽

Cited By ~ 1

Author(s):

Sanket Nagarkar ◽

Ruchi Wasnik ◽

Pravallika Govada ◽

Stephen Cohen ◽

L. S. Shashidhara

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Gene Expression Regulation ◽

Regulation Of Gene Expression ◽

Elongation Factor ◽

Imaginal Discs ◽

Link Type ◽

Genome Wide ◽

Wing Imaginal Discs ◽

Tumorous Growth

Promoter proximal pausing (PPP) of RNA polymerase II has emerged as a crucial rate-limiting step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT), and the negative elongation factor (NELF), which are highly conserved from Drosophila to humans. Here, we show that RNAi-mediated depletion of bin3 or Hexim of the 7SK snRNP complex or depletion of individual components of the NELF complex enhances Yki-driven growth, leading to neoplastic transformation of Drosophila wing imaginal discs. We also show that increased CDK9 expression cooperates with Yki in driving neoplastic growth. Interestingly, overexpression of CDK9 on its own or in the background of depletion of one of the components of 7SK snRNP or the NELF complex necessarily, and specifically, needed Yki overexpression to cause tumorous growth. Genome-wide gene expression analyses suggested that deregulation of protein homeostasis is associated with tumorous growth of wing imaginal discs. As both Fat/Hippo/Yki pathway and PPP are highly conserved, our observations may provide insights into mechanisms of oncogenic function of YAP—the ortholog of Yki in humans.

Download Full-text

High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME)

Blood ◽

10.1182/blood.v118.21.2392.2392 ◽

2011 ◽

Vol 118 (21) ◽

pp. 2392-2392 ◽

Cited By ~ 1

Author(s):

Ilango Balakrishnan ◽

Xiaodong Yang ◽

Beverly Torok-Storb ◽

Jay Hesselberth ◽

Manoj M Pillai

Keyword(s):

Gene Expression ◽

High Throughput ◽

Stromal Cells ◽

False Positive ◽

High Throughput Sequencing ◽

Regulation Of Gene Expression ◽

Negative Results ◽

Genome Wide ◽

Direct Binding

Abstract Abstract 2392 There is increasing recognition of the role of small noncoding RNAs in post-transcriptional regulation of gene expression in diverse tissues of eukaryotic organisms including vertebrates. MicroRNAs (miRNAs) are the best studied amongst these small RNAs and are thought to act by binding to the 3' untranslated regions (3' UTRs) of mature mRNAs in a sequence-specific fashion and preventing the initiation of peptide translation and/ or initiating mRNA degradation. Recent evidence suggests that miRNA-based regulation might involve binding to regions other than 3' UTRs including coding regions. Current approaches to defining miRNA-mRNA interactions are mostly restricted to those based on bio-informatic prediction, protein down-regulation following in-vitro transfection of miRNA precursors and luciferase assays to determine binding to 3' UTRs. None of these methods however show direct interaction between a specific miRNA and its purported target RNA. Bio-informatics-based approaches are also prone to false positive and negative results given the short length of sequence matching, and reliance on heuristics and cross-species conservation. Newer genome-wide approaches like HITS-CLIP (High Throughput Sequencing following Cross Linked Immuno Precipitation, or CLIP-Seq) overcome some of these limitations by directly isolating the miRNA-mRNA interactome bound to argonaute (AGO), a critical component of the rna-induced silencing complex (RISC)1. HITS-CLIP utilizes the ability of ultraviolet (UV) light to cross-link RNAs to proteins in their close proximity. The crosslinked miRNA-mRNA-Ago complexes are then isolated and the RNA reverse transcribed to cDNA libraries and sequenced by next generation sequencing (NGS). Given the widespread role of miRNAs in several vertebrate tissues, we hypothesized that miRNA-regulation of gene expression is operant in the hematopoietic microenvironment (ME) and thus contributes to regulation of hematopoiesis. We hence used HITS-CLIP to analyze the miRNA-mRNA interactome of three key cellular components of the ME: stromal cells, endothelium and macrophages. We have previously reported on the use of the stromal cell lines Hs27a and Hs5 to define specific functional niches within the ME. Hs27a can functionally support primitive hematopoietic stem and progenitor cells (HSPC) in cobblestone areas (CSAs) and express high levels of factors known to support HSPC such as SDF1, Jagged1 and Angiopoietin1. In contrast, Hs5 drives HSPC to mature lineages and secretes high levels of cytokines like IL1, IL6 and GCSF. Human umbilical vein endothelial cells (HUVECs) and MCSF-treated CD14+ cells were utilized for the endothelial and macrophage cultures respectively. The HITS-CLIP datasets from each of these populations were enriched for a putative binding site for miR-9 in the coding region of Matrix Metalloproteinase 2 (MMP2) mRNA. MMP2 belongs to a family of endopeptidases critical in the remodeling of extracellular matrix in several tissues and in the egress/ homing of HSPC to their functional niches in the ME. Functional binding of miR-9 to MMP2 was validated by Western-blotting of stromal cells transfected with miR-9 which revealed > 50% reduction of protein levels when compared to control-transfected cells. This was also confirmed by gelatin zymography which showed significantly reduced MMP2 activity in stromal cells transfected with miR-9. Finally, to confirm direct binding of miR-9 to the putative binding region on the MMP2 transcript, we cloned this microRNA responsive region (MRE) downstream of the Renilla luciferase gene and assayed its activity by luciferase assays. MiR-9 transfection down-regulated luciferase activity > 50% confirming direct binding to the MRE. Our results show that genome-wide approaches such as HITS-CLIP can be used to define in vivo miRNA-mRNA interactions in the ME and should be considered in studies that define such interactions given the significant false-positive and false negative results associated with approaches based on bio-informatics alone. The approach can also define specific interactions between miRNAs and mRNAs such as MMP2, of relevance to regulation of the hematopoietic ME. Disclosures: No relevant conflicts of interest to declare.

Download Full-text

Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression

DNA Research ◽

10.1093/dnares/dsu044 ◽

2015 ◽

Vol 22 (1) ◽

pp. 109-119 ◽

Cited By ~ 13

Author(s):

Y. V. Kravatsky ◽

V. R. Chechetkin ◽

N. A. Tchurikov ◽

G. I. Kravatskaya

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Genomic Features ◽

Genome Wide ◽

Genome Wide Study

Download Full-text

Thiol peroxidases mediate specific genome-wide regulation of gene expression in response to hydrogen peroxide

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1010721108 ◽

2011 ◽

Vol 108 (7) ◽

pp. 2729-2734 ◽

Cited By ~ 101

Author(s):

D. E. Fomenko ◽

A. Koc ◽

N. Agisheva ◽

M. Jacobsen ◽

A. Kaya ◽

...

Keyword(s):

Gene Expression ◽

Hydrogen Peroxide ◽

Regulation Of Gene Expression ◽

Genome Wide

Download Full-text

Chromatin is an ancient innovation conserved between Archaea and Eukarya

eLife ◽

10.7554/elife.00078 ◽

2012 ◽

Vol 1 ◽

Cited By ~ 48

Author(s):

Ron Ammar ◽

Dax Torti ◽

Kyle Tsui ◽

Marinella Gebbia ◽

Tanja Durbic ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Structure ◽

Nucleosome Occupancy ◽

Regulation Of Gene Expression ◽

Haloferax Volcanii ◽

Dna Compaction ◽

Genome Wide ◽

Eukaryotic Chromatin ◽

Transcriptional Start Sites

The eukaryotic nucleosome is the fundamental unit of chromatin, comprising a protein octamer that wraps ∼147 bp of DNA and has essential roles in DNA compaction, replication and gene expression. Nucleosomes and chromatin have historically been considered to be unique to eukaryotes, yet studies of select archaea have identified homologs of histone proteins that assemble into tetrameric nucleosomes. Here we report the first archaeal genome-wide nucleosome occupancy map, as observed in the halophile Haloferax volcanii. Nucleosome occupancy was compared with gene expression by compiling a comprehensive transcriptome of Hfx. volcanii. We found that archaeal transcripts possess hallmarks of eukaryotic chromatin structure: nucleosome-depleted regions at transcriptional start sites and conserved −1 and +1 promoter nucleosomes. Our observations demonstrate that histones and chromatin architecture evolved before the divergence of Archaea and Eukarya, suggesting that the fundamental role of chromatin in the regulation of gene expression is ancient.

Download Full-text