In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

AbstractThe molecular mechanisms responsible for Topologically Associated Domains (TADs) formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by Architectural Proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence on the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.

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Selective Requirement for SAGA in Hog1-Mediated Gene Expression Depending on the Severity of the External Osmostress Conditions

Molecular and Cellular Biology ◽

10.1128/mcb.00089-07 ◽

2007 ◽

Vol 27 (11) ◽

pp. 3900-3910 ◽

Cited By ~ 68

Author(s):

Meritxell Zapater ◽

Marc Sohrmann ◽

Matthias Peter ◽

Francesc Posas ◽

Eulàlia de Nadal

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Genetic Screening ◽

Essential Role ◽

Regulation Of Gene Expression ◽

Transcriptional Program ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Transcriptional Complex

ABSTRACT Regulation of gene expression by the Hog1 stress-activated protein kinase is essential for proper cell adaptation to osmostress. Hog1 coordinates an extensive transcriptional program through the modulation of transcription. To identify systematically novel components of the transcriptional machinery required for osmostress-mediated gene expression, we performed an exhaustive genome-wide genetic screening, searching for mutations that render cells osmosensitive at high osmolarity and that are associated with reduced expression of osmoresponsive genes. The SAGA and Mediator complexes were identified as putative novel regulators of osmostress-mediated transcription. Interestingly, whereas Mediator is essential for osmostress gene expression, the requirement for SAGA is different depending on the strength of the extracellular osmotic conditions. At mild osmolarity, SAGA mutants show only very slight defects on RNA polymerase II (Pol II) recruitment and gene expression, whereas at severe osmotic conditions, SAGA mutants show completely impaired RNA Pol II recruitment and transcription of osmoresponsive genes. Thus, our results define an essential role for Mediator in osmostress gene expression and a selective role for SAGA under severe osmostress. Our results indicate that the requirement for a transcriptional complex to regulate a promoter might be determined by the strength of the stimuli perceived by the cell through the regulation of interactions between transcriptional complexes.

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The Role of Translation Initiation Regulation in Haematopoiesis

Comparative and Functional Genomics ◽

10.1155/2012/576540 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 7

Author(s):

Godfrey Grech ◽

Marieke von Lindern

Keyword(s):

Gene Expression ◽

Translation Initiation ◽

Translational Control ◽

Molecular Mechanisms ◽

Rna Binding ◽

Regulation Of Gene Expression ◽

Mrna Translation ◽

Translation Control ◽

Haematological Disorders

Organisation of RNAs into functional subgroups that are translated in response to extrinsic and intrinsic factors underlines a relatively unexplored gene expression modulation that drives cell fate in the same manner as regulation of the transcriptome by transcription factors. Recent studies on the molecular mechanisms of inflammatory responses and haematological disorders indicate clearly that the regulation of mRNA translation at the level of translation initiation, mRNA stability, and protein isoform synthesis is implicated in the tight regulation of gene expression. This paper outlines how these posttranscriptional control mechanisms, including control at the level of translation initiation factors and the role of RNA binding proteins, affect hematopoiesis. The clinical relevance of these mechanisms in haematological disorders indicates clearly the potential therapeutic implications and the need of molecular tools that allow measurement at the level of translational control. Although the importance of miRNAs in translation control is well recognised and studied extensively, this paper will exclude detailed account of this level of control.

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Active transgenes in zebrafish are enriched in acetylated histone H4 and dynamically associate with RNA Pol II and splicing complexes

Journal of Cell Science ◽

10.1242/jcs.112.7.1045 ◽

1999 ◽

Vol 112 (7) ◽

pp. 1045-1054 ◽

Cited By ~ 1

Author(s):

P. Collas ◽

M.R. Liang ◽

M. Vincent ◽

P. Alestrom

Keyword(s):

Transgene Expression ◽

Functional Organization ◽

Histone Deacetylation ◽

Splicing Factors ◽

Histone H4 ◽

Rna Pol Ii ◽

Pol Ii ◽

Acetylated Histone H4 ◽

Co Precipitation

We have investigated the functional organization of active and silent integrated luciferase transgenes in zebrafish, with the aim of accounting for the variegation of transgene expression in this species. We demonstrate the enrichment of transcriptionally active transgenes in acetylated histone H4 and the dynamic association of the transgenes with splicing factor SC35 and RNA Pol II. Analysis of interphase nuclei and extended chromatin fibers by immunofluorescence and in situ hybridization reveals a co-localization of transgenes with acetylated H4 in luciferase-expressing animals only. Enrichment of expressed transgenes in acetylated H4 is further demonstrated by their co-precipitation from chromatin using anti-acetylated H4 antibodies. Little correlation exists, however, between the level of histone acetylation and the degree of transgene expression. In transgene-expressing zebrafish, most transgenes co-localize with Pol II and SC35, whereas no such association occurs in non-expressing individuals. Inhibition of Pol II abolishes transgene expression and disrupts association of transgenes with SC35, although inactivated transgenes remains enriched in acetylated histones. Exposure of embryos to the histone deacetylation inhibitor TSA induces expression of most silent transgenes. Chromatin containing activated transgenes becomes enriched in acetylated histones and the transgenes recruit SC35 and Pol II. The results demonstrate a correlation between H4 acetylation and transgene activity, and argue that active transgenes dynamically recruit splicing factors and Pol II. The data also suggest that dissociation of splicing factors from transgenes upon Pol II inhibition is not a consequence of changes in H4 acetylation.

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Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1912459116 ◽

2019 ◽

Vol 116 (39) ◽

pp. 19490-19499 ◽

Cited By ~ 76

Author(s):

Chenglong Xia ◽

Jean Fan ◽

George Emanuel ◽

Junjie Hao ◽

Xiaowei Zhuang

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Spatial Information ◽

Detection Efficiency ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Rna Profiling ◽

Spatially Resolved ◽

Cycle Dependent

The expression profiles and spatial distributions of RNAs regulate many cellular functions. Image-based transcriptomic approaches provide powerful means to measure both expression and spatial information of RNAs in individual cells within their native environment. Among these approaches, multiplexed error-robust fluorescence in situ hybridization (MERFISH) has achieved spatially resolved RNA quantification at transcriptome scale by massively multiplexing single-molecule FISH measurements. Here, we increased the gene throughput of MERFISH and demonstrated simultaneous measurements of RNA transcripts from ∼10,000 genes in individual cells with ∼80% detection efficiency and ∼4% misidentification rate. We combined MERFISH with cellular structure imaging to determine subcellular compartmentalization of RNAs. We validated this approach by showing enrichment of secretome transcripts at the endoplasmic reticulum, and further revealed enrichment of long noncoding RNAs, RNAs with retained introns, and a subgroup of protein-coding mRNAs in the cell nucleus. Leveraging spatially resolved RNA profiling, we developed an approach to determine RNA velocity in situ using the balance of nuclear versus cytoplasmic RNA counts. We applied this approach to infer pseudotime ordering of cells and identified cells at different cell-cycle states, revealing ∼1,600 genes with putative cell cycle-dependent expression and a gradual transcription profile change as cells progress through cell-cycle stages. Our analysis further revealed cell cycle-dependent and cell cycle-independent spatial heterogeneity of transcriptionally distinct cells. We envision that the ability to perform spatially resolved, genome-wide RNA profiling with high detection efficiency and accuracy by MERFISH could help address a wide array of questions ranging from the regulation of gene expression in cells to the development of cell fate and organization in tissues.

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HNF4A Regulates the Formation of Hepatic Progenitor Cells from Human iPSC-Derived Endoderm by Facilitating Efficient Recruitment of RNA Pol II

Genes ◽

10.3390/genes10010021 ◽

2018 ◽

Vol 10 (1) ◽

pp. 21 ◽

Cited By ~ 12

Author(s):

Ann DeLaForest ◽

Francesca Di Furio ◽

Ran Jing ◽

Amy Ludwig-Kubinski ◽

Kirk Twaroski ◽

...

Keyword(s):

Cell Differentiation ◽

Chromatin Immunoprecipitation ◽

Molecular Mechanisms ◽

Cell Formation ◽

Rna Pol Ii ◽

Pol Ii ◽

High Throughput Dna Sequencing ◽

Hepatocyte Nuclear Factor 4 ◽

Induced Pluripotent ◽

Human Ipsc

Elucidating the molecular basis of cell differentiation will advance our understanding of organ development and disease. We have previously established a protocol that efficiently produces cells with hepatocyte characteristics from human induced pluripotent stem cells. We previously used this cell differentiation model to identify the transcription factor hepatocyte nuclear factor 4 α (HNF4A) as being essential during the transition of the endoderm to a hepatic fate. Here, we sought to define the molecular mechanisms through which HNF4A controls this process. By combining HNF4A chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) analyses at the onset of hepatic progenitor cell formation with transcriptome data collected during early stages of differentiation, we identified genes whose expression is directly dependent upon HNF4A. By examining the dynamic changes that occur at the promoters of these HNF4A targets we reveal that HNF4A is essential for recruitment of RNA polymerase (RNA pol) II to genes that are characteristically expressed as the hepatic progenitors differentiate from the endoderm.

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Molecular Mechanisms, Diagnostic Aspects and Therapeutic Opportunities of Micro Ribonucleic Acids in Atrial Fibrillation

International Journal of Molecular Sciences ◽

10.3390/ijms21082742 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2742 ◽

Cited By ~ 1

Author(s):

Allan Böhm ◽

Marianna Vachalcova ◽

Peter Snopek ◽

Ljuba Bacharova ◽

Dominika Komarova ◽

...

Keyword(s):

Gene Expression ◽

Atrial Fibrillation ◽

Molecular Mechanisms ◽

Wide Spectrum ◽

Regulation Of Gene Expression ◽

Review Article ◽

Ribonucleic Acids ◽

Rna Molecules ◽

Diagnostic Aspects ◽

Non Coding Rna

Micro ribonucleic acids (miRNAs) are short non-coding RNA molecules responsible for regulation of gene expression. They are involved in many pathophysiological processes of a wide spectrum of diseases. Recent studies showed their involvement in atrial fibrillation. They seem to become potential screening biomarkers for atrial fibrillation and even treatment targets for this arrhythmia. The aim of this review article was to summarize the latest knowledge about miRNA and their molecular relation to the pathophysiology, diagnosis and treatment of atrial fibrillation.

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Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression

Nature Communications ◽

10.1038/s41467-019-13394-w ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 4

Author(s):

Nicola P. Montaldo ◽

Diana L. Bordin ◽

Alessandro Brambilla ◽

Marcel Rösinger ◽

Sarah L. Fordyce Martin ◽

...

Keyword(s):

Gene Expression ◽

Genome Stability ◽

Genome Instability ◽

Excision Repair ◽

Regulation Of Gene Expression ◽

Direct Interaction ◽

Dna Glycosylase ◽

Pol Ii ◽

Naked Dna ◽

Alkyladenine Dna Glycosylase

AbstractBase excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3′end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression.

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MAP Kinase Pathways in the YeastSaccharomyces cerevisiae

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.62.4.1264-1300.1998 ◽

1998 ◽

Vol 62 (4) ◽

pp. 1264-1300 ◽

Cited By ~ 660

Author(s):

Michael C. Gustin ◽

Jacobus Albertyn ◽

Matthew Alexander ◽

Kenneth Davenport

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Current Knowledge ◽

Regulation Of Gene Expression ◽

Mapk Cascade ◽

Mitogen Activated Protein Kinase ◽

Future Research ◽

Mapk Pathways ◽

Mapk Cascades

SUMMARY A cascade of three protein kinases known as a mitogen-activated protein kinase (MAPK) cascade is commonly found as part of the signaling pathways in eukaryotic cells. Almost two decades of genetic and biochemical experimentation plus the recently completed DNA sequence of the Saccharomyces cerevisiae genome have revealed just five functionally distinct MAPK cascades in this yeast. Sexual conjugation, cell growth, and adaptation to stress, for example, all require MAPK-mediated cellular responses. A primary function of these cascades appears to be the regulation of gene expression in response to extracellular signals or as part of specific developmental processes. In addition, the MAPK cascades often appear to regulate the cell cycle and vice versa. Despite the success of the gene hunter era in revealing these pathways, there are still many significant gaps in our knowledge of the molecular mechanisms for activation of these cascades and how the cascades regulate cell function. For example, comparison of different yeast signaling pathways reveals a surprising variety of different types of upstream signaling proteins that function to activate a MAPK cascade, yet how the upstream proteins actually activate the cascade remains unclear. We also know that the yeast MAPK pathways regulate each other and interact with other signaling pathways to produce a coordinated pattern of gene expression, but the molecular mechanisms of this cross talk are poorly understood. This review is therefore an attempt to present the current knowledge of MAPK pathways in yeast and some directions for future research in this area.

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Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽

10.1534/genetics.119.302749 ◽

2019 ◽

Vol 213 (4) ◽

pp. 1545-1563 ◽

Cited By ~ 2

Author(s):

Ramona Lütkenhaus ◽

Stefanie Traeger ◽

Jan Breuer ◽

Laia Carreté ◽

Alan Kuo ◽

...

Keyword(s):

Gene Expression ◽

Fruiting Body ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Regulation Of Gene Expression ◽

Comparative Transcriptomics ◽

Fruiting Bodies ◽

Body Development ◽

Fruiting Body Development ◽

Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

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Hepatic Gene Expression Changes in Hypothyroid Juvenile Mice: Characterization of a Novel Negative Thyroid-Responsive Element

Endocrinology ◽

10.1210/en.2007-0452 ◽

2007 ◽

Vol 148 (8) ◽

pp. 3932-3940 ◽

Cited By ~ 19

Author(s):

Hongyan Dong ◽

Carole L. Yauk ◽

Andrew Williams ◽

Alice Lee ◽

George R. Douglas ◽

...

Keyword(s):

Gene Expression ◽

Dna Microarrays ◽

Molecular Mechanisms ◽

Regulation Of Gene Expression ◽

Transient Gene Expression ◽

Early Response ◽

Response Element ◽

Gene Expression Studies ◽

Maternal Thyroid ◽

Responsive Element

The molecular mechanisms involved in the response of developing mice to disruptions in maternal thyroid hormone (TH) homeostasis are poorly characterized. We used DNA microarrays to examine a broad spectrum of genes from the livers of mice rendered hypothyroid by treating pregnant mice from gestational d 13 to postnatal d 15 with 6-propyl-2-thiouracil in drinking water. Twenty-four individuals (one male and one female pup from six litters of control or 6-propyl-2-thiouracil treatment groups, respectively) were profiled using Agilent oligonucleotide microarrays. MAANOVA identified 96 differentially expressed genes (false discovery rate adjusted P < 0.1 and fold change > 2 in at least one gender). Of these, 72 genes encode proteins of known function, 15 of which had previously been identified as regulated by TH. Pathway analysis revealed these genes are involved in metabolism, development, cell proliferation, apoptosis, and signal transduction. An immediate-early response gene, Nr4a1 (nuclear receptor subfamily 4, group A, member 1), was up-regulated by 3-fold in hypothyroid juvenile mouse liver; treatment of HepG2 cells with T3 resulted in down-regulation of Nr4a1. A potential thyroid response element −1218 to −1188 bp upstream of the promoter region of Nr4a1 was identified and demonstrated to bind TH receptor (TR)-α and TRβ. Point mutation or deletion of the sequence containing the potential Nr4a1-thyroid response element in transient gene expression studies resulted in both higher basal expression and loss of T3 regulatory capacity, suggesting that this site is responsible for the negative regulation of gene expression by TR and TH.

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