scholarly journals Transcriptional regulatory logic of the diurnal cycle in the mouse liver

2016 ◽  
Author(s):  
Jonathan Aryeh Sobel ◽  
Irina Krier ◽  
Teemu Andersin ◽  
Sunil Raghav ◽  
Donatella Canella ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Rna Polymerase Ii ◽  
Diurnal Cycle ◽  
Mouse Liver ◽  
Regulatory Elements ◽  
Dnase I ◽  
Diurnal Rhythms ◽  
Dynamic Binding ◽  
Pol Ii ◽  
The Core

AbstractMany organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription. Using ChIP-seq, we found that hypersensitivity cycled in phase with RNA polymerase II (Pol II) loading and H3K27ac histone marks. We then combined the DHSs with temporal Pol II profiles in wild-type (WT) and Bmal1-/- livers to computationally identify transcription factors through which the core clock and feeding-fasting cycles control diurnal rhythms in transcription. While a similar number of mRNAs accumulated rhythmically in Bmal1-/- compared to WT livers, the amplitudes in Bmal1-/- were generally lower. The residual rhythms in Bmal1-/- reflected transcriptional regulators mediating feeding-fasting responses as well as responses to rhythmic systemic signals. Finally, the analysis of DNase I cuts at nucleotide resolution showed dynamically changing footprint consistent with dynamic binding of CLOCK:BMAL1 complexes. Structural modeling suggested that these footprints are driven by a transient hetero-tetramer binding configuration at peak activity. Together, our temporal DNase I mappings allowed us to decipher the global regulation of diurnal transcription rhythms in mouse liver.

scholarly journals Molecular Genetics of the RNA Polymerase II General Transcriptional Machinery

1998 ◽  
Vol 62 (2) ◽  
pp. 465-503 ◽  
Author(s):  
Michael Hampsey
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Regulatory Elements ◽  
Transcriptional Repressors ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
The Core ◽  
General Transcription Factors ◽  
Transcriptional Machinery

SUMMARY Transcription initiation by RNA polymerase II (RNA pol II) requires interaction between cis-acting promoter elements and trans-acting factors. The eukaryotic promoter consists of core elements, which include the TATA box and other DNA sequences that define transcription start sites, and regulatory elements, which either enhance or repress transcription in a gene-specific manner. The core promoter is the site for assembly of the transcription preinitiation complex, which includes RNA pol II and the general transcription fctors TBP, TFIIB, TFIIE, TFIIF, and TFIIH. Regulatory elements bind gene-specific factors, which affect the rate of transcription by interacting, either directly or indirectly, with components of the general transcriptional machinery. A third class of transcription factors, termed coactivators, is not required for basal transcription in vitro but often mediates activation by a broad spectrum of activators. Accordingly, coactivators are neither gene-specific nor general transcription factors, although gene-specific coactivators have been described in metazoan systems. Transcriptional repressors include both gene-specific and general factors. Similar to coactivators, general transcriptional repressors affect the expression of a broad spectrum of genes yet do not repress all genes. General repressors either act through the core transcriptional machinery or are histone related and presumably affect chromatin function. This review focuses on the global effectors of RNA polymerase II transcription in yeast, including the general transcription factors, the coactivators, and the general repressors. Emphasis is placed on the role that yeast genetics has played in identifying these factors and their associated functions.

scholarly journals Computational identification and experimental characterization of preferred downstream positions in human core promoters

2021 ◽  
Author(s):  
René Dreos ◽  
Nati Malachi ◽  
Anna Sloutskin ◽  
Philipp Bucher ◽  
Tamar Juven-Gershon
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Motif Discovery ◽  
Core Promoter ◽  
Sequence Motifs ◽  
Promoter Element ◽  
Pol Ii ◽  
Core Promoters ◽  
The Core

AbstractMetazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a strict spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters.Author summaryTranscription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properties to it. Interestingly, core promoter motifs can be located both upstream and downstream of the transcription start site. Variable compositions of core promoter elements have been identified. The initiator (Inr) motif and the downstream core promoter element (DPE) is a combination of elements that has been identified and extensively characterized in fruit flies. Although a few Inr+DPE - containing human promoters have been identified, the presence of transcriptionally important downstream core promoter positions within human promoters has been a matter of controversy in the literature. Here, using a newly-designed motif discovery strategy, we discovered preferred downstream positions in human promoters that resemble fruit fly DPE. Clustering of the corresponding sequence motifs in eight additional species indicated that such promoters could be common to multicellular non-plant organisms. Importantly, functional characterization of the newly discovered preferred downstream positions supports the existence of Inr+DPE-containing promoters in human genes.

scholarly journals Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Science ◽  
2009 ◽  
Vol 325 (5940) ◽  
pp. 626-628 ◽  
Author(s):  
Courtney Hodges ◽  
Lacramioara Bintu ◽  
Lucyna Lubkowska ◽  
Mikhail Kashlev ◽  
Carlos Bustamante
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Optical Tweezers ◽  
Direct Evidence ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
The Core ◽  
Nucleosomal Dna ◽  
Dna Loop ◽  
Core Histones

RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.

scholarly journals Stress-Induced Transcriptional Memory Accelerates Promoter-Proximal Pause-Release and Decelerates Termination over Mitotic Divisions

2019 ◽  
Author(s):  
Anniina Vihervaara ◽  
Dig Bijay Mahat ◽  
Samu V. Himanen ◽  
Malin A.H. Blom ◽  
John T. Lis ◽  
...  
Keyword(s):  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Transcriptional Response ◽  
Regulatory Elements ◽  
List Type ◽  
Pol Ii ◽  
Daughter Cells ◽  
Heat Shocks ◽  
Transcriptional Memory ◽  
Pol Ii Pausing

SummaryHeat shock triggers an instant reprogramming of gene and enhancer transcription, but whether cells encode a memory to stress, at the level of nascent transcription, has remained unknown. Here, we measured transcriptional response to acute heat stress in unconditioned cells and in daughters of cells that had been exposed to a single or multiple heat shocks. Tracking RNA Polymerase II (Pol II) genome-wide at nucleotide-resolution revealed that cells precisely remember their transcriptional identity throughout stress, restoring Pol II distribution at gene bodies and enhancers upon recovery. However, single heat shock primed faster gene-induction in the daughter cells by increasing promoter-proximal Pol II pausing, and accelerating the pause-release. In repeatedly stressed cells, both basal and inducible transcription was refined, and pre-mRNA processing decelerated, which retained transcripts on chromatin and reduced recycling of the transcription machinery. These results mechanistically uncovered how the steps of pause-release and termination maintain transcriptional memory over mitosis.Highlights-Cell type-specific transcription precisely recovers after heat-induced reprogramming-Single heat shock primes genes for accelerated induction over mitotic divisionsviaincreased promoter-proximal Pol II pausing and faster pause-release-Multiple heat shocks refine basal and inducible transcription over mitotic divisions to support survival of the daughter cells-Decelerated termination at active genes reduces recycling of Pol II to heat-activated promoters and enhancers-HSF1 increases the rate of promoter-proximal pause-releaseviadistal and proximal regulatory elements

scholarly journals Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells

2020 ◽  
Vol 6 (50) ◽  
pp. eaaz7420
Author(s):  
Ryo Onishi ◽  
Kaoru Sato ◽  
Kensaku Murano ◽  
Lumi Negishi ◽  
Haruhiko Siomi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Adenosine Triphosphatase ◽  
Somatic Cells ◽  
Pol Ii ◽  
Heterochromatin Formation ◽  
Rna Transcripts ◽  
The Core ◽  
Chromatin Remodeling Complex

Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. Bioinformatic analyses indicated that Piwi, once bound to target RNAs, reduced the occupancies of SWI/SNF and RNA polymerase II (Pol II) on target loci, abrogating transcription. Artificial piRNA-driven targeting of Piwi to RNA transcripts enhanced repression of Brm-dependent reporters compared with Brm-independent reporters. This was dependent on Piwi cofactors, Gtsf1/Asterix (Gtsf1), Panoramix/Silencio (Panx), and Maelstrom (Mael), but not Eggless/dSetdb (Egg)–mediated H3K9me3 deposition. The λN-box B–mediated tethering of Mael to reporters repressed Brm-dependent genes in the absence of Piwi, Panx, and Gtsf1. We propose that Piwi, via Mael, can rapidly suppress transcription of Brm-dependent genes to facilitate heterochromatin formation.

scholarly journals Genomewide Recruitment Analysis of Rpb4, a Subunit of Polymerase II in Saccharomyces cerevisiae, Reveals Its Involvement in Transcription Elongation

2008 ◽  
Vol 7 (6) ◽  
pp. 1009-1018 ◽  
Author(s):  
Jiyoti Verma-Gaur ◽  
Sudha Narayana Rao ◽  
Toshiki Taya ◽  
Parag Sadhale
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Normal Growth ◽  
Growth Conditions ◽  
Pol Ii ◽  
Coding Regions ◽  
The Core ◽  
A Subunit ◽  
On Chip

ABSTRACT The Rpb4/Rpb7 subcomplex of yeast RNA polymerase II (Pol II) has counterparts in all multisubunit RNA polymerases from archaebacteria to higher eukaryotes. The Rpb4/7 subcomplex in Saccharomyces cerevisiae is unique in that it easily dissociates from the core, unlike the case in other organisms. The relative levels of Rpb4 and Rpb7 in yeasts affect the differential gene expression and stress response. Rpb4 is nonessential in S. cerevisiae and affects expression of a small number of genes under normal growth conditions. Here, using a chromatin immunoprecipitation (“ChIP on-chip”) technique, we compared genomewide binding of Rpb4 to that of a core Pol II subunit, Rpb3. Our results showed that in spite of being nonessential for survival, Rpb4 was recruited on coding regions of most transcriptionally active genes, similar to the case with the core Pol II subunit, Rpb3, albeit to a lesser extent. The extent of Rpb4 recruitment increased with increasing gene length. We also observed Pol II lacking Rpb4 to be defective in transcribing long, GC-rich transcription units, suggesting a role for Rpb4 in transcription elongation. This role in transcription elongation was supported by the observed 6-azauracil (6AU) sensitivity of the rpb4Δ mutant. Unlike most phenotypes of rpb4Δ, the 6AU sensitivity of the rpb4Δ strain was not rescued by overexpression of RPB7. This report provides the first instance of a distinct role for Rpb4 in transcription, which is independent of its interacting partner, Rpb7.

Long Distance Cyclin D1 Activation in B Cell Malignancies: Role of RNA Polymerase II.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1113-1113
Author(s):  
Hui Liu ◽  
Jin Wang ◽  
Richard T. Maziarz ◽  
Elliot M. Epner
Keyword(s):  
B Cells ◽  
Rna Polymerase ◽  
B Cell ◽  
Cyclin D1 ◽  
Rna Polymerase Ii ◽  
Gene Locus ◽  
Regulatory Elements ◽  
Long Distance ◽  
B Cell Malignancies ◽  
Pol Ii

Abstract Translocations involving the immunoglobulin heavy chain gene locus (IgH) are common in B cell malignancies. One common target gene is cyclin D1, which is deregulated in most patients with mantle cell lymphoma (MCL) and approximately 15–20% of patients with multiple myeloma (MM). Cyclin D1 is not expressed in normal lymphocytes; cyclin D1 expression in B cell malignancies is deregulated by IgH translocations and insertions. We have shown that the cyclin D1 locus, including the promoter and upstream regions, are acetylated and DNA hypomethylated in both malignant and nonmalignant B cells (Liu et al, Blood in press). Using chromatin immunoprecipitation (ChIP) assays, we have found that RNA polymerase II (Pol II) is a) present at the cyclin D1 promoter b) located at regions far upstream of the cyclin D1 gene and c) present at 3′ Cα IgH regulatory elements only in cyclin D1 expressing malignant B cells. Pol II is present at the translocation breakpoint in a MCL cell line, but we do not find Pol II present continuously from the IgH regulatory regions to the cyclin D1 promoter. Confirmatory RT-PCR analyses also do not demonstrate continous evidence of RNA transcripts extending from the IgH regulatory elements to the cyclin D1 promoter. Mutants derived from gene targeting experiments that have lost the translocated chromosome show Pol II binding only at the Eu intronic enhancer, consistent with known promoter acivity and sterile transcripts originating at this location. Our data suggest that Pol II may play a important role in initiating long distance cyclin D1 deregulation by translocated IgH sequences. Analogous to the mouse β-globin gene locus, a polymerase transfer (LPT) model may be invoked, where other proteins such as CTCF effect Pol II transfer from 3′ Cα IgH regulatory sequences to the cyclin D1 promoter and initiate cyclin D1 transcription.

Cooperative Silencing of Chicken ρ- and βH- Globin Gene Expression by Chicken β-Globin Regulatory Elements: Involvement of GATA-1, NF-E2, and RNA Polymerase II.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1214-1214
Author(s):  
Jin Wang ◽  
Hui Liu ◽  
Elliot Epner
Keyword(s):  
Rna Polymerase Ii ◽  
Selectable Marker ◽  
Globin Gene ◽  
Marker Gene ◽  
K562 Cells ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Selectable Marker Gene ◽  
Pol Ii ◽  
Globin Gene Expression

Abstract The chicken β-globin locus represents a well characterized, model system where the relationship between chromatin structure, transcription and DNA replication can be studied. The locus contains several regulatory elements including an intergenic enhancer as well as upstream regulatory elements that may function either alone or in combination with the intergenic enhancer as an LCR. The availability of the recombination proficient chicken B cell line DT40 has allowed the introduction of mutations into the endogenous chicken β-globin locus and phenotypic analysis after microcell mediated chromosome transfer into human erythroleukemia (K562) cells. Using this system, we have introduced deletions in the chicken β-globin intergenic enhancer as well as 5′ HS 1,2, and 3. A chicken chromosome marked by insertion of a selectable marker gene into the upstream folate receptor gene locus or 5′ HS1 followed by Cre recombinase mediated removal of the selectable marker gene served as control “wild type” chromosomes. Expression of the embryonic ρ and fetal βH chicken globin genes were repressed by the intergenic enhancer, 5′ HS1, or 5′HS2. No ρ or βH globin gene expression was detected in K562 cells containing control chicken chromosomes, while ρ and βH mRNA were activated when the intergenic enhancer, 5′ HS1, or 5′HS2 were deleted. Transcriptional activation of the ρ and βH genes correlated with hyperacetylation of histones H3 and H4, loss of methylated K9 histone H3, and binding of RNA polymerase II to the gene promoters. The status of methylated CpG dinucleotides at the promoters did not correlate with the transcriptional status of the genes. The phenotype of the 5′ HS1, and HS2 deletions were surprisingly similar to that of the intergenic enhancer, which suggested these elements may function either in the same pathway or complex. Chromatin immunoprecipitation (ChIP) experiments that assayed RNA polmerase II (pol II), GATA-1 and NF-E2 p45/ p18 binding at regulatory elements and gene promoters in targeted cell lines supported this hypothesis and suggested a potential role for 5′HS3 in gene activation. However, targeted deletion of 5′ HS3, unlike the other chicken β-globin regulatory elements, showed no transcriptional phenotype. Our results demonstrate the intergenic enhancer, 5′HS1, and 5′ HS2 function through a common silencing mechanism involving pol II, GATA-1, and NF-E2/P18.

scholarly journals Intron-driven gene expression in the absence of a core promoter in Arabidopsis thaliana

2016 ◽  
Author(s):  
Jenna E Gallegos ◽  
Alan B Rose
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Regulatory Elements ◽  
Intron Position ◽  
Mrna Accumulation ◽  
Practical Applications ◽  
Promoter Sequences ◽  
The Core

AbstractIn diverse eukaryotes, certain introns increase mRNA accumulation through the poorly understood mechanism of intron-mediated enhancement (IME). A distinguishing feature of IME is that these introns have no effect from upstream or more than 1 Kb downstream of the transcription start site (TSS). To more precisely define the intron position requirements for IME in Arabidopsis, we tested the effect of the UBQ10 intron on gene expression from 6 different positions surrounding the TSS of a TRP1:GUS fusion. The intron strongly increased expression from all transcribed positions, but had no effect when 204 nt or more upstream of the 5’-most TSS. When the intron was located in the 5’ UTR, the TSS unexpectedly changed, resulting in longer transcripts. Remarkably, deleting 303 nt of the core promoter, including all known TSS’s and all but 18 nt of the 5’ UTR, had virtually no effect on the level of gene expression as long as a stimulating intron was included in the gene. When the core promoter was deleted, transcription initiated in normally untranscribed sequences the same distance upstream of the intron as when the promoter was intact. Together, these results suggest that certain introns play unexpectedly large roles in directing transcription initiation and represent a previously unrecognized type of downstream regulatory elements for genes transcribed by RNA polymerase II. This study also demonstrates considerable flexibility in the sequences surrounding the TSS, indicating that the TSS is not determined by promoter sequences alone. These findings are relevant in practical applications where introns are used to increase gene expression and contribute to our general understanding of gene structure and regulation in eukaryotes.

scholarly journals The synchronization and adaptation of Neurospora crassa circadian and conidiation rhythms to short light-dark cycles

2018 ◽  
Author(s):  
Huan Ma ◽  
Luyao Li ◽  
Jie Yan ◽  
Yin Zhang ◽  
Weirui Shi ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Neurospora Crassa ◽  
Metabolic Pathways ◽  
Diurnal Rhythms ◽  
Daily Rhythms ◽  
The Core ◽  
Ubiquitin E3 Ligase ◽  
Modeling And Experiments ◽  
High Intensity Light ◽  
Clock Protein

ABSTRACTCircadian clocks control the physiological and behavioral daily rhythms to adapt to the changing environment with a period of ~24 h. However, the influence and mechanism of extreme light-dark cycles on the circadian clock remain unclear. We show that, in the fungus Neurospora crassa under short LD cycles, both the growth rate and the ratio of microconidia production contributes to adaptation in LD12:12 (light for 12 h and dark for 12 h, periodically). Mathematical modeling and experiments demonstrate that in short LD cycles, the expression of the core clock protein FREQUENCY is entrained to the LD cycles when LD>3:3 while it free runs when T≤ LD3:3. We investigated the changes in circadian/diurnal rhythms under a series of different LD conditions, and the results showed that conidial rhythmicity can be adapted to the short LD cycles. We further demonstrate that the existence of unknown blue light photoreceptor(s) and the circadian clock might promote the conidiation rhythms that resonate with the environment. A high-intensity light induced the expression of a set of downstream genes involved in various metabolic pathways. The ubiquitin E3 ligase FWD-1 and the previously described CRY-dependent oscillator system were implicated in regulating conidiation under short LD conditions.

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