Fsh–Pc–Sce complex mediates active transcription of Cubitus interruptus (Ci)

Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA to regulate its targets frequently becomes a challenge. Previously, we developed the ASSA algorithm that detects statistically significant inter-molecular RNA-RNA interactions. Here we designed a workflow that uses ASSA predictions to estimate the ability of an lncRNA to function via direct base pairing with the target transcripts (co- or post-transcriptionally). The workflow was applied to 300+ lncRNA knockdown experiments from the FANTOM6 pilot project producing statistically significant predictions for 71 unique lncRNAs (104 knockdowns). Surprisingly, the majority of these lncRNAs were likely to function co-transcriptionally, i.e., hybridize with the nascent transcripts of the target genes. Moreover, a number of the obtained predictions were supported by independent iMARGI experimental data on co-localization of lncRNA and chromatin. We detected an evolutionarily conserved lncRNA CHASERR (AC013394.2 or LINC01578) that could regulate target genes co-transcriptionally via interaction with a nascent transcript by directing CHD2 helicase. The obtained results suggested that this nuclear lncRNA may be able to activate expression of the target genes in trans by base-pairing with the nascent transcripts and directing the CHD2 helicase to the regulated promoters leading to open the chromatin and active transcription. Our study highlights the possible importance of base-pairing between nuclear lncRNAs and nascent transcripts for the regulation of gene expression.

Download Full-text

EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2

Cell Death and Disease ◽

10.1038/s41419-021-03538-6 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Shuang Cui ◽

Qiong Wu ◽

Ming Liu ◽

Mu Su ◽

ShiYou Liu ◽

...

Keyword(s):

Tumor Progression ◽

Tumor Cells ◽

Target Gene ◽

Super Enhancer ◽

Proliferation And Metastasis ◽

Active Transcription ◽

Hct 116 ◽

Large Clusters

AbstractSuper-enhancers or stretch enhancers (SEs) consist of large clusters of active transcription enhancers which promote the expression of critical genes that define cell identity during development and disease. However, the role of many super-enhancers in tumor cells remains unclear. This study aims to explore the function and mechanism of a new super-enhancer in various tumor cells. A new super-enhancer that exists in a variety of tumors named EphA2-Super-enhancer (EphA2-SE) was found using multiple databases and further identified. CRISPR/Cas9-mediated deletion of EphA2-SE results in the significant downregulation of its target gene EphA2. Mechanistically, we revealed that the core active region of EphA2-SE comprises E1 component enhancer, which recruits TCF7L2 and FOSL2 transcription factors to drive the expression of EphA2, induce cell proliferation and metastasis. Bioinformatics analysis of RNA-seq data and functional experiments in vitro illustrated that EphA2-SE deletion inhibited cell growth and metastasis by blocking PI3K/AKT and Wnt/β-catenin pathway in HeLa, HCT-116 and MCF-7 cells. Overexpression of EphA2 in EphA2-SE−/− clones rescued the effect of EphA2-SE deletion on proliferation and metastasis. Subsequent xenograft animal model revealed that EphA2-SE deletion suppressed tumor proliferation and survival in vivo. Taken together, these findings demonstrate that EphA2-SE plays an oncogenic role and promotes tumor progression in various tumors by recruiting FOSL2 and TCF7L2 to drive the expression of oncogene EphA2.

Download Full-text

Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

Nature Communications ◽

10.1038/s41467-021-24815-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yisrael Rappaport ◽

Hanna Achache ◽

Roni Falk ◽

Omer Murik ◽

Oren Ram ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Rna Polymerase Ii ◽

X Chromosome ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Transcription Analysis ◽

X Chromosomes ◽

Unique Character ◽

Active Transcription ◽

Heterogametic Sex

AbstractDuring meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

Download Full-text

Visualization of Chromatin in the Yeast Nucleus and Nucleolus Using Hyperosmotic Shock

International Journal of Molecular Sciences ◽

10.3390/ijms22031132 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1132

Author(s):

Nicolas Thelen ◽

Jean Defourny ◽

Denis L. J. Lafontaine ◽

Marc Thiry

Keyword(s):

Osmotic Shock ◽

Size Composition ◽

Yeast Cells ◽

Exponential Growth Phase ◽

Cell Nuclei ◽

Hyperosmotic Shock ◽

Christmas Trees ◽

Transmission Electron ◽

Active Transcription ◽

Decondensed Chromatin

Unlike in most eukaryotic cells, the genetic information of budding yeast in the exponential growth phase is only present in the form of decondensed chromatin, a configuration that does not allow its visualization in cell nuclei conventionally prepared for transmission electron microscopy. In this work, we studied the distribution of chromatin and its relationships to the nucleolus using different cytochemical and immunocytological approaches applied to yeast cells subjected to hyperosmotic shock. Our results show that osmotic shock induces the formation of heterochromatin patches in the nucleoplasm and intranucleolar regions of the yeast nucleus. In the nucleolus, we further revealed the presence of osmotic shock-resistant DNA in the fibrillar cords which, in places, take on a pinnate appearance reminiscent of ribosomal genes in active transcription as observed after molecular spreading (“Christmas trees”). We also identified chromatin-associated granules whose size, composition and behaviour after osmotic shock are reminiscent of that of mammalian perichromatin granules. Altogether, these data reveal that it is possible to visualize heterochromatin in yeast and suggest that the yeast nucleus displays a less-effective compartmentalized organization than that of mammals.

Download Full-text

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication

Cell Discovery ◽

10.1038/s41421-021-00279-w ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Wen Juan Tu ◽

Robert D. McCuaig ◽

Michelle Melino ◽

Daniel J. Rawle ◽

Thuy T. Le ◽

...

Keyword(s):

Viral Replication ◽

Treatment Options ◽

Critical Role ◽

Post Exposure Prophylaxis ◽

Nuclear Entry ◽

Importin Α ◽

Active Transcription ◽

Nuclear Shuttling ◽

Asymptomatic Phase ◽

Exposure Prophylaxis

AbstractTreatment options for COVID-19 remain limited, especially during the early or asymptomatic phase. Here, we report a novel SARS-CoV-2 viral replication mechanism mediated by interactions between ACE2 and the epigenetic eraser enzyme LSD1, and its interplay with the nuclear shuttling importin pathway. Recent studies have shown a critical role for the importin pathway in SARS-CoV-2 infection, and many RNA viruses hijack this axis to re-direct host cell transcription. LSD1 colocalized with ACE2 at the cell surface to maintain demethylated SARS-CoV-2 spike receptor-binding domain lysine 31 to promote virus–ACE2 interactions. Two newly developed peptide inhibitors competitively inhibited virus–ACE2 interactions, and demethylase access to significantly inhibit viral replication. Similar to some other predominantly plasma membrane proteins, ACE2 had a novel nuclear function: its cytoplasmic domain harbors a nuclear shuttling domain, which when demethylated by LSD1 promoted importin-α-dependent nuclear ACE2 entry following infection to regulate active transcription. A novel, cell permeable ACE2 peptide inhibitor prevented ACE2 nuclear entry, significantly inhibiting viral replication in SARS-CoV-2-infected cell lines, outperforming other LSD1 inhibitors. These data raise the prospect of post-exposure prophylaxis for SARS-CoV-2, either through repurposed LSD1 inhibitors or new, nuclear-specific ACE2 inhibitors.

Download Full-text

Histone methyltransferase WHSC1 inhibits colorectal cancer cell apoptosis via targeting anti-apoptotic BCL2

Cell Death Discovery ◽

10.1038/s41420-021-00402-6 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Yu Wang ◽

Liming Zhu ◽

Mei Guo ◽

Gang Sun ◽

Kun Zhou ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Cell ◽

Cell Apoptosis ◽

B Cell Lymphoma ◽

Histone Methyltransferase ◽

Chemotherapeutic Agents ◽

Cancer Cell Apoptosis ◽

Active Transcription

AbstractWHSC1 is a histone methyltransferase that facilitates histone H3 lysine 36 dimethylation (H3K36me2), which is a permissive mark associated with active transcription. In this study, we revealed how WHSC1 regulates tumorigenesis and chemosensitivity of colorectal cancer (CRC). Our data showed that WHSC1 as well as H3K36me2 were highly expressed in clinical CRC samples, and high WHSC1 expression is associated with poorer prognosis in CRC patients. WHSC1 reduction promoted colon cancer cell apoptosis both in vivo and in vitro. We found that B cell lymphoma-2 (BCL2) expression, an anti-apoptotic protein, is markedly decreased in after WHSC1 depletion. Mechanistic characterization indicated that WHSC1 directly binds to the promoter region of BCL2 gene and regulate its H3K36 dimethylation level. What’s more, our study indicated that WHSC1 depletion promotes chemosensitivity in CRC cells. Together, our results suggested that WHSC1 and H3K36me2 modification might be optimal therapeutic targets to disrupt CRC progression and WHSC1-targeted therapy might potentially overcome the resistance of chemotherapeutic agents.

Download Full-text

Roles of XBP1s in Transcriptional Regulation of Target Genes

Biomedicines ◽

10.3390/biomedicines9070791 ◽

2021 ◽

Vol 9 (7) ◽

pp. 791

Author(s):

Sung-Min Park ◽

Tae-Il Kang ◽

Jae-Seon So

Keyword(s):

Transcriptional Regulation ◽

Er Stress ◽

Target Genes ◽

Inflammatory Diseases ◽

Vital Role ◽

Genes Encoding ◽

Autoimmune And Inflammatory Diseases ◽

Active Transcription ◽

Transcriptional Regulatory Mechanisms ◽

The Unfolded Protein Response

The spliced form of X-box binding protein 1 (XBP1s) is an active transcription factor that plays a vital role in the unfolded protein response (UPR). Under endoplasmic reticulum (ER) stress, unspliced Xbp1 mRNA is cleaved by the activated stress sensor IRE1α and converted to the mature form encoding spliced XBP1 (XBP1s). Translated XBP1s migrates to the nucleus and regulates the transcriptional programs of UPR target genes encoding ER molecular chaperones, folding enzymes, and ER-associated protein degradation (ERAD) components to decrease ER stress. Moreover, studies have shown that XBP1s regulates the transcription of diverse genes that are involved in lipid and glucose metabolism and immune responses. Therefore, XBP1s has been considered an important therapeutic target in studying various diseases, including cancer, diabetes, and autoimmune and inflammatory diseases. XBP1s is involved in several unique mechanisms to regulate the transcription of different target genes by interacting with other proteins to modulate their activity. Although recent studies discovered numerous target genes of XBP1s via genome-wide analyses, how XBP1s regulates their transcription remains unclear. This review discusses the roles of XBP1s in target genes transcriptional regulation. More in-depth knowledge of XBP1s target genes and transcriptional regulatory mechanisms in the future will help develop new therapeutic targets for each disease.

Download Full-text

Adenovirus 2 peptide IX gene is expressed only on replicated DNA molecules

Molecular and Cellular Biology ◽

10.1128/mcb.6.12.4149-4154.1986 ◽

1986 ◽

Vol 6 (12) ◽

pp. 4149-4154

Author(s):

T Matsui ◽

M Murayama ◽

T Mita

Keyword(s):

Quantitative Analysis ◽

Cytosine Arabinoside ◽

Plasmid Dna ◽

Adenovirus Type ◽

Plasmid Replication ◽

Gene Transcript ◽

Dna Molecules ◽

Transfected Cells ◽

Active Transcription

Transcription of the adenovirus type 2 peptide IX (pIX) gene was examined in transient expression assays. When a nonreplicating plasmid DNA containing the pIX gene was introduced into HeLa cells by the DEAE-dextran method, no pIX gene transcript was detected. In contrast, efficient transcription was observed in the cells transfected with a replicating plasmid containing the pIX gene. Adenovirus early genes did not affect the level of transcription of the pIX gene on either a nonreplicating or a replicating plasmid. Inhibition of plasmid replication with cytosine arabinoside prevented transcription of the pIX gene. By quantitative analysis of the amount of the pIX gene and its transcript in transfected cells, it was concluded that active transcription of the pIX gene occurred only on DNA molecules replicated in the cell.

Download Full-text

Deregulated expression of the RanBP1 gene alters cell cycle progression in murine fibroblasts

Journal of Cell Science ◽

10.1242/jcs.110.19.2345 ◽

1997 ◽

Vol 110 (19) ◽

pp. 2345-2357 ◽

Cited By ~ 1

Author(s):

A. Battistoni ◽

G. Guarguaglini ◽

F. Degrassi ◽

C. Pittoggi ◽

A. Palena ◽

...

Keyword(s):

Cell Cycle ◽

Dna Replication ◽

Cell Cycle Progression ◽

Protein Import ◽

Proliferating Cells ◽

Cycle Progression ◽

Ran Gtpase ◽

Genes Encoding ◽

Active Transcription ◽

Gtpase Cycle

RanBP1 is a molecular partner of the Ran GTPase, which is implicated in the control of several processes, including DNA replication, mitotic entry and exit, cell cycle progression, nuclear structure, protein import and RNA export. While most genes encoding Ran-interacting partners are constitutively active, transcription of the RanBP1 mRNA is repressed in non proliferating cells, is activated at the G1/S transition in cycling cells and peaks during S phase. We report here that forced expression of the RanBP1 gene disrupts the orderly execution of the cell division cycle at several stages, causing inhibition of DNA replication, defective mitotic exit and failure of chromatin decondensation during the telophase-to-interphase transition in cells that achieve nuclear duplication and chromosome segregation. These results suggest that deregulated RanBP1 activity interferes with the Ran GTPase cycle and prevents the functioning of the Ran signalling system during the cell cycle.

Download Full-text