DOCSLIB.ORG

A Conserved Module in SWI2/SNF2 DNA Damage Tolerance Proteins

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Conserved Module in SWI2/SNF2 DNA Damage Tolerance Proteins J Biomol NMR (2016) 66:209–219 DOI 10.1007/s10858-016-0070-9 ARTICLE Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins 1 2 3 Dmitry M. Korzhnev • Dante Neculai • Sirano Dhe-Paganon • 4,5 1 Cheryl H. Arrowsmith • Irina Bezsonova Received: 30 June 2016 / Accepted: 17 October 2016 / Published online: 22 October 2016 Ó Springer Science+Business Media Dordrecht 2016 Abstract HLTF is a SWI2/SNF2-family ATP-dependent DNA bound form, while the NMR analysis also reveals chromatin remodeling enzyme that acts in the error-free that the DNA binding site of the free domain exhibits branch of DNA damage tolerance (DDT), a cellular conformational heterogeneity. Sequence comparison of mechanism that enables replication of damaged DNA N-terminal regions of HLTF, SHPRH and Rad5 aided by while leaving damage repair for a later time. Human HLTF knowledge of the HLTF HIRAN structure suggests that the and a closely related protein SHPRH, as well as their yeast SHPRH N-terminus also includes an uncharacterized homologue Rad5, are multi-functional enzymes that share structured module, exhibiting weak sequence similarity E3 ubiquitin-ligase activity required for activation of the with HIRAN regions of HLTF and Rad5, and potentially error-free DDT. HLTF and Rad5 also function as ATP- playing a similar functional role. dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped repli- Keywords DNA replication Á DNA damage tolerance Á cation forks into X-shaped Holliday junction structures that Helicase-like transcription factor Á HLTF allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 30-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we Introduction present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organ- Human HLTF (Helicase-Like Transcription Factor) and its isms from bacteria (as a stand-alone domain) to plants, functional homologues, S. cerevisiae Rad5 and human fungi and metazoan (in combination with SWI2/SNF2 SHPRH (SNF2, histone linker, PHD, RING, helicase), are helicase-like domain). The obtained structure of free HLTF SWI2/SNF2-family ATP-dependent chromatin remodeling HIRAN is similar to recently reported structures of its factors that promote error-free DNA damage tolerance (DDT) in eukaryotes (Chang and Cimprich 2009; Unk et al. 2010). To cope with exogenous and endogenous DNA & Irina Bezsonova damage that creates DNA replication blocks, cells have [email protected] evolved DDT mechanisms that enable bypass replication 1 Department of Molecular Biology and Biophysics, University over sites of DNA damage lesions (Chang and Cimprich of Connecticut Health, Farmington, CT 06030, USA 2009; Waters et al. 2009; Unk et al. 2010; Sale et al. 2012). 2 School of Medicine, Zhejiang University, Hangzhou, China The error-prone branch of DDT, which involves DNA lesion bypass by mutagenic translesion synthesis (TLS) 3 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA DNA polymerases (Waters et al. 2009; Sale et al. 2012), is activated by mono-ubiquitination of the DNA-sliding 4 Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada clamp PCNA by the Rad6/Rad18 E2/E3 enzyme pair (Hoege et al. 2002). Subsequently, the error-free DDT that 5 Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, utilizes a template switching mechanism can be activated ON M5S 1A8, Canada by K63-polyubiquitination of PCNA catalyzed by the 123 210 J Biomol NMR (2016) 66:209–219 RING E3 ligases HLTF, SHPRH or Rad5 and the Ubc13/ predicted to recognize DNA features at stalled replication Mms2 E2 conjugating enzyme (Motegi et al. 2006, 2008; forks such as ssDNA stretches or DNA lesions (Iyer et al. Unk et al. 2006, 2008, 2010; Chang and Cimprich 2009). 2006). Although the HIRAN domain was also found in S. One possible mechanism of the error-free DDT is cerevisiae Rad5, this module is reportedly lacking in the replication fork reversal that involves conversion of a HLTF’s human homologue SHPRH (Unk et al. Y-shaped DNA structure into an X-shaped four-way Hol- 2008, 2010). liday junction structure with one arm composed of the Recently, we and others have demonstrated that the newly synthesized daughter DNA strands annealed against HLTF HIRAN domain is involved in 30 ssDNA end one another (Chang and Cimprich 2009; Unk et al. 2010). recognition at replication forks and is required for fork Such a ‘chicken foot’ intermediate allows switching DNA reversal, but not for other activities of HLTF (Achar et al. synthesis blocked by DNA damage from the lesion-con- 2015; Hishiki et al. 2015; Kile et al. 2015). These works taining strand to the undamaged template newly synthe- have also reported structures of the HLTF HIRAN domain sized at the complementary DNA strand. Beyond serving in complexes with DNA substrates revealing structural as E3 ligases that polyubiquitinate PCNA and trigger basis of the 30 DNA end recognition. Here we complement switching to the error-free DDT (Motegi et al. 2006, 2008; these studies by reporting a high-resolution structure of the Unk et al. 2006, 2008), HLTF and Rad5 function as ATP- free HIRAN domain from human HLTF determined by dependent dsDNA translocases and can catalyze replica- solution NMR spectroscopy. Based on the obtained struc- tion fork reversal into a Holliday-like structure (Blastyak ture and sequence alignment of the N-terminal regions of et al. 2007, 2010). The fork reversal activity, however, has HLTF, SHPRH and Rad5 we predict that the N-terminal not yet been demonstrated for SHPRH. region of human SHPRH preceding the core helicase-like The core helicase-like domains of HLTF, SHPRH and domain also includes yet uncharacterized structured mod- Rad5 consist of the two recA-like domains and share ule, exhibiting weak sequence similarity with HIRAN SWI2/SNF2 architectures, featuring seven conserved heli- regions of HLTF and Rad5. These findings highlight a case motifs (Thoma et al. 2005; Flaus et al. 2006). The potential conserved role of the N-terminal regions of helicase motifs are separated by the two (‘minor’ and SWI2/SNF2 chromatin remodeling enzymes in mediating ‘major’) insert regions that may include additional domains error-free DNA damage tolerance. embedded into a core domain (Flaus et al. 2006). The ‘major’ insert regions of HLTF, SHPRH and Rad5 harbor RING-finger domains characteristic of the E3 ubiquitin Materials and Methods ligases, while the ‘minor’ insert region of SHPRH also includes H1.5 and PHD finger domains. Such a discontin- Protein sample preparation uous arrangement complicates structural studies of SWI2/ SNF2 DDT enzymes; at this time, the only structure 15N/13C labeled human HLTF HIRAN (residues 50–171) available from the core helicase-like regions is that of PHD was expressed in BL21 (DE3) E. coli cells transformed domain embedded in the ‘minor’ insert region of human with pET28a-LIC based plasmid encoding the domain SHPRH (Machado et al. 2013). (Addgene plasmid # 28152). Cells were grown in minimal 15 13 HLTF, also called HIP116, SMARCA3 and other M9 medium supplemented with NH4Cl and C-glucose alternative names, was first identified as a transcription as sole nitrogen and carbon sources, respectively. The factor for plasminogen activator inhibitor 1 (PAI-1) (Ding protein was affinity purified on a Ni–NTA agarose beads et al. 1996, 1999) and b-globin genes (Mahajan and (GE Healthcare), followed by cleavage of a hexahistidine Weissman 2002) capable of binding specific DNA target tag by Thrombin (MP Biomedicals) and a second purifi- sequences (Sheridan et al. 1995; Ding et al. 1996, 1999; cation step on a size-exclusion Superdex 75 HiLoad 16/60 Mahajan and Weissman 2002). In these original studies, chromatography column (GE Healthcare). The final NMR the DNA-binding region of HLTF was mapped to its sample of the free HIRAN domain contained 1.0 mM N-terminal part encompassing residues 38–219 (Sheridan protein, 20 mM sodium phosphate pH 6.8, 100 mM NaCl, et al. 1995; Ding et al. 1996) preceding the core helicase- 2 mM DTT and 10 % v/v D2O. like domain. Later, this N-terminal region was shown to include a standalone b-strand rich domain conserved in NMR spectroscopy and protein structure calculation eukaryotic SWI2/SNF2 DNA-dependent ATPases dubbed as HIRAN (HIP116, Rad5p N-terminal domain) (Iyer et al. The backbone and side-chain 15N, 13C and 1H NMR res- 2006). This domain was also found as a standalone protein onance assignments of the HLTF HIRAN domain were in a range of bacteria (Iyer et al. 2006). Based on its obtained from a set of 2D 1H–15N HSQC, 1H–13C HSQC contextual information network, the HIRAN domain was and 3D HNCA, HNCACB, HNCO, HBHA(CO)NH, 123 J Biomol NMR (2016) 66:209–219 211 15 13 HC(C)H-TOCSY, (H)CCH-TOCSY and N- and C- Table 1 Summary of NMR-based restrains used for structure cal- edited NOESY-HSQC (150 ms mixing time) spectra (Kay culation of the human HLTF HIRAN domain and structure refinement 1995, 1997; Kanelis et al. 2001) collected at 25 °C on the statistics Agilent VNMRS 800 MHz spectrometer equipped with a Summary of restraints cold probe. NMR spectra were processed with NMRPipe NOE distance restraints (Delaglio et al. 1995) and analyzed with Sparky software Short range (|i - j| B 1) 1186 (Goddard and Kneller), resulting in 86 % assignment of all Medium range (1 \ |i - j| \ 5) 387 expected NMR chemical shifts, including 98 % of back- Long range (|i - j| C 5) 770 bone, 82 % of aliphatic and 53 % of aromatic side-chain.
Load more

Recommended publications
  • UBE2N Antibody (N-Term) Blocking Peptide Synthetic Peptide Catalog # Bp13846a
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 UBE2N Antibody (N-term) Blocking peptide Synthetic peptide Catalog # BP13846a Specification UBE2N Antibody (N-term) Blocking UBE2N Antibody (N-term) Blocking peptide - peptide - Background Product Information The modification of proteins with ubiquitin is Primary Accession P61088 animportant cellular mechanism for targeting abnormal or short-livedproteins for degradation. Ubiquitination involves at least UBE2N Antibody (N-term) Blocking peptide - Additional Information threeclasses of enzymes: ubiquitin-activating enzymes, or E1s,ubiquitin-conjugating enzymes, or E2s, and ubiquitin-proteinligases, Gene ID 7334 or E3s. This gene encodes a member of the E2ubiquitin-conjugating enzyme family. Other Names Studies in mouse suggest thatthis protein plays Ubiquitin-conjugating enzyme E2 N, a role in DNA postreplication repair. Bendless-like ubiquitin-conjugating enzyme, [providedby RefSeq]. Ubc13, UbcH13, Ubiquitin carrier protein N, Ubiquitin-protein ligase N, UBE2N, BLU UBE2N Antibody (N-term) Blocking Target/Specificity peptide - References The synthetic peptide sequence used to generate the antibody AP13846a was Zhao, J., et al. BMC Med. Genet. 11, 96 (2010) selected from the N-term region of UBE2N. :Markson, G., et al. Genome Res. A 10 to 100 fold molar excess to antibody is 19(10):1905-1911(2009)Topisirovic, I., et al. recommended. Precise conditions should be Proc. Natl. Acad. Sci. U.S.A. optimized for a particular assay. 106(31):12676-12681(2009)Yin, Q., et al. Nat. Struct. Mol. Biol. 16(6):658-666(2009)van Wijk, Format S.J., et al. Mol. Syst. Biol. 5, 295 (2009) : Peptides are lyophilized in a solid powder format.
    [Show full text]
  • Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass
    cancers Review Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass Nicole A. Wilkinson y, Katherine S. Mnuskin y, Nicholas W. Ashton * and Roger Woodgate * Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA; [email protected] (N.A.W.); [email protected] (K.S.M.) * Correspondence: [email protected] (N.W.A.); [email protected] (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.) Co-first authors. y Received: 29 August 2020; Accepted: 29 September 2020; Published: 2 October 2020 Simple Summary: Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract: Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs).
    [Show full text]
  • Identification and Characterisation of Human Cytomegalovirus-Mediated Degradation of Helicase-Like Transcription Factor
    Identification and Characterisation of Human Cytomegalovirus-Mediated Degradation of Helicase-Like Transcription Factor Kai-Min Lin Department of Medicine Cambridge Institute for Medical Research University of Cambridge This dissertation is submitted for the degree of Doctor of Philosophy Fitzwilliam College September 2020 Declaration I hereby declare, that except where specific reference is made to the work of others, the contents of this dissertation are original and have not been submitted in whole or in part for consideration for any other degree of qualification in this, or any other university. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except as where specified in the text and acknowledgments. This dissertation does not exceed the specified word limit of 60,000 words as defined by the Degree Committee, excluding figures, photographs, tables, appendices and bibliography. Kai-Min Lin September, 2020 I Summary Identification and characterisation of human cytomegalovirus-mediated degradation of helicase-like transcription factor Kai-Min Lin Viruses are known to degrade host factors that are important in innate antiviral immunity in order to infect successfully. To systematically identify host proteins targeted for early degradation by human cytomegalovirus (HCMV), the lab developed orthogonal screens using high resolution multiplexed mass spectrometry. Taking advantage of broad and selective proteasome and lysosome inhibitors, proteasomal degradation was found to be heavily exploited by HCMV. Several known antiviral restriction factors, including components of cellular promyelocytic leukemia (PML) were enriched in a shortlist of proteasomally degraded proteins during infection. A particularly robust novel ‘hit’ was helicase-like transcription factor (HLTF), a DNA repair protein that participates in error-free repair of stalled replication forks.
    [Show full text]
  • Loss of HLTF Function Promotes Intestinal Carcinogenesis Sumit Sandhu1, Xiaoli Wu1, Zinnatun Nabi1, Mojgan Rastegar1,3,4, Sam Kung3, Sabine Mai1,2 and Hao Ding1*
    Sandhu et al. Molecular Cancer 2012, 11:18 http://www.molecular-cancer.com/content/11/1/18 RESEARCH Open Access Loss of HLTF function promotes intestinal carcinogenesis Sumit Sandhu1, Xiaoli Wu1, Zinnatun Nabi1, Mojgan Rastegar1,3,4, Sam Kung3, Sabine Mai1,2 and Hao Ding1* Abstract Background: HLTF (Helicase-like Transcription Factor) is a DNA helicase protein homologous to the SWI/SNF family involved in the maintenance of genomic stability and the regulation of gene expression. HLTF has also been found to be frequently inactivated by promoter hypermethylation in human colon cancers. Whether this epigenetic event is required for intestinal carcinogenesis is unknown. Results: To address the role of loss of HLTF function in the development of intestinal cancer, we generated Hltf deficient mice. These mutant mice showed normal development, and did not develop intestinal tumors, indicating that loss of Hltf function by itself is insufficient to induce the formation of intestinal cancer. On the Apcmin/+ mutant background, Hltf- deficiency was found to significantly increase the formation of intestinal adenocarcinoma and colon cancers. Cytogenetic analysis of colon tumor cells from Hltf -/-/Apcmin/+ mice revealed a high incidence of gross chromosomal instabilities, including Robertsonian fusions, chromosomal fragments and aneuploidy. None of these genetic alterations were observed in the colon tumor cells derived from Apcmin/+ mice. Increased tumor growth and genomic instability was also demonstrated in HCT116 human colon cancer cells in which HLTF expression was significantly decreased. Conclusion: Taken together, our results demonstrate that loss of HLTF function promotes the malignant transformation of intestinal or colonic adenomas to carcinomas by inducing genomic instability.
    [Show full text]
  • Lymph Node Metastasis Is Infrequent in Patients with Highly-Methylated Colorectal Cancer
    ANTICANCER RESEARCH 26: 55-58 (2006) Lymph Node Metastasis is Infrequent in Patients with Highly-methylated Colorectal Cancer KENJI HIBI1 and AKIMASA NAKAO2 1Department of Surgery, Seirei Hospital, 56 Kawanayama-machi, Showa-ku, Nagoya 466-8633; 2Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan Abstract. In this study, the combined methylation status of p16, was found to harbor promoter hypermethylation p16, p14, HLTF, CDH13 and RUNX3 was examined in 59 associated with the loss of protein expression in cancer cells resected primary colorectal cancers using methylation-specific (7). Though homozygous deletions of the p16 locus were not PCR and the methylation status was correlated with the present (8), p16 promoter methylation was detected in clinicopathological features of the affected patients. A colorectal cancer (9). Subsequently, it has been found that significant difference was found in lymph node metastasis human p14 was also silenced by promoter hypermethylation (p=0.0359) on comparing the methylation status in in colorectal cancer (10). p14 interacts with the MDM2 colorectal cancers with lymph node metastasis to those protein and neutralizes the MDM2-mediated degradation without. There was also a significant gender difference of p53. Thus, p14 acts as a tumor suppressor gene via (p=0.0248) when the methylation status was compared. inhibition of p53 degradation. These studies indicated that Colorectal cancer without lymph node metastasis frequently p16 and p14 inactivation due to promoter methylation was exhibited aberrant methylation of the p16, p14, HLTF, important for colorectal tumorigenesis. We previously CDH13 and RUNX3 genes. examined the methylation status of these genes in 86 primary colorectal cancers using methylation-specific PCR There is now strong evidence that a series of genetic (MSP) (11).
    [Show full text]
  • Fission Yeast Rad8/HLTF Facilitates Rad52-Dependent Chromosomal
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.05.425428; this version posted January 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Fission yeast Rad8/HLTF facilitates Rad52-dependent 2 chromosomal rearrangements through PCNA lysine 107 3 ubiquitination 4 5 Jie Su, Naoko Toyofuku, Takuro Nakagawa * 6 Department of Biological Sciences, Graduate School of Science, Osaka University, Japan 7 *For correspondence: [email protected] 8 9 10 Abstract 11 Rad52 recombinase can cause gross chromosomal rearrangements (GCRs). However, the 12 mechanism of Rad52-dependent GCRs remains unclear. Here, we show that fission yeast 13 Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) 14 of PCNA, a DNA sliding clamp. Loss of Rad8 reduced isochromosomes resulting from 15 centromere inverted repeat recombination. Rad8 HIRAN and RING finger mutations reduced 16 GCRs, suggesting that Rad8 facilitates GCRs through 3' DNA-end binding and ubiquitin ligase 17 activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating proteins were required for GCRs. 18 Consistent with this, PCNA K107R but not K164R mutation greatly reduced GCRs. Rad8- 19 dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, 20 rad8, and rad52 mutations epistatically reduced GCRs. Remarkably, K107 is located at the 21 interface between PCNA subunits, and an interface mutation D150E bypassed the requirement 22 of PCNA K107 ubiquitination for GCRs.
    [Show full text]
  • UBE2N Antibody Order 021-34695924 [email protected] Support 400-6123-828 50Ul [email protected] 100 Ul √ √ Web
    TD8193 UBE2N Antibody Order 021-34695924 [email protected] Support 400-6123-828 50ul [email protected] 100 uL √ √ Web www.ab-mart.com.cn Description: The UBE2V1-UBE2N and UBE2V2-UBE2N heterodimers catalyze the synthesis of non- canonical 'Lys-63'-linked polyubiquitin chains. This type of polyubiquitination does not lead to protein degradation by the proteasome. Mediates transcriptional activation of target genes. Plays a role in the control of progress through the cell cycle and differentiation. Plays a role in the error-free DNA repair pathway and contributes to the survival of cells after DNA damage. Acts together with the E3 ligases, HLTF and SHPRH, in the 'Lys-63'- linked poly-ubiquitination of PCNA upon genotoxic stress, which is required for DNA repair. Appears to act together with E3 ligase RNF5 in the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD. Promotes TRIM5 capsid-specific restriction activity and the UBE2V1-UBE2N heterodimer acts in concert with TRIM5 to generate 'Lys-63'-linked polyubiquitin chains which activate the MAP3K7/TAK1 complex which in turn results in the induction and expression of NF-kappa-B and MAPK-responsive inflammatory genes. Together with RNF135 and UB2V1, catalyzes the viral RNA-dependent 'Lys-63'-linked polyubiquitination of RIG-I/DDX58 to activate the downstream signaling pathway that leads to interferon beta production. Uniprot:P61088 Alternative Names： Bendless like ubiquitin conjugating enzyme;
    [Show full text]
  • Highly-Methylated Colorectal Cancers Show Poorly-Differentiated Phenotype
    ANTICANCER RESEARCH 26: 4263-4266 (2006) Highly-methylated Colorectal Cancers Show Poorly-differentiated Phenotype KENJI HIBI1,2 and AKIMASA NAKAO2 1Department of Surgery, Showa University Fujigaoka Hospital, 1-30 Fujigaoka, Aoba-ku, Yokohama 227-8501; 2Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan Abstract. The combined methylation status of p16, p14, HLTF, human p14 was also silenced by promoter hypermethylation SOCS-1, CDH13, RUNX3 and CHFR was examined in 58 in colorectal cancer (10). p14 interacts with the MDM2 resected primary colorectal cancers using methylation-specific protein and neutralizes the MDM2-mediated degradation of PCR, and the methylation status was correlated with the p53. Thus, p14 acts as a tumor suppressor gene via inhibition clinicopathological features of the affected patients. A significant of p53 degradation. These studies indicated that p16 and p14 difference in histology (p=0.0041) was observed when the number inactivation due to promoter methylation was important for of methylated genes of poorly-differentiated colorectal cancers was colorectal tumorigenesis. We previously examined the compared to that of other differentiated ones. Poorly-differentiated methylation status of these genes in 86 primary colorectal colorectal cancers preferentially exhibited gene methylation. cancers using methylation-specific PCR (MSP) (11). Aberrant promoter methylation of p16 and p14 genes was detected in There is now strong evidence that a series of genetic 43 out of 86 (50 %) and 25 out of 86 (29%) colorectal cancer alterations in both dominant oncogenes and tumor suppressor specimens, respectively. genes are involved in the pathogenesis of human colorectal The loss of expression of a helicase-like transcription factor cancer.
    [Show full text]
  • Temporal Epigenomic Profiling Identifies AHR As a Dynamic Super-Enhancer Controlled Regulator of Mesenchymal Multipotency
    bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Gerard et al.: Time-series epigenomic profiles of mesenchymal differentiation 1 Temporal epigenomic profiling identifies AHR as a 2 dynamic super-enhancer controlled regulator of 3 mesenchymal multipotency 4 Deborah Gérard1, Florian Schmidt2,3, Aurélien Ginolhac1, Martine Schmitz1, 5 Rashi Halder4, Peter Ebert3, Marcel H. Schulz2,3, Thomas Sauter1 and Lasse 6 Sinkkonen1* 7 1Life Sciences Research Unit, University of Luxembourg, L-4367 Belvaux, 8 Luxembourg 9 2Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics 10 Campus, Germany 11 3Computational Biology & Applied Algorithmics, Max Planck Institute for 12 Informatics, Saarland Informatics Campus, Germany 13 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur- 14 Alzette, L-4362, Luxembourg 15 16 [email protected]; [email protected]; [email protected]; 17 [email protected]; [email protected]; [email protected]; 18 [email protected]; [email protected]; [email protected] 19 20 *Corresponding author: Dr. Lasse Sinkkonen 21 Life Sciences Research Unit, University of Luxembourg 22 6, Avenue du Swing, L-4367 Belvaux, Luxembourg 23 Tel.: +352-4666446839 24 E-mail: [email protected] 25 1 bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017.
    [Show full text]
  • The Role of SMARCAD1 During Replication Stress Sarah Joseph
    The role of SMARCAD1 during replication stress Sarah Joseph Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2020 © 2020 Sarah Joseph All Rights Reserved Abstract The role of SMARCAD1 during replication stress Sarah Joseph Heterozygous mutations in BRCA1 or BRCA2 predispose carriers to an increased risk for breast or ovarian cancer. Both BRCA1 and BRCA2 (BRCA1/2) play an integral role in promoting genomic stability through their respective actions during homologous recombination (HR) mediated repair and stalled replication fork protection from nucleolytic degradation. SMARCAD1 (SD1) is a SWI/SNF chromatin remodeler that has been implicated in promoting long-range end resection and contributes to HR. Using human cell lines, we show that SMARCAD1 promotes nucleolytic degradation in BRCA1/2-deficient cells dependent on its chromatin remodeling activity. Moreover, SMARCAD1 prevents DNA break formation and promotes fork restart at stalled replication forks. These studies identify a new role for SMARCAD1 at the replication fork. In addition to the work presented here, I discuss a method for introducing stop codons (nonsense mutations) into genes using CRISPR-mediated base editing, called iSTOP, and provide an online resource for accessing the sequence of iSTOP sgRNASs (sgSTOPs) for five base editor variants (VQR-BE3, EQR-BE3, VRER-BE3, SaBE3, and SaKKH-BE3) in humans and over 3 million targetable gene coordinates for eight eukaryotic species. Ultimately, with improvements to CRISPR base editors this method can help model and study nonsense mutations in human disease. Table of Contents List of Figures .................................................................................................................
    [Show full text]
  • Gene Section Review
    Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review HLTF (helicase-like transcription factor) Ludovic Dhont, Alexandra Belayew Molecular Biology, Health Institute, University of Mons, Mons, Belgium. [email protected] Published in Atlas Database: November 2016 Online updated version : http://AtlasGeneticsOncology.org/Genes/HLTFID42332ch3q24.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/68527/11-2016-HLTFID42332ch3q24.pdf DOI: 10.4267/2042/68527 This article is an update of : HLTF (helicase-like transcription factor). Atlas Genet Cytogenet Oncol Haematol Dimitrova J, Belayew A. HLTF (helicase-like transcription factor). Atlas Genet Cytogenet Oncol Haematol 2010;14(10) This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract domains involved in DNA repair. HLTF is a transcription factor - The Helicase-Like These data support a role of tumor suppressor gene Transcription Factor (HLTF/SMARCA3) belongs to for HLTF. the family of SWI/SNF proteins that use the energy The first association between HLTF inactivation and of ATP hydrolysis to remodel chromatin in a variety tumorigenesis was shown when hypermethylation of of cellular processes. the HLTF promoter was detected in 43% of primary Several groups independently isolated HLTF colon tumors and 22-55% of gastric cancers. through its capacity to selectively interact with a Moreover, HLTF deficiency in Apc-/+ mice induced DNA cis-element in the promoter or enhancer of the transition from colon adenocarcinoma to a different genes involved in cardiac development carcinoma with high chromosomal instability.
    [Show full text]
  • Methylation of Serum DNA Is an Independent Prognostic Marker In
    Imaging, Diagnosis, Prognosis Methylation of Serum DNA Is an Independent Prognostic Marker in Colorectal Cancer Maike Wallner,1Andreas Herbst,1Andrea Behrens,1Alexander Crispin,2 Petra Stieber,3 Burkhard Go« ke,1RolfLamerz, 1and Frank T. Kolligs1 Abstract Purpose: Aberrant CpG island hypermethylation is a feature of a subgroup of colorectal cancers, which can be detected in the serum ofaffected patients. This study was designed to identify methylation targets with prognostic significance in the serum of patients with colorectal cancer. Experimental Design: In a gene evaluation set consisting ofsera from 24 patients with local colorectal cancers, 14 with metastasized disease, and 20 healthy controls, the genes HPP1/TPEF, HLTF,andhMLH1were identified as potential serum DNA methylation markers.These genes were further analyzed in a test set of sera of 104 patients with colorectal cancer. Results: Methylation of HLTF, HPP1/TPEF,andhMLH1 was found to be significantly correlated with tumor size, and methylation of HLTF and HPP1/TPEF was significantly associated with metastatic disease and tumor stage. Moreover, methylation of HPP1/TPEF was also associated with serum carcinoembryonic antigen. The prognostic relevance ofmethylation ofthese genes was tested in pretherapeutic sera of77 patients with known follow-up. Patients with methylation of HPP1/TPEF or HLTF were found to have unfavorable prognosis (P = 0.001 and 0.008). In contrast, serum methylation of hMLH1was not associated with a higher risk ofdeath. Multivariate analysis showed methylated HPP1 and/or HLTF serum DNA to be independently associated with poor outcome and a relative risk ofdeath of3.4 (95% confidence interval, 1.4-8.1; P = 0.007).
    [Show full text]