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Taka JRH, Sun Y, Goldstone DC. Mapping the interaction between Trim28 and the
KRAB
domain at the center of Trim28 silencing of endogenous retroviruses. Protein Sci 2022; 31:e4436. [PMID: 36173157 PMCID: PMC9601868 DOI: 10.1002/pro.4436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022]
Abstract
Transcription of endogenous retroviral elements are tightly regulated during development by members of the KRAB‐containing zinc finger proteins (KRAB‐ZFPs) and the co‐repressor Trim28 (also known as Kap‐1 or Tif1β). KRAB‐ZFPs form the largest family of transcription regulators in mammals and initiate transcriptional silencing by tethering Trim28 to a target locus. Subsequently, Trim28 recruits chromatin modifying effectors resulting in the formation of heterochromatin. In the present study, we identify surface exposed residues on the central six turns of the Trim28 coiled‐coil region forming the binding interface for the KRAB domain. Using AlphaFold2 (AF2) we provide high confidence models of the interface between Trim28 and the KRAB domain and identified leucine 301 on each chain of the Trim28 monomer to act as a pin extending into a hydrophobic pocket on the KRAB domain surface. Site directed mutations in the Trim28‐KRAB binding interface abolished binding to the KRAB domain. Our work provides a detailed understanding of the specific interactions between the KRAB domain and the Trim28 coiled‐coil and how this interaction may be regulated during silencing events.
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Affiliation(s)
- Jamie R. H. Taka
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Yunyuan Sun
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - David C. Goldstone
- School of Biological Sciences University of Auckland Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery Auckland New Zealand
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2
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Zhou YH, Gallins PJ, Etheridge AS, Jima D, Scholl E, Wright FA, Innocenti F. A resource for integrated genomic analysis of the human liver. Sci Rep 2022; 12:15151. [PMID: 36071064 PMCID: PMC9452507 DOI: 10.1038/s41598-022-18506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we generated whole-transcriptome RNA-Seq from n = 192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq) and previous liver eQTL (microarray) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response. The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.
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Affiliation(s)
- Yi-Hui Zhou
- Department of Biological Sciences, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA.
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Amy S Etheridge
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Elizabeth Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
- Department of Statistics, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.
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3
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Mariot V, Dumonceaux J. Gene Editing to Tackle Facioscapulohumeral Muscular Dystrophy. Front Genome Ed 2022; 4:937879. [PMID: 35910413 PMCID: PMC9334676 DOI: 10.3389/fgeed.2022.937879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is a skeletal muscle disease caused by the aberrant expression of the DUX4 gene in the muscle tissue. To date, different therapeutic approaches have been proposed, targeting DUX4 at the DNA, RNA or protein levels. The recent development of the clustered regularly interspaced short-palindromic repeat (CRISPR) based technology opened new avenues of research, and FSHD is no exception. For the first time, a cure for genetic muscular diseases can be considered. Here, we describe CRISPR-based strategies that are currently being investigated for FSHD. The different approaches include the epigenome editing targeting the DUX4 gene and its promoter, gene editing targeting the polyadenylation of DUX4 using TALEN, CRISPR/cas9 or adenine base editing and the CRISPR-Cas9 genome editing for SMCHD1. We also discuss challenges facing the development of these gene editing based therapeutics.
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Affiliation(s)
- Virginie Mariot
- NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, University College London, London, United Kingdom
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, University College London, London, United Kingdom
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Li C, Xia P, Ma Y, Zhang X, Liu Y. Expression pattern of ZNF33B in bovine ovaries and the effect of its polymorphism on superovulation traits. Arch Anim Breed 2022; 65:69-77. [PMID: 35252544 PMCID: PMC8889308 DOI: 10.5194/aab-65-69-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/24/2022] [Indexed: 11/11/2022] Open
Abstract
ZNF33B belongs to recently duplicated Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs), which
is widely present in various organs, and some evidence showed that its
expression is altered in the ovary undergoing superovulation. In this study,
the expression of ZNF33B in ovary and early embryo was determined by
immunohistochemistry and immunofluorescence techniques. Results showed that
the expression of ZNF33B in the ovary was mainly in the cytoplasm of oocytes
and granulosa luteal cells of ovarian corpus luteum and significantly
reduced during follicular ovulation to luteal degeneration. The expression
of ZNF33B in the early embryo transferred from the nucleus to the whole
cell, suggesting that the expression of ZNF33B is spatiotemporally specific.
Then, in combination with the single nucleotide polymorphism (SNP) database, the g.-61G>T mutant
of the 5′-untranslated region (5′ UTR) of the ZNF33B gene was screened out from 556
Changbaishan black cattle, and the frequency of the mutant gene was counted.
The statistics of superovulation and superovulation traits confirmed
significant differences between the two genotypes in the quantity and
quality of oocytes obtained after superovulation. This study confirmed, for
the first time, the effect of ZNF33B gene polymorphism on superovulation
traits and suggested that the mutation could provide a basis for cattle
breeding and improving animal fertility.
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Affiliation(s)
- Changhong Li
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun, Jilin, China
| | - Yijuan Ma
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Xinyue Zhang
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Yijia Liu
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
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Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma. Proc Natl Acad Sci U S A 2011; 108:8212-7. [PMID: 21531907 DOI: 10.1073/pnas.1101544108] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
TRIM24 (TIF1α), TRIM28 (TIF1β), and TRIM33 (TIF1γ) are three related cofactors belonging to the tripartite motif superfamily that interact with distinct transcription factors. TRIM24 interacts with the liganded retinoic acid (RA) receptor to repress its transcriptional activity. Germ line inactivation of TRIM24 in mice deregulates RA-signaling in hepatocytes leading to the development of hepatocellular carcinoma (HCC). Here we show that TRIM24 can be purified as at least two macromolecular complexes comprising either TRIM33 or TRIM33 and TRIM28. Somatic hepatocyte-specific inactivation of TRIM24, TRIM28, or TRIM33 all promote HCC in a cell-autonomous manner in mice. Moreover, HCC formation upon TRIM24 inactivation is strongly potentiated by further loss of TRIM33. These results demonstrate that the TIF1-related subfamily of TRIM proteins interact both physically and functionally to modulate HCC formation in mice.
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Abstract
The cis-acting regulatory sequences of imprinted gene loci, called imprinting control regions (ICRs), acquire specific imprint marks in germ cells, including DNA methylation. These epigenetic imprints ensure that imprinted genes are expressed exclusively from either the paternal or the maternal allele in offspring. The last few years have witnessed a rapid increase in studies on how and when ICRs become marked by and subsequently maintain such epigenetic modifications. These novel findings are summarised in this review, which focuses on the germline acquisition of DNA methylation imprints and particularly on the combined role of primary sequence specificity, chromatin configuration, non-histone proteins and transcriptional events.
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West JT, Wood C. The role of Kaposi's sarcoma-associated herpesvirus/human herpesvirus-8 regulator of transcription activation (RTA) in control of gene expression. Oncogene 2003; 22:5150-63. [PMID: 12910252 DOI: 10.1038/sj.onc.1206555] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mechanisms that control the replication state, latency versus lytic, of human herpesviruses have been under intense investigations. Here we summarize some of the recent findings that help define such mechanisms for Kaposi's sarcoma-associated herpesvirus/human herpesvirus type 8 (KSHV/HHV-8). For HHV-8, the viral regulator of transcription activation (RTA) is a key mediator of the switch from latency to lytic gene expression in infected cells. RTA is necessary and sufficient to drive HHV-8 lytic replication and the production of viral progeny. The RTA is an immediate-early gene product, it is the initial activator of expression of a multitude of viral and cellular genes that have been implicated in the replication of HHV-8 and pathogenesis of KS. Interactions of RTA with a number of viral promoters, and with a number of transcription factors or transcriptional co-activators are highlighted. Modulation of transactivation, through alternate RTA-protein, or RTA-promoter interactions, is hypothesized to participate in the selective tissue tropism and differential pathogenesis observed in KS.
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Affiliation(s)
- John T West
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska, Lincoln, 1901 Vine Street, Lincoln, NE 68588, USA
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