51
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The Drosophila CLAMP protein associates with diverse proteins on chromatin. PLoS One 2017; 12:e0189772. [PMID: 29281702 PMCID: PMC5744976 DOI: 10.1371/journal.pone.0189772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/13/2017] [Indexed: 11/29/2022] Open
Abstract
Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that regulates chromatin accessibility at promoters genome-wide. To identify associations between CLAMP and other factors in both male and female cells, we used two complementary mass spectrometry approaches. We demonstrate that CLAMP associates with the transcriptional regulator complex Negative Elongation Factor (NELF) in both sexes and determine that CLAMP reduces NELF recruitment to several target genes. In sum, we have identified many new CLAMP-associated factors and provide a resource for further study of this little understood essential protein.
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52
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Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, Adelman K, Tolstorukov M, Larschan E. Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS One 2017; 12:e0186855. [PMID: 29077765 PMCID: PMC5659772 DOI: 10.1371/journal.pone.0186855] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes. Here, we demonstrate that the non-sex-specific CLAMP (Chromatin-linked adaptor for MSL proteins) zinc finger protein that recognizes GA-rich sequences genome-wide promotes the specialized chromatin environment on the male X-chromosome and can act over long genomic distances (~14 kb). Although MSL complex is required for increasing transcript levels of X-linked genes, it is not required for enhancing global male X-chromosome chromatin accessibility, and instead works cooperatively with CLAMP to facilitate an accessible chromatin configuration at its sites of highest occupancy. Furthermore, CLAMP regulates chromatin structure at strong MSL complex binding sites through promoting recruitment of the Nucleosome Remodeling Factor (NURF) complex. In contrast to the X-chromosome, CLAMP regulates chromatin and gene expression on autosomes through a distinct mechanism that does not involve NURF recruitment. Overall, our results support a model where synergy between a non-sex-specific transcription factor (CLAMP) and a sex-specific cofactor (MSL) creates a specialized chromatin domain on the male X-chromosome.
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Affiliation(s)
- Jennifer Urban
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sarah Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Robert Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Michael Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MT); (EL)
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (MT); (EL)
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53
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. Mol Cell 2017; 68:491-503.e5. [PMID: 29056321 DOI: 10.1016/j.molcel.2017.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 11/21/2022]
Abstract
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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54
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Drosophila Dosage Compensation Loci Associate with a Boundary-Forming Insulator Complex. Mol Cell Biol 2017; 37:MCB.00253-17. [PMID: 28784719 DOI: 10.1128/mcb.00253-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
Chromatin entry sites (CES) are 100- to 1,500-bp elements that recruit male-specific lethal (MSL) complexes to the X chromosome to upregulate expression of X-linked genes in male flies. CES contain one or more ∼20-bp GA-rich sequences called MSL recognition elements (MREs) that are critical for dosage compensation. Recent studies indicate that CES also correspond to boundaries of X-chromosomal topologically associated domains (TADs). Here, we show that an ∼1,000-kDa complex called the late boundary complex (LBC), which is required for the functioning of the Bithorax complex boundary Fab-7, interacts specifically with a special class of CES that contain multiple MREs. Mutations in the MRE sequences of three of these CES that disrupt function in vivo abrogate interactions with the LBC. Moreover, reducing the levels of two LBC components compromises MSL recruitment. Finally, we show that several of the CES that are physically linked to each other in vivo are LBC interactors.
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55
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Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response. PLoS One 2017; 12:e0186435. [PMID: 29028826 PMCID: PMC5640250 DOI: 10.1371/journal.pone.0186435] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/29/2017] [Indexed: 01/26/2023] Open
Abstract
The innate immune response of Anopheles gambiae involves the transcriptional upregulation of effector genes. Therefore, the cis-regulatory sequences and their cognate binding factors play essential roles in the mosquito’s immune response. However, the genetic control of the mosquito’s innate immune response is not yet fully understood. To gain further insight on the elements, the factors and the potential mechanisms involved, an open chromatin profiling was carried out on A. gambiae-derived immune-responsive cells. Here, we report the identification of cis-regulatory sites, immunity-related transcription factor binding sites, and cis-regulatory modules. A de novo motif discovery carried out on this set of cis-regulatory sequences identified immunity-related motifs and cis-regulatory modules. These modules contain motifs that are similar to binding sites for REL-, STAT-, lola- and Deaf1-type transcription factors. Sequence motifs similar to the binding sites for GAGA were found within a cis-regulatory module, together with immunity-related transcription factor binding sites. The presence of Deaf1- and lola-type binding sites, along with REL- and STAT-type binding sites, suggests that the immunity function of these two factors could have been conserved both in Drosophila and Anopheles gambiae.
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56
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Li W, Zhang H, Qi S, Qin J, Guan H, Li J, An X, Du R. Molecular Cloning and Motif Identification of the Sheep Musclin Gene Promoter. DNA Cell Biol 2017; 36:1093-1098. [PMID: 28981327 DOI: 10.1089/dna.2017.3762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Musclin is a bioactive factor that functions in regulating the muscle growth and metabolism. To investigate the transcriptional regulatory mechanism of the gene, the 1.4 kb musclin promoter in sheep was cloned (GenBank accession: JX966391) and the sequence was analyzed to predict the motifs associated with muscle growth. Next the enhanced green fluorescent protein (EGFP) was selected as the reporter gene and various wild-type and motif-mutant vectors were constructed. The transcriptional regulatory activities were compared by observing the fluorescence strength and detecting the EGFP mRNA expression in C2C12 myoblasts transfected with the vectors. The results showed that the different lengths of promoters could drive the transcription of EGFP and the mutation of some motifs up- or downregulated the activity of the promoter. Furthermore, the electrophoresis mobility shift assay showed that these motifs regulated the musclin gene transcription through binding to the corresponding transcriptional factors in sheep muscle tissue.
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Affiliation(s)
- Weizhen Li
- 1 College of Animal Science and Veterinary Medicine, Shanxi Agricultural University , Shanxi, People's Republic of China
| | - Hongqiang Zhang
- 1 College of Animal Science and Veterinary Medicine, Shanxi Agricultural University , Shanxi, People's Republic of China
| | - Shuai Qi
- 1 College of Animal Science and Veterinary Medicine, Shanxi Agricultural University , Shanxi, People's Republic of China
| | - Jian Qin
- 2 Centre of Experiment Teaching, Shanxi Agricultural University , Shanxi, People's Republic of China .,3 College of Life Science, Shanxi Agricultural University , Shanxi, People's Republic of China
| | - Hong Guan
- 4 State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University , Beijing, People's Republic of China
| | - Jianwei Li
- 4 State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University , Beijing, People's Republic of China
| | - Xiaorong An
- 4 State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University , Beijing, People's Republic of China
| | - Rong Du
- 1 College of Animal Science and Veterinary Medicine, Shanxi Agricultural University , Shanxi, People's Republic of China
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57
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Bunch H. Gene regulation of mammalian long non-coding RNA. Mol Genet Genomics 2017; 293:1-15. [PMID: 28894972 DOI: 10.1007/s00438-017-1370-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development. In this review, the newly discovered transcription mechanisms, characteristics, and functions of lncRNA are discussed.
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Affiliation(s)
- Heeyoun Bunch
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Agriculture & Life Sciences Building 1, Room 207, 80 Dae-Hak Ro, Daegu, Republic of Korea.
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58
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Zouaz A, Auradkar A, Delfini MC, Macchi M, Barthez M, Ela Akoa S, Bastianelli L, Xie G, Deng WM, Levine SS, Graba Y, Saurin AJ. The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription. EMBO J 2017; 36:2887-2906. [PMID: 28871058 DOI: 10.15252/embj.201695751] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature. We found that AbdA binding to M1BP-regulated genes results in reduction in PcG binding, the release of paused Pol II, increases in promoter H3K4me3 histone marks and increased gene transcription. Linking transcription factors, PcG proteins and paused Pol II states, these data identify a two-step mechanism of Hox-driven transcription, with M1BP binding leading to Pol II recruitment followed by AbdA targeting, which results in a change in the chromatin landscape and enhanced transcription.
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Affiliation(s)
- Amel Zouaz
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Ankush Auradkar
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | | | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Marine Barthez
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Serge Ela Akoa
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Leila Bastianelli
- MGX-Montpellier GenomiX c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
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59
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Bagshaw AT. Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. Genome Biol Evol 2017; 9:2428-2443. [PMID: 28957459 PMCID: PMC5622345 DOI: 10.1093/gbe/evx164] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 02/06/2023] Open
Abstract
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.
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60
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Rieder LE, Koreski KP, Boltz KA, Kuzu G, Urban JA, Bowman SK, Zeidman A, Jordan WT, Tolstorukov MY, Marzluff WF, Duronio RJ, Larschan EN. Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP. Genes Dev 2017; 31:1494-1508. [PMID: 28838946 PMCID: PMC5588930 DOI: 10.1101/gad.300855.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/25/2017] [Indexed: 01/13/2023]
Abstract
Rieder et al. report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct histone locus body (HLB) formation in Drosophila. In addition, the CLAMP zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct HLB formation in Drosophila. In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We demonstrated previously that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X chromosome. Therefore, CLAMP binding to GA repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.
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Affiliation(s)
- Leila E Rieder
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kara A Boltz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jennifer A Urban
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Sarah K Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Anna Zeidman
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - William T Jordan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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61
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Uyehara CM, Nystrom SL, Niederhuber MJ, Leatham-Jensen M, Ma Y, Buttitta LA, McKay DJ. Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev 2017; 31:862-875. [PMID: 28536147 PMCID: PMC5458754 DOI: 10.1101/gad.298182.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/26/2017] [Indexed: 11/24/2022]
Abstract
Uyehara et al. show that hormone-induced transcription factors control temporal gene expression by regulating accessibility of DNA regulatory elements. Using the Drosophila wing, they demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility.
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Affiliation(s)
- Christopher M Uyehara
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Spencer L Nystrom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Matthew J Niederhuber
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Mary Leatham-Jensen
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Yiqin Ma
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Laura A Buttitta
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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62
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Boldyreva LV, Goncharov FP, Demakova OV, Zykova TY, Levitsky VG, Kolesnikov NN, Pindyurin AV, Semeshin VF, Zhimulev IF. Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines. Curr Genomics 2017; 18:214-226. [PMID: 28367077 PMCID: PMC5345337 DOI: 10.2174/1389202917666160512164913] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5' untranslated regions (5'UTRs) of the genes, is enriched in diverse "open" chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the "closed" chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Igor F. Zhimulev
- Address correspondence to this author at the Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Tel: +7 383 363-90-41; Fax: +7 383 363-90-78; E-mail:
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63
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Yeung K, Boija A, Karlsson E, Holmqvist PH, Tsatskis Y, Nisoli I, Yap D, Lorzadeh A, Moksa M, Hirst M, Aparicio S, Fanto M, Stenberg P, Mannervik M, McNeill H. Atrophin controls developmental signaling pathways via interactions with Trithorax-like. eLife 2017; 6:e23084. [PMID: 28327288 PMCID: PMC5409829 DOI: 10.7554/elife.23084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.
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Affiliation(s)
- Kelvin Yeung
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ann Boija
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Per-Henrik Holmqvist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yonit Tsatskis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ilaria Nisoli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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64
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Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov AV, Moresco JJ, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates JR, Shidlovskii YV, Georgiev P, Schedl P, Chetverina D. The GAGA factor regulatory network: Identification of GAGA factor associated proteins. PLoS One 2017; 12:e0173602. [PMID: 28296955 PMCID: PMC5351981 DOI: 10.1371/journal.pone.0173602] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Drosophila GAGA factor (GAF) has an extraordinarily diverse set of functions that include the activation and silencing of gene expression, nucleosome organization and remodeling, higher order chromosome architecture and mitosis. One hypothesis that could account for these diverse activities is that GAF is able to interact with partners that have specific and dedicated functions. To test this possibility we used affinity purification coupled with high throughput mass spectrometry to identify GAF associated partners. Consistent with this hypothesis the GAF interacting network includes a large collection of factors and complexes that have been implicated in many different aspects of gene activity, chromosome structure and function. Moreover, we show that GAF interactions with a small subset of partners is direct; however for many others the interactions could be indirect, and depend upon intermediates that serve to diversify the functional capabilities of the GAF protein.
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Affiliation(s)
- Dmitry Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mikhailova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J. Moresco
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tatiana Blokhina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Vladimir Ryabykh
- Institute of Animal Physiology, Biochemistry and Nutrition, Borovsk, Russia
| | - John R. Yates
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | | | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
- * E-mail: (DC); (PS); (PG)
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
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65
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Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development. Genetics 2016; 205:605-620. [PMID: 28007888 DOI: 10.1534/genetics.116.195685] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.
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66
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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67
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Li J, Chauve L, Phelps G, Brielmann RM, Morimoto RI. E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response. Genes Dev 2016; 30:2062-2075. [PMID: 27688402 PMCID: PMC5066613 DOI: 10.1101/gad.283317.116] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/06/2016] [Indexed: 01/08/2023]
Abstract
Heat-shock factor (HSF) is the master transcriptional regulator of the heat-shock response (HSR) and is essential for stress resilience. HSF is also required for metazoan development; however, its function and regulation in this process are poorly understood. Here, we characterize the genomic distribution and transcriptional activity of Caenorhabditis elegans HSF-1 during larval development and show that the developmental HSF-1 transcriptional program is distinct from the HSR. HSF-1 developmental activation requires binding of E2F/DP to a GC-rich motif that facilitates HSF-1 binding to a heat-shock element (HSE) that is degenerate from the consensus HSE sequence and adjacent to the E2F-binding site at promoters. In contrast, induction of the HSR is independent of these promoter elements or E2F/DP and instead requires a distinct set of tandem canonical HSEs. Together, E2F and HSF-1 directly regulate a gene network, including a specific subset of chaperones, to promote protein biogenesis and anabolic metabolism, which are essential in development.
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Affiliation(s)
- Jian Li
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laetitia Chauve
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Grace Phelps
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Renée M Brielmann
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
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68
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Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. Genes Dev 2016; 30:1731-46. [PMID: 27492368 PMCID: PMC5002978 DOI: 10.1101/gad.284430.116] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/11/2016] [Indexed: 12/24/2022]
Abstract
The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.
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Affiliation(s)
- Fabiana M Duarte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Nicholas J Fuda
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Dig B Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
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69
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Tsai SY, Chang YL, Swamy KBS, Chiang RL, Huang DH. GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. Epigenetics Chromatin 2016; 9:32. [PMID: 27468311 PMCID: PMC4962548 DOI: 10.1186/s13072-016-0082-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing. RESULTS Using newly isolated mutants that retain only ~3 % normal GAF level, we analyzed its impacts on transcriptional regulation in whole animals. We first examined the abundance of three major isoforms of RNA-Pol on Hsp70 during heat shock. By cytogenetic analyses on polytene chromosomes and chromatin immunoprecipitation (ChIP), we show that paused RNA-Pol of Hsp70 is substantially reduced in mutants. Conversely, a global increase in paused RNA-Pol is observed when GAF is over-expressed. Coupled analyses of transcriptome and GAF genomic distribution show that 269 genes enriched for upstream GAF binding are down-regulated in mutants. Interestingly, ~15 % of them encode transcriptional factors, which might control ~2000 additional genes down-regulated in mutants. Further examination of RNA-Pol distribution in GAF targets reveals that a positive correlation exists between promoter-proximal RNA-Pol density and GAF occupancy in WT, but not in mutants. Comparison of nucleosome profiles indicates that nucleosome occupancy is preferentially attenuated by GAF in the upstream region that strongly favors nucleosome assembly. Using a dominant eye phenotype caused by GAF over-expression, we detect significant genetic interactions between GAF and the nucleosome remodeler NURF, the pausing factor NELF, and BAB1 whose binding sites are enriched specifically in genes displaying GAF-dependent pausing. CONCLUSION Our results provide direct evidence to support a critical role of GAF in global gene expression, transcriptional pausing and upstream nucleosome organization of a group of genes. By cooperating with factors acting at different levels, GAF orchestrates a series of events from local nucleosome displacement to paused transcription. The use of whole animals containing broad tissue types attests the physiological relevance of this regulatory network.
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Affiliation(s)
- Shih-Ying Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC ; Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yuh-Long Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Ruei-Lin Chiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
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70
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Deignan L, Pinheiro MT, Sutcliffe C, Saunders A, Wilcockson SG, Zeef LAH, Donaldson IJ, Ashe HL. Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PLoS Genet 2016; 12:e1006164. [PMID: 27379389 PMCID: PMC4933369 DOI: 10.1371/journal.pgen.1006164] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The BMP signaling pathway has a conserved role in dorsal-ventral axis patterning during embryonic development. In Drosophila, graded BMP signaling is transduced by the Mad transcription factor and opposed by the Brinker repressor. In this study, using the Drosophila embryo as a model, we combine RNA-seq with Mad and Brinker ChIP-seq to decipher the BMP-responsive transcriptional network underpinning differentiation of the dorsal ectoderm during dorsal-ventral axis patterning. We identify multiple new BMP target genes, including positive and negative regulators of EGF signaling. Manipulation of EGF signaling levels by loss- and gain-of-function studies reveals that EGF signaling negatively regulates embryonic BMP-responsive transcription. Therefore, the BMP gene network has a self-regulating property in that it establishes a balance between its activity and that of the antagonistic EGF signaling pathway to facilitate correct patterning. In terms of BMP-dependent transcription, we identify key roles for the Zelda and Zerknüllt transcription factors in establishing the resulting expression domain, and find widespread binding of insulator proteins to the Mad and Brinker-bound genomic regions. Analysis of embryos lacking the BEAF-32 insulator protein shows reduced transcription of a peak BMP target gene and a reduction in the number of amnioserosa cells, the fate specified by peak BMP signaling. We incorporate our findings into a model for Mad-dependent activation, and discuss its relevance to BMP signal interpretation in vertebrates. Embryogenesis involves the patterning of many different cell fates by a limited number of types of signals. One way that these signals promote a particular cell fate is through the induction of a complex, yet highly reproducible, gene expression programme that instructs changes in the cell. For example, there is a conserved role for BMP signals in specifying cell fates during dorsal-ventral axis patterning. Here, we have used genomics approaches to identify the gene expression programme implemented in response to BMP signaling during axis patterning in the Drosophila embryo. Part of the gene network downstream of BMP signaling includes members of the EGF signaling pathway, with our data highlighting reciprocal interactions between these two pathways. We have also determined genome-wide binding of BMP-responsive transcription factors to gain new insights into how the BMP gene network is activated. Our data reveal roles for specific transcription factors and insulator binding proteins, with the latter traditionally associated with the separation of transcriptional domains. Overall, our data will provide a platform for exploiting the tractability of the Drosophila embryo to determine which features of the network are critical drivers of BMP-induced cell fate changes during embryogenesis.
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Affiliation(s)
- Lisa Deignan
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Marco T. Pinheiro
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Catherine Sutcliffe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Scott G. Wilcockson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Leo A. H. Zeef
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian J. Donaldson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Hilary L. Ashe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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71
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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72
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Scheidegger A, Nechaev S. RNA polymerase II pausing as a context-dependent reader of the genome. Biochem Cell Biol 2015; 94:82-92. [PMID: 26555214 DOI: 10.1139/bcb-2015-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.
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Affiliation(s)
- Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
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73
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Liu X, Kraus WL, Bai X. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci 2015; 40:516-25. [PMID: 26254229 DOI: 10.1016/j.tibs.2015.07.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/07/2015] [Accepted: 07/06/2015] [Indexed: 01/06/2023]
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a well-established mechanism to control the timing, rate, and possibly the magnitude of transcriptional responses. Recent studies have shown that cellular signaling pathways can regulate gene transcription and signaling outcomes by controlling Pol II pausing in a wide array of biological systems. Identification of the proteins and small molecules that affect the establishment and release of paused Pol II is shedding new light on the mechanisms and biology of Pol II pausing. This review focuses on the interplay between cellular signaling pathways and Pol II pausing during normal development and under disease conditions.
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Affiliation(s)
- Xiuli Liu
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Signaling and Gene Regulation Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoying Bai
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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