LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription

2018 ◽  
Author(s):  
Gary LeRoy ◽  
Ozgur Oksuz ◽  
Nicolas Descostes ◽  
Yuki Aoi ◽  
Rais Ganai ◽  
...  
Keyword(s):  
Protein Complex ◽  
Target Genes ◽  
Cell Types ◽  
Undifferentiated Cells ◽  
Genomic Regions ◽  
Active Genes ◽  
Facilitates Chromatin Transcription

FACT (facilitates chromatin transcription) is a protein complex that allows RNAPII to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is absent in most tissues. Therefore, we screened for additional proteins that might replace FACT upon differentiation. Here we report the identification of two such proteins, LEDGF and HDGF2, each containing two HMGA-like AT-hooks and a PWWP methyl-lysine reading domain known to bind to H3K36me2 and H3K36me3. LEDGF and HDGF2 localize with H3K36me2/3 at genomic regions containing active genes, usually adjacent to H3K27me3 domains. In myoblasts, where FACT expression is low, LEDGF and HDGF2 are enriched on most active genes. Upon differentiation to myotubes, LEDGF levels decrease across the genome while HDGF2 levels are maintained. Moreover, HDGF2 is recruited to the majority of myotube up-regulated genes and is required for their proper expression. HDGF2 knockout myoblasts exhibit an accumulation of paused RNAPII proximal to the first nucleosome within the transcribed region of many HDGF2 target genes, indicating a defect in early elongation. We propose that LEDGF and HDGF2 substitute for FACT in differentiated tissues and that their distribution on the genome helps maintain transcriptional programs unique to particular cell types.

scholarly journals LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells

2019 ◽  
Vol 5 (10) ◽  
pp. eaay3068 ◽  
Author(s):  
Gary LeRoy ◽  
Ozgur Oksuz ◽  
Nicolas Descostes ◽  
Yuki Aoi ◽  
Rais A. Ganai ◽  
...  
Keyword(s):  
Growth Factor ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
High Mobility ◽  
Pwwp Domain ◽  
Differentiated Cells ◽  
Undifferentiated Cells ◽  
Group A ◽  
Genomic Regions ◽  
Active Genes

FACT (facilitates chromatin transcription) is a protein complex that allows RNA polymerase II (RNAPII) to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is absent in most tissues. Therefore, we screened for additional proteins that might replace FACT upon differentiation. We identified two proteins, lens epithelium-derived growth factor (LEDGF) and hepatoma-derived growth factor 2 (HDGF2), each containing two high mobility group A (HMGA)–like AT-hooks and a methyl-lysine reading Pro-Trp-Trp-Pro (PWWP) domain that binds to H3K36me2 and H3K36me3.LEDGF and HDGF2 colocalize with H3K36me2/3 at genomic regions containing active genes. In myoblasts, LEDGF and HDGF2 are enriched on most active genes. Upon differentiation to myotubes, LEDGF levels decrease, while HDGF2 levels are maintained. Moreover, HDGF2 is required for their proper expression. HDGF2 knockout myoblasts exhibit an accumulation of paused RNAPII within the transcribed region of many HDGF2 target genes, indicating a defect in early elongation.

scholarly journals JAZF1-SUZ12 dysregulates PRC2 function and gene expression during cell differentiation

2021 ◽  
Author(s):  
Manuel Tavares ◽  
Garima Khandelwal ◽  
Joanne Mutter ◽  
Keijo Viiri ◽  
Manuel Beltran ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Target Genes ◽  
Histone H3 ◽  
Endometrial Stromal Sarcoma ◽  
Cell Types ◽  
Polycomb Repressive Complex 2 ◽  
Stromal Sarcoma ◽  
N Terminus ◽  
Undifferentiated Cells

Polycomb repressive complex 2 (PRC2) methylates histone H3 lysine 27 (H3K27me3) to maintain repression of genes specific for other cell types and is essential for cell differentiation. In endometrial stromal sarcoma, the PRC2 subunit SUZ12 is often fused with the NuA4/TIP60 subunit JAZF1. Here, we show that JAZF1-SUZ12 dysregulates PRC2 composition, recruitment, histone modification, gene expression and cell differentiation. The loss of the SUZ12 N-terminus in the fusion protein disrupted interaction with the PRC2 accessory factors JARID2, EPOP and PALI1 and prevented recruitment of PRC2 from RNA to chromatin. In undifferentiated cells, JAZF1-SUZ12 occupied PRC2 target genes but gained a JAZF1-like binding profile during cell differentiation. JAZF1-SUZ12 reduced H3K27me3 and increased H4Kac at PRC2 target genes, and this was associated with disruption in gene expression and cell differentiation programs. These results reveal the defects in chromatin regulation caused by JAZF1-SUZ12, which may underlie its role in oncogenesis.

scholarly journals EpiRegio: analysis and retrieval of regulatory elements linked to genes

2020 ◽  
Vol 48 (W1) ◽  
pp. W193-W199 ◽  
Author(s):  
Nina Baumgarten ◽  
Dennis Hecker ◽  
Sivarajan Karunanithi ◽  
Florian Schmidt ◽  
Markus List ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Association Studies ◽  
Web Server ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Genome Wide Association Studies ◽  
Coding Regions ◽  
Genomic Regions

Abstract A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM’s activity and its estimated cell type-specific contribution to its target gene’s expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.

scholarly journals Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics

2021 ◽  
Author(s):  
Yan Wu ◽  
Blue Lake ◽  
Brandon Sos ◽  
Song Chen ◽  
Thu E. Duong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Human Brain ◽  
Single Cell ◽  
Target Genes ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Specific Sequence ◽  
Enhancer Activity ◽  
Genomic Regions ◽  
Human Specific

AbstractHuman behaviors are at least partially driven by genomic regions that influence human-specific neurodevelopment. This includes genomic regions undergoing human specific sequence acceleration (Human Accelerated Regions or HARs) and regions showing human-specific enhancer activity (Human Gained Enhancers or HGEs) not present in other primates. However, prior studies on HAR/HGE activities involved mixtures of brain cell types and focused only on putative downstream target genes. Here, we directly measured cell type specific HAR/HGE activity in the developing fetal human brain using two independent single-cell chromatin accessibility datasets with matching single-cell gene expression data. Transcription factor (TF) motif analyses identified upstream TFs binding to HARs/HGEs and identified LHX2, a key regulator of forebrain development, as an active HGE regulator in neuronal progenitors. We integrated our TF motif analyses with published chromatin interaction maps to build detailed regulatory networks where TFs are linked to downstream genes via HARs/HGEs. Through these networks, we identified a potential regulatory role for NFIC in human neuronal progenitor networks via modulating the Notch signaling and cell adhesion pathways. Therefore, by using a single cell multi-omics approach, we were able to capture both the upstream and downstream regulatory context of HARs/HGEs, which may provide a more comprehensive picture of the roles HARs/HGEs play amongst diverse fetal cell types of the developing human brain.

scholarly journals OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data

2018 ◽  
Author(s):  
Parisa Shooshtari ◽  
Samantha Feng ◽  
Viswateja Nelakuditi ◽  
Justin Foong ◽  
Michael Brudno ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Large Scale ◽  
Target Genes ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Sequencing Data ◽  
Genomic Regions ◽  
Multiple Samples ◽  
Regulatory Sites

ABSTRACTInternational consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.

A Deficiency Screen for Zygotic Loci Required for Establishment and Patterning of the Epidermis in Caenorhabditis elegans

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 185-206 ◽  
Author(s):  
Rebecca M Terns ◽  
Peggy Kroll-Conner ◽  
Jiangwen Zhu ◽  
Sooyoun Chung ◽  
Joel H Rothman
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Types ◽  
Epidermal Cells ◽  
Epidermal Differentiation ◽  
Apparent Effect ◽  
Internal Organs ◽  
C Elegans ◽  
Seam Cell ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome

To identify genomic regions required for establishment and patterning of the epidermis, we screened 58 deficiencies that collectively delete at least ∼67% of the Caenorhabditis elegans genome. The epidermal pattern of deficiency homozygous embryos was analyzed by examining expression of a marker specific for one of the three major epidermal cell types, the seam cells. The organization of the epidermis and internal organs was also analyzed using a monoclonal antibody specific for epithelial adherens junctions. While seven deficiencies had no apparent effect on seam cell production, 21 were found to result in subnormal, and five in excess numbers of these cells. An additional 23 deficiencies blocked expression of the seam cell marker, in some cases without preventing cell proliferation. Two deficiencies result in multinucleate seam cells. Deficiencies were also identified that result in subnormal numbers of epidermal cells, hyperfusion of epidermal cells into a large syncytium, or aberrant epidermal differentiation. Finally, analysis of internal epithelia revealed deficiencies that cause defects in formation of internal organs, including circularization of the intestine and bifurcation of the pharynx lumen. This study reveals that many regions of the C. elegans genome are required zygotically for patterning of the epidermis and other epithelia.

Drosophila Gain-of-Function Mutant RTK Torso Triggers Ectopic Dpp and STAT Signaling

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 247-258 ◽  
Author(s):  
Jinghong Li ◽  
Willis X Li
Keyword(s):  
Tyrosine Kinases ◽  
Target Genes ◽  
Tor Signaling ◽  
Gain Of Function ◽  
Essential Requirement ◽  
Downstream Target ◽  
Rtk Signaling ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Overactivation of receptor tyrosine kinases (RTKs) has been linked to tumorigenesis. To understand how a hyperactivated RTK functions differently from wild-type RTK, we conducted a genome-wide systematic survey for genes that are required for signaling by a gain-of-function mutant Drosophila RTK Torso (Tor). We screened chromosomal deficiencies for suppression of a gain-of-function mutation tor (torGOF), which led to the identification of 26 genomic regions that, when in half dosage, suppressed the defects caused by torGOF. Testing of candidate genes in these regions revealed many genes known to be involved in Tor signaling (such as those encoding the Ras-MAPK cassette, adaptor and structural molecules of RTK signaling, and downstream target genes of Tor), confirming the specificity of this genetic screen. Importantly, this screen also identified components of the TGFβ (Dpp) and JAK/STAT pathways as being required for TorGOF signaling. Specifically, we found that reducing the dosage of thickveins (tkv), Mothers against dpp (Mad), or STAT92E (aka marelle), respectively, suppressed torGOF phenotypes. Furthermore, we demonstrate that in torGOF embryos, dpp is ectopically expressed and thus may contribute to the patterning defects. These results demonstrate an essential requirement of noncanonical signaling pathways for a persistently activated RTK to cause pathological defects in an organism.

scholarly journals Annotation of chromatin states in 66 complete mouse epigenomes during development

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Arjan van der Velde ◽  
Kaili Fan ◽  
Junko Tsuji ◽  
Jill E. Moore ◽  
Michael J. Purcaro ◽  
...  
Keyword(s):  
Target Genes ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Phase Iii ◽  
Chromatin State ◽  
Mammalian Development ◽  
Chromatin States ◽  
Transcription Start Sites ◽  
Repressive Mark ◽  
Distinct Cell

AbstractThe morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development.

scholarly journals Thyroid Hormone Action in Cerebellum and Cerebral Cortex Development

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Fabrice Chatonnet ◽  
Frédéric Picou ◽  
Teddy Fauquier ◽  
Frédéric Flamant
Keyword(s):  
Cerebral Cortex ◽  
Thyroid Hormone ◽  
Thyroid Hormones ◽  
Glial Cell ◽  
Nuclear Receptors ◽  
Target Genes ◽  
Cell Types ◽  
Hormone Action ◽  
Cerebral Cortex Development ◽  
Thyroid Hormone Action

Thyroid hormones (TH, including the prohormone thyroxine (T4) and its active deiodinated derivative 3,,5-triiodo-L-thyronine (T3)) are important regulators of vertebrates neurodevelopment. Specific transporters and deiodinases are required to ensure T3 access to the developing brain. T3 activates a number of differentiation processes in neuronal and glial cell types by binding to nuclear receptors, acting directly on transcription. Only few T3 target genes are currently known. Deeper investigations are urgently needed, considering that some chemicals present in food are believed to interfere with T3 signaling with putative neurotoxic consequences.

Homeotic response elements are tightly linked to tissue-specific elements in a transcriptional enhancer of the teashirt gene

Development ◽  
1995 ◽  
Vol 121 (9) ◽  
pp. 2799-2812 ◽  
Author(s):  
A. McCormick ◽  
N. Core ◽  
S. Kerridge ◽  
M.P. Scott
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Hox Genes ◽  
Zinc Finger Protein ◽  
Cell Types ◽  
Transcriptional Enhancer ◽  
Hox Proteins ◽  
Tissue Specific ◽  
Conserved Sequences

Along the anterior-posterior axis of animal embryos, the choice of cell fates, and the organization of morphogenesis, is regulated by transcription factors encoded by clustered homeotic or ‘Hox’ genes. Hox genes function in both epidermis and internal tissues by regulating the transcription of target genes in a position- and tissue-specific manner. Hox proteins can have distinct targets in different tissues; the mechanisms underlying tissue and homeotic protein specificity are unknown. Light may be shed by studying the organization of target gene enhancers. In flies, one of the target genes is teashirt (tsh), which encodes a zinc finger protein. tsh itself is a homeotic gene that controls trunk versus head development. We identified a tsh gene enhancer that is differentially activated by Hox proteins in epidermis and mesoderm. Sites where Antennapedia (Antp) and Ultrabithorax (Ubx) proteins bind in vitro were mapped within evolutionarily conserved sequences. Although Antp and Ubx bind to identical sites in vitro, Antp activates the tsh enhancer only in epidermis while Ubx activates the tsh enhancer in both epidermis and in somatic mesoderm. We show that the DNA elements driving tissue-specific transcriptional activation by Antp and Ubx are separable. Next to the homeotic protein-binding sites are extensive conserved sequences likely to control tissue activation by different homeodomain proteins. We propose that local interactions between homeotic proteins and other factors effect activation of targets in proper cell types.

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