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TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish

https://doi.org/10.1101/720102

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-0177(200001)217:1<109::aid-dvdy10>3.0.co;2-8openalex-snapshot

A Novel Pbx family member expressed during early zebrafish embryogenesis forms trimeric complexes with Meis3 and Hoxb1b

inferredcites →https://doi.org/10.1002/dvdy.23997openalex-snapshot

Hox regulation of transcription: More complex(es)

inferredcites →https://doi.org/10.1016/j.bone.2009.01.374openalex-snapshot

Novel and unexpected functions of zebrafish CCAAT box binding transcription factor (NF-Y) B subunit during cartilages development

inferredcites →https://doi.org/10.1016/j.cell.2012.09.045openalex-snapshot

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

inferredcites →https://doi.org/10.1016/j.cell.2012.11.047openalex-snapshot

Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination

inferredcites →https://doi.org/10.1016/j.cell.2015.03.017openalex-snapshot

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

inferredcites →https://doi.org/10.1016/j.cell.2016.05.050openalex-snapshot

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

inferredcites →https://doi.org/10.1016/j.cell.2018.02.028openalex-snapshot

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

inferredcites →https://doi.org/10.1016/j.celrep.2013.03.029openalex-snapshot

Analysis of the DNA-Binding Profile and Function of TALE Homeoproteins Reveals Their Specialization and Specific Interactions with Hox Genes/Proteins

inferredcites →https://doi.org/10.1016/j.devcel.2009.08.007openalex-snapshot

Meis Cofactors Control HDAC and CBP Accessibility at Hox-Regulated Promoters during Zebrafish Embryogenesis

inferredcites →https://doi.org/10.1016/j.devcel.2013.12.011openalex-snapshot

TALE Factors Poise Promoters for Activation by Hox Proteins

inferredcites →https://doi.org/10.1016/j.devcel.2014.12.024openalex-snapshot

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.molcel.2014.07.005openalex-snapshot

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

inferredcites →https://doi.org/10.1016/j.tig.2016.03.004openalex-snapshot

To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins

inferredcites →https://doi.org/10.1016/j.ydbio.2006.10.029openalex-snapshot

Expression of Hoxa2 in rhombomere 4 is regulated by a conserved cross-regulatory mechanism dependent upon Hoxb1

inferredcites →https://doi.org/10.1016/j.ydbio.2009.10.019openalex-snapshot

A systematic approach to identify functional motifs within vertebrate developmental enhancers

inferredcites →https://doi.org/10.1016/s0021-9258(17)31997-xopenalex-snapshot

Dominant negative analogs of NF-YA.

inferredcites →https://doi.org/10.1016/s0092-8674(05)80008-xopenalex-snapshot

Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx

inferredcites →https://doi.org/10.1016/s0968-0004(98)01201-8openalex-snapshot

Role of the CCAAT-binding protein CBF/NF-Y in transcription

inferredcites →https://doi.org/10.1016/s1097-2765(00)00027-7openalex-snapshot

lazarus Is a Novel pbx Gene that Globally Mediates hox Gene Function in Zebrafish

inferredcites →https://doi.org/10.1016/s1097-2765(02)00459-8openalex-snapshot

Opening of Compacted Chromatin by Early Developmental Transcription Factors HNF3 (FoxA) and GATA-4

inferredcites →https://doi.org/10.1016/s1534-5807(02)00319-2openalex-snapshot

Eliminating Zebrafish Pbx Proteins Reveals a Hindbrain Ground State

inferredcites →https://doi.org/10.1038/418037aopenalex-snapshot

Conserved function for embryonic nodal cilia

inferredcites →https://doi.org/10.1038/nature07388openalex-snapshot

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

inferredcites →https://doi.org/10.1038/nature12632openalex-snapshot

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

inferredcites →https://doi.org/10.1038/nbt.1630openalex-snapshot

GREAT improves functional interpretation of cis-regulatory regions

inferredcites →https://doi.org/10.1038/ng.3844openalex-snapshot

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

inferredcites →https://doi.org/10.1038/ng.3858openalex-snapshot

DUX-family transcription factors regulate zygotic genome activation in placental mammals

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nprot.2008.211openalex-snapshot

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

inferredcites →https://doi.org/10.1038/s41588-019-0418-7openalex-snapshot

Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development

inferredcites →https://doi.org/10.1038/sj.onc.1201097openalex-snapshot

The highest affinity DNA element bound by Pbx complexes in t(1;19) leukemic cells fails to mediate cooperative DNA-binding or cooperative transactivation by E2a-Pbx1 and Class I Hox proteins – evidence for selective targetting of E2a-Pbx1 to a subset of Pbx-recognition elements

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btr189openalex-snapshot

MEME-ChIP: motif analysis of large DNA datasets

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/emboj/16.24.7402openalex-snapshot

Synergistic activation of a Drosophila enhancer by HOM/EXD and DPP signaling

inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot

MEME SUITE: tools for motif discovery and searching

inferredcites →https://doi.org/10.1093/nar/gkt557openalex-snapshot

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot

deepTools: a flexible platform for exploring deep-sequencing data

inferredcites →https://doi.org/10.1093/nar/gkw1134openalex-snapshot

OUP accepted manuscript

inferredcites →https://doi.org/10.1101/gad.10.13.1670openalex-snapshot

Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control.

inferredcites →https://doi.org/10.1101/gad.13.13.1704openalex-snapshot

The control of trunk Hox specificity and activity by Extradenticle

inferredcites →https://doi.org/10.1101/gad.321174.118openalex-snapshot

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

inferredcites →https://doi.org/10.1101/gr.133546.111openalex-snapshot

Coding exons function as tissue-specific enhancers of nearby genes

inferredcites →https://doi.org/10.1101/gr.134833.111openalex-snapshot

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

inferredcites →https://doi.org/10.1101/gr.153692.112openalex-snapshot

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

inferredcites →https://doi.org/10.1101/gr.157750.113openalex-snapshot

Canonical nucleosome organization at promoters forms during genome activation

inferredcites →https://doi.org/10.1101/gr.192542.115openalex-snapshot

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

inferredcites →https://doi.org/10.1126/science.1242527openalex-snapshot

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

inferredcites →https://doi.org/10.1128/mcb.17.10.5679openalex-snapshot

Meis Proteins are Major In Vivo DNA Binding Partners for Wild-Type but Not Chimeric Pbx Proteins

inferredcites →https://doi.org/10.1128/mcb.19.7.5134openalex-snapshot

Trimeric Association of Hox and TALE Homeodomain Proteins Mediates Hoxb2 Hindbrain Enhancer Activity

inferredcites →https://doi.org/10.1128/mcb.20.22.8623-8633.2000openalex-snapshot

Cell Signaling Switches HOX-PBX Complexes from Repressors to Activators of Transcription Mediated by Histone Deacetylases and Histone Acetyltransferases

inferredcites →https://doi.org/10.1128/mcb.25.19.8541-8552.2005openalex-snapshot

Hoxb1 Enhancer and Control of Rhombomere 4 Expression: Complex Interplay between PREP1-PBX1-HOXB1 Binding Sites

inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot

Differential expression analysis for sequence count data

inferredcites →https://doi.org/10.1186/gb-2010-11-8-r86openalex-snapshot

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

inferredcites →https://doi.org/10.1186/s12864-018-5362-xopenalex-snapshot

DEBrowser: interactive differential expression analysis and visualization tool for count data

inferredcites →https://doi.org/10.1242/dev.00948openalex-snapshot

Prep1.1 has essential genetic functions in hindbrain development and cranial neural crest cell differentiation

inferredcites →https://doi.org/10.1242/dev.066498openalex-snapshot

pTransgenesis: a cross-species, modular transgenesis resource

inferredcites →https://doi.org/10.1242/dev.125.3.393openalex-snapshot

Zebrafish hox genes: expression in the hindbrain region of wild-type and mutants of the segmentation gene, valentino

inferredcites →https://doi.org/10.1242/dev.125.3.407openalex-snapshot

Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk

inferredcites →https://doi.org/10.1242/dev.127.1.155openalex-snapshot

Segmental expression of Hoxb2 in r4 requires two separate sites that integrate cooperative interactions between Prep1, Pbx and Hox proteins

inferredcites →https://doi.org/10.1242/dev.128.21.4139openalex-snapshot

Zebrafish Meis functions to stabilize Pbx proteins and regulate hindbrain patterning

inferredcites →https://doi.org/10.1242/dev.129.3.585openalex-snapshot

Meis family proteins are required for hindbrain development in the zebrafish

inferredcites →https://doi.org/10.1242/dev.133900openalex-snapshot

Cell fate control by pioneer transcription factors

inferredcites →https://doi.org/10.1242/dev.147793openalex-snapshot

The primary role of zebrafish nanog is in extra-embryonic tissue

inferredcites →https://doi.org/10.1242/dev.161471openalex-snapshot

The maternal-to-zygotic transition revisited

inferredcites →https://doi.org/10.1371/journal.pgen.1002266openalex-snapshot

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

inferredcites →https://doi.org/10.1371/journal.pgen.1002339openalex-snapshot

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

inferredcites →https://doi.org/10.1371/journal.pgen.1002368openalex-snapshot

PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer

inferredcites →https://doi.org/10.15252/embr.201847382openalex-snapshot

DPPA2 and DPPA4 are necessary to establish a 2C‐like state in mouse embryonic stem cells

inferredcites →https://doi.org/10.17615/nvtt-9k83openalex-snapshot

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo

inferredcites →https://doi.org/10.3109/10409238.2011.628970openalex-snapshot

NF-Y and the transcriptional activation of CCAAT promoters

inferredcites →https://doi.org/10.7554/elife.36144openalex-snapshot

TALE factors use two distinct functional modes to control an essential zebrafish gene expression program

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008546openalex-snapshot

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

inferred← citeshttps://doi.org/10.3410/f.737214548.793573559openalex-snapshot

Faculty Opinions recommendation of Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.

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