ArticleGenome research2006
Experimental validation of predicted mammalian erythroid cis-regulatory modules.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Trial
- Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions.iScience · 2023Article
- Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?Current opinion in plant biology · 2022Review
- RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse.Genome research · 2022Article
- An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.Genome research · 2020Article
- Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells.IUBMB life · 2020Review
- Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.Human mutation · 2016Article
- Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.Molecular biology and evolution · 2016Article
- Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.Epigenetics & chromatin · 2015Article
- X-linked sideroblastic anemia due to ALAS2 intron 1 enhancer element GATA-binding site mutations.American journal of hematology · 2014Article
- Genomic approaches towards finding cis-regulatory modules in animals.Nature reviews. Genetics · 2012Review
- Article
- What fraction of the human genome is functional?Genome research · 2011Review
- Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.Genome research · 2011Article
- Assessing computational methods of cis-regulatory module prediction.PLoS computational biology · 2010Article
- A single cis element maintains repression of the key developmental regulator Gata2.PLoS genetics · 2010Article
- Hypoxia regulates BMP4 expression in the murine spleen during the recovery from acute anemia.PloS one · 2010Article
- Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.Genome research · 2009Article
- The role and regulation of friend of GATA-1 (FOG-1) during blood development in the zebrafish.Blood · 2009Article
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Authors and funding
16 authors.
Funding
Abstract
Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis-regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict CRMs for mammalian genes expressed in red blood cells by combining two properties gleaned from aligned, noncoding genome sequences: a positive regulatory potential (RP) score, which detects similarity to patterns in alignments distinctive for regulatory regions, and conservation of a binding site motif for the essential erythroid transcription factor GATA-1. Within eight target loci, we tested 75 noncoding segments by reporter gene assays in transiently transfected human K562 cells and/or after site-directed integration into murine erythroleukemia cells. Segments with a high RP score and a conserved exact match to the binding site consensus are validated at a good rate (50%-100%, with rates increasing at higher RP), whereas segments with lower RP scores or nonconsensus binding motifs tend to be inactive. Active DNA segments were shown to be occupied by GATA-1 protein by chromatin immunoprecipitation, whereas sites predicted to be inactive were not occupied. We verify four previously known erythroid CRMs and identify 28 novel ones. Thus, high RP in combination with another feature of a CRM, such as a conserved transcription factor binding site, is a good predictor of functional CRMs. Genome-wide predictions based on RP and a large set of well-defined transcription factor binding sites are available through servers at http://www.bx.psu.edu/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.