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Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-022084]

ABSTRACT: Genomic copy number analysis in patients with ACD/MPV. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.potentially cause many disorders of human development. CNVs were identified by array CGH with custom-designed 16q24.1 region specific (1Mb flanking FOXF1) 44K oligonucleotide microarrays (Agilent technologies) in 3 patients with ACD. This Series contains data for only two patients

ORGANISM(S): Homo sapiens

PROVIDER: GSE38978 | GEO | 2012/07/06

SECONDARY ACCESSION(S): PRJNA170042

REPOSITORIES: GEO

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Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-030795]

Project description:Genomic copy number analysis in patients with ACD/MPV. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.potentially cause many disorders of human development. CNVs were identified by array CGH with custom-designed 16q24.1 region specific (1Mb flanking FOXF1) 44K oligonucleotide microarrays (Agilent technologies) in 3 patients with ACD.

2012-07-10 | E-GEOD-39254 | biostudies-arrayexpress

Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-022084]

2012-07-05 | E-GEOD-38978 | biostudies-arrayexpress

Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-030795]

2012-07-11 | GSE39254 | GEO

ChIP-chip analysis to determine GLI2 binding sites

Project description:Chromatin immunoprecipitation with anti-GLI2 antibody was conducted in human pulomonary microvascular endothelial cells (HPMECs) to determine GLI2 binding sites upstream of FOXF1. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development. ChIP-chip HPMECs transfected to overxpress GLI2; 2 biological replicates

2012-07-10 | E-GEOD-39255 | biostudies-arrayexpress

Genomic copy-number analysis in Alveolar capillary dysplasia (ACD) patient samples

Project description:Non-coding copy number changes in 16q24.1 upstream of FOXF1 were identified in two patients with ACD. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.

2012-07-11 | GSE39257 | GEO

FOXF1 promoter-putative enhancer chromatin looping

Project description:To determine if there is a physical interaction between the FOXF1 promoter and putative enhancer sequences ~250kb upstream of the promoter chromosome conformation capture-on-chip (4C) analysis was performed. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development. 4C analysis using 16q24.1 specific 3x720K arrays demonstrated physical interaction between the FOXF1 promoter and distant putative regulatory sequences, about 250 kb upstream in human pulomonary microvascular endothelial cells; 2 biological replicates performed; this chromatin looping was not detected in lymphoblasts that do not express FOXF1 and hence serve as a negative control.

2012-07-10 | E-GEOD-39256 | biostudies-arrayexpress

FOXF1 promoter-putative enhancer chromatin looping

2012-07-11 | GSE39256 | GEO

ChIP-chip analysis to determine GLI2 binding sites

2012-07-11 | GSE39255 | GEO

Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

Project description:Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

| PRJNA565194 | ENA

A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure.

Project description:Prader-Willi syndrome (PWS), a genetic cause of childhood obesity, is characterized by intellectual disabilities and sleep abnormalities. PWS-causing deletions include a neuronal long, non-coding RNA (lncRNA) processed into small nucleolar RNAs and a spliced lncRNA,116HG. We show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in postnatal neurons. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1, and Per2. Genomic and metabolic analyses demonstrate altered diurnal energy regulation in the Snord116del mouse cortex and link the loss of 116HG to the energy imbalance observed in PWS. Examination of lncRNA binding sites by ChIRP-seq using an oligo-based purification method from WT and Snord116del (+/-) mouse brain with specific and nonspecific control oligos. Transcript abundance levels by RNA-seq analysis of 3 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+6 and 2 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+16.

2013-06-20 | E-GEOD-43575 | biostudies-arrayexpress

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