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Structural disruption of genomic regions containing ultraconserved elements is associated with neurodevelopmental phenotypes

https://doi.org/10.1101/233197
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What this work says

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

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Complex chromosomal rearrangement in a girl with psychomotor‐retardation and a de novo inversion: inv(2)(p15;q24.2)
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Clinical Significance of De Novo and Inherited Copy-Number Variation
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Identification of a Novel Gene on Chromosome 7q11.2 Interrupted by a Translocation Breakpoint in a Pair of Autistic Twins
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Sixteen Years of Meiotic Silencing by Unpaired DNA
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Understanding the Genomic Ultraconservations: T-UCRs and Cancer
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Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation
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Disruption of Autoregulatory Feedback by a Mutation in a Remote, Ultraconserved PAX6 Enhancer Causes Aniridia
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Cryptic and Complex Chromosomal Aberrations in Early-Onset Neuropsychiatric Disorders
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BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription
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Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements
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Common fragile sites, extremely large genes, neural development and cancer
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Chromothripsis in congenital disorders and cancer: similarities and differences
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Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries
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Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells
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Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior
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When a Stomach Bug Comes Calling
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The Sestrins Interact with GATOR2 to Negatively Regulate the Amino-Acid-Sensing Pathway Upstream of mTORC1
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Genomic and Functional Overlap between Somatic and Germline Chromosomal Rearrangements
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LIMITED CONTRIBUTION OF RARE, NONCODING VARIATION TO AUTISM SPECTRUM DISORDER FROM SEQUENCING OF 2,076 GENOMES IN QUARTET FAMILIES
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Pairing and anti-pairing: a balancing act in the diploid genome
inferredcites →https://doi.org/10.1016/j.gene.2016.02.022openalex-snapshot
Fractality and entropic scaling in the chromosomal distribution of conserved noncoding elements in the human genome
inferredcites →https://doi.org/10.1016/j.molcel.2014.05.005openalex-snapshot
Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region
inferredcites →https://doi.org/10.1016/j.neuron.2011.05.002openalex-snapshot
Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism
inferredcites →https://doi.org/10.1016/j.neuron.2011.05.015openalex-snapshot
Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders
inferredcites →https://doi.org/10.1016/j.neuron.2012.04.009openalex-snapshot
De Novo Gene Disruptions in Children on the Autistic Spectrum
inferredcites →https://doi.org/10.1016/j.neuron.2015.09.016openalex-snapshot
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci
inferredcites →https://doi.org/10.1016/j.tig.2008.04.005openalex-snapshot
Tuning in to the signals: noncoding sequence conservation in vertebrate genomes
inferredcites →https://doi.org/10.1016/j.tig.2016.01.003openalex-snapshot
Breaking TADs: How Alterations of Chromatin Domains Result in Disease
inferredcites →https://doi.org/10.1016/j.ygeno.2005.03.003openalex-snapshot
In vivo characterization of a vertebrate ultraconserved enhancer
inferredcites →https://doi.org/10.1016/j.ygeno.2010.01.002openalex-snapshot
Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites
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HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts
inferredcites →https://doi.org/10.1038/ejhg.2013.147openalex-snapshot
The strength of combined cytogenetic and mate-pair sequencing techniques illustrated by a germline chromothripsis rearrangement involving FOXP2
inferredcites →https://doi.org/10.1038/ejhg.2013.220openalex-snapshot
Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations
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Molecular evolution of FOXP2, a gene involved in speech and language
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An RNA gene expressed during cortical development evolved rapidly in humans
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Origins and functional impact of copy number variation in the human genome
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Functional impact of global rare copy number variation in autism spectrum disorders
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De novo mutations revealed by whole-exome sequencing are strongly associated with autism
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An integrated encyclopedia of DNA elements in the human genome
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Topoisomerases facilitate transcription of long genes linked to autism
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Synaptic, transcriptional and chromatin genes disrupted in autism
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The contribution of de novo coding mutations to autism spectrum disorder
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Parent–progeny sequencing indicates higher mutation rates in heterozygotes
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Analysis of protein-coding genetic variation in 60,706 humans
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De novo mutations in regulatory elements in neurodevelopmental disorders
inferredcites →https://doi.org/10.1038/ng.2007.55openalex-snapshot
Ultraconservation identifies a small subset of extremely constrained developmental enhancers
inferredcites →https://doi.org/10.1038/ng.2202openalex-snapshot
Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration
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Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
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A framework for the interpretation of de novo mutation in human disease
inferredcites →https://doi.org/10.1038/ng.3720openalex-snapshot
The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies
inferredcites →https://doi.org/10.1038/ng.712openalex-snapshot
A de novo paradigm for mental retardation
inferredcites →https://doi.org/10.1038/ng1888openalex-snapshot
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants
inferredcites →https://doi.org/10.1038/nrg.2015.25openalex-snapshot
Mechanisms underlying structural variant formation in genomic disorders
inferredcites →https://doi.org/10.1038/nrg3585openalex-snapshot
The role of de novo mutations in the genetics of autism spectrum disorders
inferredcites →https://doi.org/10.1038/onc.2010.361openalex-snapshot
CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer
inferredcites →https://doi.org/10.1073/pnas.1011098108openalex-snapshot
Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma
inferredcites →https://doi.org/10.1093/bioinformatics/btl048openalex-snapshot
The UCSC Known Genes
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/btr539openalex-snapshot
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
inferredcites →https://doi.org/10.1093/bioinformatics/bts400openalex-snapshot
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
inferredcites →https://doi.org/10.1093/hmg/ddl232openalex-snapshot
Conserved distances between vertebrate highly conserved elements
inferredcites →https://doi.org/10.1093/hmg/ddr073openalex-snapshot
Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline†
inferredcites →https://doi.org/10.1093/molbev/msr093openalex-snapshot
Positive and Negative Selection in Murine Ultraconserved Noncoding Elements
inferredcites →https://doi.org/10.1093/nar/gkn148openalex-snapshot
An ultraconserved Hox–Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4
inferredcites →https://doi.org/10.1093/nar/gkp1124openalex-snapshot
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1098/rsbl.2015.0929openalex-snapshot
Heterozygosity increases microsatellite mutation rate
inferredcites →https://doi.org/10.1098/rstb.2013.0021openalex-snapshot
The mystery of extreme non-coding conservation
inferredcites →https://doi.org/10.1101/gr.129346.111openalex-snapshot
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
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Large transcription units unify copy number variants and common fragile sites arising under replication stress
inferredcites →https://doi.org/10.1101/gr.6086307openalex-snapshot
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
inferredcites →https://doi.org/10.1126/science.1098119openalex-snapshot
Ultraconserved Elements in the Human Genome
inferredcites →https://doi.org/10.1126/science.1138659openalex-snapshot
Strong Association of De Novo Copy Number Mutations with Autism
inferredcites →https://doi.org/10.1126/science.1142430openalex-snapshot
Human Genome Ultraconserved Elements Are Ultraselected
inferredcites →https://doi.org/10.1126/science.aab3897openalex-snapshot
Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders
inferredcites →https://doi.org/10.1128/9781555819583.ch33openalex-snapshot
Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi
inferredcites →https://doi.org/10.1128/microbiolspec.funk-0042-2017openalex-snapshot
Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi
inferredcites →https://doi.org/10.1136/jmg.2006.043166openalex-snapshot
Array-based comparative genomic hybridisation identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders
inferredcites →https://doi.org/10.1146/annurev-genom-090413-025600openalex-snapshot
The Diverse Genetic Landscape of Neurodevelopmental Disorders
inferredcites →https://doi.org/10.1146/annurev-genom-091212-153431openalex-snapshot
The Genetic Landscapes of Autism Spectrum Disorders
inferredcites →https://doi.org/10.1159/000336479openalex-snapshot
Expression Levels of Transcribed Ultraconserved Regions uc.73 and uc.388 Are Altered in Colorectal Cancer
inferredcites →https://doi.org/10.1186/1471-2164-5-99openalex-snapshot
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
inferredcites →https://doi.org/10.1186/1471-2350-11-128openalex-snapshot
Important role of indels in somatic mutations of human cancer genes
inferredcites →https://doi.org/10.1186/1476-4598-12-13openalex-snapshot
Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer
inferredcites →https://doi.org/10.1186/1755-8794-3-54openalex-snapshot
Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies
inferredcites →https://doi.org/10.1186/gb-2006-7-11-r105openalex-snapshot
Patterns of sequence conservation in presynaptic neural genes
inferredcites →https://doi.org/10.1242/dev.051052openalex-snapshot
An SNP in an ultraconserved regulatory element affects Dlx5/Dlx6 regulation in the forebrain
inferredcites →https://doi.org/10.1371/journal.pbio.0030007openalex-snapshot
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
inferredcites →https://doi.org/10.1371/journal.pbio.0050234openalex-snapshot
Deletion of Ultraconserved Elements Yields Viable Mice
inferredcites →https://doi.org/10.1371/journal.pgen.1003484openalex-snapshot
From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes
inferredcites →https://doi.org/10.1371/journal.pgen.1004646openalex-snapshot
Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells
inferredcites →https://doi.org/10.1371/journal.pone.0017634openalex-snapshot
Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions between Human Conserved Non-Coding Sequences
inferredcites →https://doi.org/10.1371/journal.pone.0028616openalex-snapshot
DNaseI Hypersensitivity and Ultraconservation Reveal Novel, Interdependent Long-Range Enhancers at the Complex Pax6 Cis-Regulatory Region
inferredcites →https://doi.org/10.1371/journal.pone.0095437openalex-snapshot
Conserved Noncoding Elements Follow Power-Law-Like Distributions in Several Genomes as a Result of Genome Dynamics
inferredcites →https://doi.org/10.1371/journal.pone.0110692openalex-snapshot
Allele Frequencies of Variants in Ultra Conserved Elements Identify Selective Pressure on Transcription Factor Binding
inferredcites →https://doi.org/10.1371/journal.pone.0179006openalex-snapshot
Childhood cancer risk in those with chromosomal and non-chromosomal congenital anomalies in Washington State: 1984-2013
inferredcites →https://doi.org/10.1534/genetics.108.096537openalex-snapshot
Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries
inferredcites →https://doi.org/10.1534/genetics.112.141945openalex-snapshot
Ultraconserved Elements in the Human Genome: Association and Transmission Analyses of Highly Constrained Single-Nucleotide Polymorphisms
inferredcites →https://doi.org/10.18632/oncotarget.7833openalex-snapshot
Long non-coding RNA containing ultraconserved genomic region 8 promotes bladder cancer tumorigenesis
inferredcites →https://doi.org/10.4161/rna.5.3.6673openalex-snapshot
Ultraconserved elements: Genomics, function and disease

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41576-021-00424-xopenalex-snapshot
Perfect and imperfect views of ultraconserved sequences
inferred← citeshttps://doi.org/10.1101/2022.02.15.22270795openalex-snapshot
Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders
inferred← citeshttps://doi.org/10.1101/2024.03.17.585403openalex-snapshot
Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease
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