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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Related Experiment Video

Updated: Jul 5, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.

Arthur S Lee1,2,3,4, Lauren J Ayers1, Michael Kosicki5

  • 1Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA.

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Researchers developed a single-cell multi-omic framework to identify non-coding variants in congenital cranial dysinnervation disorders (CCDDs). This approach aids in diagnosing rare genetic conditions by pinpointing regulatory elements affecting gene expression.

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Area of Science:

  • Genomics and Developmental Biology: Focuses on understanding gene regulation in neural development and its role in genetic disorders.

Background:

  • Many Mendelian disorders lack identifiable coding variants, suggesting non-coding regions are implicated.
  • Congenital cranial dysinnervation disorders (CCDDs) are a group of Mendelian disorders affecting cranial motor neuron development.

Approach:

  • Developed a single-cell multi-omic framework integrating chromatin accessibility, histone modification, and gene expression data from embryonic mouse models.
  • Profiled approximately 86,000 cranial motor neurons (cMNs) and related cell types to identify regulatory elements.
  • Validated enhancer activity using in vivo transgenic reporter assays, confirming single-cell accessibility as a predictor.

Key Points:

  • Identified ~250,000 accessible regulatory elements and ~145,000 putative enhancers in cMNs.
  • Successfully nominated candidate non-coding variants in known CCDD genes (MAFB, PHOX2A, CHN1, EBF3) and novel candidates.
  • Demonstrated the framework's utility by applying it to 899 whole genome sequences from 270 unsolved CCDD pedigrees.

Conclusions:

  • The study provides novel non-coding variant discoveries relevant to CCDDs.
  • Presents a generalizable framework for nominating high-impact non-coding variants in other Mendelian disorders.