Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
Project description:The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195–base pair (bp) duplication in HoxC10 intron. Micro-C analyses show that HoxC-containing topologically associating domain (TAD) is normally closed in the scalp but open in the dorsal and tail regions, allowing multiple long-distance contacts. In the PC scalp, the TAD is open, resulting in high HoxC expression. CRISPR-Cas9 deletion of the 195-bp duplication reduces crest feather formation, and HoxC misexpression alters feather shapes. The 195-bp sequence is found only in Archelosauria (crocodilians and birds) and not in mammals. These findings suggest that higher-order regulation of the HoxC cluster modulates gene expression, driving the evolution of adaptive integumentary appendages in birds.
Project description:Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. We named these molecularly coordinated regions “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect an uncharacterized VCM-modulating non-coding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a big change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with long-range chromatin compaction and AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.