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Principal Investigator: WENYI FENG
Organization: UPSTATE MEDICAL UNIVERSITY
Fiscal Year: 2024
Award: $448,250
Funding agency: National Human Genome Research Institute
PROJECT SUMMARY/ABSTRACT
Common fragile sites (CFSs) are recurrent “wounds” in every person's genome that predispose
the chromosomes to DNA double strand breaks (DSBs) and rearrangements. Known features
associated with CFSs include late replication timing, which is further enhanced upon replication
stress, and large transcribed genes, which may cause replication-transcription conflict. CFS
formation/breakage underlies a wide variety of human diseases, including cancer and neurological
disorders. We recently mapped replication stress-induced DNA DSBs in a normal human
lymphoblastoid cell line, using Break-seq, a powerful NextGen-sequencing based technique
developed in my laboratory. DSBs, with or without replication stress, are associated with late
replication timing. However, these DSBs were not enriched inside large transcribing genes, nor are
they enriched inside cytologially defined CFS core sequences. We hypothesize that the differences
between Break-seq signals and CFS core sequences are attributable to the inherent differences
between technological platforms as each is biased toward a partial feature of the human CFS, with
Break-seq detecting the DSBs whereas the cytological methods detecting ssDNA gaps. The main
objective of our proposal is to directly test this hypothesis by creating an upgraded sequencing
technology, Fragile Site (FS)-seq, to simultaneously map ssDNA gaps and DSBs (Aim 1). Moreover,
preliminary evidence suggests that the ssDNA inside the CFS core sequences is a consequence of
“rogue” DNA initiation events upon high levels of DNA replication stress. Therefore, we will test if
alterations in replication timing gives rise to ssDNA at the CFS core regions (Aim 2). The proposed
project will bridge the gap in our current understanding of the mechanisms of CFS formation and
genome instability.
Terms: <Abscission><Address><Aphidicolin><Body Tissues><Cancers><Causality><Cell Body><Cell Communication and Signaling><Cell Signaling><Cells><Chemicals><Chromosome Fragile Sites><Chromosomes><Conflict><Conflict (Psychology)><Coupled><Cytology><DNA><DNA Alteration><DNA Damage><DNA Double Strand Break><DNA Hybridization Probes><DNA Injury><DNA Polymerase Inhibitor><DNA Probes><DNA Replication><DNA Replication Initiation><DNA Sequence Alteration><DNA Single Strand Break><DNA Synthesis><DNA biosynthesis><DNA mutation><Deoxyribonucleic Acid><Detection><Disease><Disorder><Effectiveness><Escalante syndrome><Etiology><Event><Excision><Extirpation><FISH Technic><FISH Technique><FISH analysis><FISH assay><Fluorescence In Situ Hybridization><Fluorescent in Situ Hybridization><Fragile Site><Fragile X><Fragile X Syndrome><Gene Transcription><Genes><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Genetic mutation><Genome><Genome Instability><Genomic Instability><Goals><Hot Spot><Human><Human Cell Line><Human Genome><Intracellular Communication and Signaling><Laboratories><Lesion><Malignant Neoplasms><Malignant Tumor><Mammalian Chromosomes><Maps><Martin-Bell Syndrome><Martin-Bell-Renpenning syndrome><Metaphase><Methodology><Methods><Mitotic Metaphase><Modern Man><Mutation><NGS Method><NGS system><Names><Nervous System Diseases><Nervous System Disorder><Neurologic Disorders><Neurological Disorders><Nucleotides><Pathway interactions><Persons><Procedures><RNA Expression><Recurrence><Recurrent><Regulation><Removal><Renpenning syndrome 2><Replication Initiation><Research Proposals><Resolution><Sequence Alteration><Signal Transduction><Signal Transduction Systems><Signaling><Single-Stranded DNA><Site><Staining method><Stains><Stress><Surgical Removal><Techniques><Technology><Testing><Time><Tissues><Transcription><X-linked mental deficiency-megalotestes syndrome><X-linked mental retardation with fragile X syndrome><X-linked mental retardation-fragile site 1 syndrome><autism-fragile X (AFRAX) syndrome><biological signal transduction><causation><cell type><detection method><detection procedure><detection technique><disease causation><fra(X) syndrome><fra(X)(28) syndrome><fra(X)(q27) syndrome><fra(X)(q27-28) syndrome><fragile X-mental retardation syndrome><fragile Xq syndrome><fragile site mental retardation 1><genome mutation><genome scale><genome wide analysis><genome wide studies><genome-wide><genome-wide analysis><genome-wide identification><genomewide><genomic alteration><human disease><human whole genome><lymphoblastoid cell line><macro-orchidism-marker X (MOMX) syndrome><macro-orchidism-marker X syndrome><malignancy><mar(X) syndrome><marker X syndrome><mental retardation-macroorchidism syndrome><name><named><naming><neoplasm/cancer><neurological disease><next gen sequencing><next generation sequencing><nextgen sequencing><pathway><replication stress><resection><resolutions><response><ssDNA><technology platform><technology system><tissue wound><tool><wound><wounding><wounds>