High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale
Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical li...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Nature
2021
|
| _version_ | 1826258483142459392 |
|---|---|
| author | Downes, DJ Beagrie, RA Gosden, ME Telenius, J Carpenter, SJ Nussbaum, L De Ornellas, S Sergeant, M Eijsbouts, CQ Schwessinger, R Kerry, J Roberts, N Shivalingam, A El-Sagheer, A Oudelaar, AM Brown, T Buckle, VJ Davies, JOJ Hughes, JR |
| author_facet | Downes, DJ Beagrie, RA Gosden, ME Telenius, J Carpenter, SJ Nussbaum, L De Ornellas, S Sergeant, M Eijsbouts, CQ Schwessinger, R Kerry, J Roberts, N Shivalingam, A El-Sagheer, A Oudelaar, AM Brown, T Buckle, VJ Davies, JOJ Hughes, JR |
| author_sort | Downes, DJ |
| collection | OXFORD |
| description | Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation. |
| first_indexed | 2024-03-06T18:34:41Z |
| format | Journal article |
| id | oxford-uuid:0ad0d13d-a54f-41c9-9089-6e9cfdb342a9 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:34:41Z |
| publishDate | 2021 |
| publisher | Nature |
| record_format | dspace |
| spelling | oxford-uuid:0ad0d13d-a54f-41c9-9089-6e9cfdb342a92022-03-26T09:26:01ZHigh-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scaleJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:0ad0d13d-a54f-41c9-9089-6e9cfdb342a9EnglishSymplectic ElementsNature2021Downes, DJBeagrie, RAGosden, METelenius, JCarpenter, SJNussbaum, LDe Ornellas, SSergeant, MEijsbouts, CQSchwessinger, RKerry, JRoberts, NShivalingam, AEl-Sagheer, AOudelaar, AMBrown, TBuckle, VJDavies, JOJHughes, JRChromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation. |
| spellingShingle | Downes, DJ Beagrie, RA Gosden, ME Telenius, J Carpenter, SJ Nussbaum, L De Ornellas, S Sergeant, M Eijsbouts, CQ Schwessinger, R Kerry, J Roberts, N Shivalingam, A El-Sagheer, A Oudelaar, AM Brown, T Buckle, VJ Davies, JOJ Hughes, JR High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title | High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title_full | High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title_fullStr | High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title_full_unstemmed | High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title_short | High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale |
| title_sort | high resolution targeted 3c interrogation of cis regulatory element organization at genome wide scale |
| work_keys_str_mv | AT downesdj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT beagriera highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT gosdenme highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT teleniusj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT carpentersj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT nussbauml highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT deornellass highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT sergeantm highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT eijsboutscq highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT schwessingerr highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT kerryj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT robertsn highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT shivalingama highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT elsagheera highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT oudelaaram highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT brownt highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT bucklevj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT daviesjoj highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale AT hughesjr highresolutiontargeted3cinterrogationofcisregulatoryelementorganizationatgenomewidescale |