PMID- 33963348
OWN - NLM
STAT- MEDLINE
DCOM- 20210727
LR  - 20221017
IS  - 1548-7105 (Electronic)
IS  - 1548-7091 (Print)
IS  - 1548-7091 (Linking)
VI  - 18
IP  - 5
DP  - 2021 May
TI  - Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
PG  - 482-490
LID - 10.1038/s41592-021-01135-1 [doi]
AB  - Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome 
      architecture mapping (GAM) are powerful technologies utilized to probe chromatin 
      interactions genome wide, but how faithfully they capture three-dimensional (3D) 
      contacts and how they perform relative to each other is unclear, as no benchmark 
      exists. Here, we compare these methods in silico in a simplified, yet controlled, 
      framework against known 3D structures of polymer models of murine and human loci, 
      which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed 
      fluorescence in situ hybridization (FISH) single-molecule conformations. We find 
      that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D 
      structures whereas single-cell data reflect strong variability among single 
      molecules. The minimal number of cells required in replicate experiments to 
      return statistically similar contacts is different across the technologies, being 
      lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal 
      levels follow an inverse power law with detection efficiency and grow with 
      genomic distance differently among the three methods, being lowest in GAM for 
      genomic separations >1 Mb.
FAU - Fiorillo, Luca
AU  - Fiorillo L
AUID- ORCID: 0000-0003-2967-0123
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Musella, Francesco
AU  - Musella F
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Conte, Mattia
AU  - Conte M
AUID- ORCID: 0000-0002-6670-9800
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Kempfer, Rieke
AU  - Kempfer R
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany.
AD  - Humboldt-Universitat zu Berlin, Berlin, Germany.
FAU - Chiariello, Andrea M
AU  - Chiariello AM
AUID- ORCID: 0000-0002-6112-0167
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Bianco, Simona
AU  - Bianco S
AUID- ORCID: 0000-0001-5819-060X
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany.
FAU - Kukalev, Alexander
AU  - Kukalev A
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany.
FAU - Irastorza-Azcarate, Ibai
AU  - Irastorza-Azcarate I
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany.
FAU - Esposito, Andrea
AU  - Esposito A
AUID- ORCID: 0000-0002-5903-8439
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Abraham, Alex
AU  - Abraham A
AUID- ORCID: 0000-0003-3533-6543
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy.
FAU - Prisco, Antonella
AU  - Prisco A
AD  - CNR-IGB, Naples, Italy.
FAU - Pombo, Ana
AU  - Pombo A
AUID- ORCID: 0000-0002-7493-6288
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany.
AD  - Humboldt-Universitat zu Berlin, Berlin, Germany.
FAU - Nicodemi, Mario
AU  - Nicodemi M
AUID- ORCID: 0000-0002-8416-6416
AD  - Dipartimento di Fisica, Universita di Napoli Federico II and INFN Napoli, 
      Complesso Universitario di Monte Sant'Angelo, Naples, Italy. 
      mario.nicodemi@na.infn.it.
AD  - Berlin Institute for Medical Systems Biology, Max-Delbruck Centre for Molecular 
      Medicine, Berlin, Germany. mario.nicodemi@na.infn.it.
AD  - Berlin Institute of Health, Berlin, Germany. mario.nicodemi@na.infn.it.
LA  - eng
GR  - U54 DK107977/DK/NIDDK NIH HHS/United States
GR  - UM1 HG011585/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20210507
PL  - United States
TA  - Nat Methods
JT  - Nature methods
JID - 101215604
RN  - 0 (Chromatin)
RN  - 0 (Polymers)
SB  - IM
CIN - Nat Methods. 2021 May;18(5):456-457. PMID: 33963351
EIN - Nat Methods. 2021 Oct;18(10):1266. PMID: 34480161
MH  - Animals
MH  - Chromatin/*chemistry
MH  - Chromosome Mapping
MH  - Computer Simulation
MH  - Humans
MH  - Mice
MH  - *Models, Chemical
MH  - Polymers/*chemistry
MH  - Single Molecule Imaging
MH  - Single-Cell Analysis
PMC - PMC8416658
COIS- A. Pombo and M.N. hold a patent on 'Genome Architecture Mapping': Pombo, A., 
      Edwards, P. A. W., Nicodemi, M., Beagrie, R. A. & Scialdone, A. Patent no. 
      PCT/EP2015/079413 (2015).
EDAT- 2021/05/09 06:00
MHDA- 2021/07/28 06:00
PMCR- 2021/05/07
CRDT- 2021/05/08 07:02
PHST- 2020/05/29 00:00 [received]
PHST- 2021/03/31 00:00 [accepted]
PHST- 2021/05/08 07:02 [entrez]
PHST- 2021/05/09 06:00 [pubmed]
PHST- 2021/07/28 06:00 [medline]
PHST- 2021/05/07 00:00 [pmc-release]
AID - 10.1038/s41592-021-01135-1 [pii]
AID - 1135 [pii]
AID - 10.1038/s41592-021-01135-1 [doi]
PST - ppublish
SO  - Nat Methods. 2021 May;18(5):482-490. doi: 10.1038/s41592-021-01135-1. Epub 2021 
      May 7.