PMID- 32864204
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20200928
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 8
DP  - 2020
TI  - Cumulative contact frequency of a chromatin region is an intrinsic property 
      linked to its function.
PG  - e9566
LID - 10.7717/peerj.9566 [doi]
LID - e9566
AB  - Regulation of gene transcription is a complex process controlled by many factors, 
      including the conformation of chromatin in the nucleus. Insights into chromatin 
      conformation on both local and global scales can be provided by the Hi-C 
      (high-throughput chromosomes conformation capture) method. One of the drawbacks 
      of Hi-C analysis and interpretation is the presence of systematic biases, such as 
      different accessibility to enzymes, amplification, and mappability of DNA 
      regions, which all result in different visibility of the regions. Iterative 
      correction (IC) is one of the most popular techniques developed for the 
      elimination of these systematic biases. IC is based on the assumption that all 
      chromatin regions have an equal number of observed contacts in Hi-C. In other 
      words, the IC procedure is equalizing the experimental visibility approximated by 
      the cumulative contact frequency (CCF) for all genomic regions. However, the 
      differences in experimental visibility might be explained by biological factors 
      such as chromatin openness, which is characteristic of distinct chromatin states. 
      Here we show that CCF is positively correlated with active transcription. It is 
      associated with compartment organization, since compartment A demonstrates higher 
      CCF and gene expression levels than compartment B. Notably, this observation 
      holds for a wide range of species, including human, mouse, and Drosophila. 
      Moreover, we track the CCF state for syntenic blocks between human and mouse and 
      conclude that active state assessed by CCF is an intrinsic property of the DNA 
      region, which is independent of local genomic and epigenomic context. Our 
      findings establish a missing link between Hi-C normalization procedures removing 
      CCF from the data and poorly investigated and possibly relevant biological 
      factors contributing to CCF.
CI  - (c)2020 Samborskaia et al.
FAU - Samborskaia, Margarita D
AU  - Samborskaia MD
AD  - Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 
      Moscow, Russia.
FAU - Galitsyna, Aleksandra
AU  - Galitsyna A
AD  - Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 
      Russia.
AD  - A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, 
      Russia.
AD  - Institute of Gene Biology, RAS, Moscow, Russia.
FAU - Pletenev, Ilya
AU  - Pletenev I
AD  - Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 
      Russia.
FAU - Trofimova, Anna
AU  - Trofimova A
AD  - Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 
      Russia.
FAU - Mironov, Andrey A
AU  - Mironov AA
AD  - Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 
      Moscow, Russia.
AD  - A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, 
      Russia.
FAU - Gelfand, Mikhail S
AU  - Gelfand MS
AD  - Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 
      Russia.
AD  - A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, 
      Russia.
FAU - Khrameeva, Ekaterina E
AU  - Khrameeva EE
AD  - Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 
      Russia.
LA  - eng
PT  - Journal Article
DEP - 20200810
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
PMC - PMC7425636
OTO - NOTNLM
OT  - Chromatin
OT  - Compartments
OT  - Conformation capture
OT  - Hi-C
COIS- Mikhail S. Gelfand is an Academic Editor for PeerJ.
EDAT- 2020/08/31 06:00
MHDA- 2020/08/31 06:01
PMCR- 2020/08/10
CRDT- 2020/09/01 06:00
PHST- 2020/01/27 00:00 [received]
PHST- 2020/06/27 00:00 [accepted]
PHST- 2020/09/01 06:00 [entrez]
PHST- 2020/08/31 06:00 [pubmed]
PHST- 2020/08/31 06:01 [medline]
PHST- 2020/08/10 00:00 [pmc-release]
AID - 9566 [pii]
AID - 10.7717/peerj.9566 [doi]
PST - epublish
SO  - PeerJ. 2020 Aug 10;8:e9566. doi: 10.7717/peerj.9566. eCollection 2020.