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Research Laboratory «‎Regulatory Genomics»

Contract number
Time span of the project

As of 01.11.2022

Number of staff members
scientific publications
General information

Name of the project: Regulatory genetic and epigenetic mechanisms of the development and the functioning of skeletal muscles and the heart muscle of humans and primates in the norm and pathology

Goals and objectives

The main objective of this research is the determination of the activity landscape of regulatory elements of the genome in the adult and developing heart muscles of humans and primates in the norm and pathology. To achieve this goal, it will be necessary to collect samples of various types of skeletal and heart muscles of humans and mammals (macaques). The organisation of a biological bank of muscle samples will be one of the important tasks. Using modern methods of the assessment of the activity of genes at the level of the whole genome (CAGE-seq RNA-seq) and their regulatory elements (ATAC-seq), as well as their variations at the level of single cells, we will be solving the problem of the collection of an array of sequencing data. The obtained data will be processed by a group of bioinformaticians possessing the experience of completion of major international projects, as well as using the FANTOM project series (2000-2018) that was based on the same technological platform (CAGE-seq), for the comparison of the results.

As a result, we are planning to create an atlas of expression activity, a reconstruction of gene networks that regulate molecular processes in muscle cells and tissues in the norm and pathology.

The practical value of the study

Scientific results:

  1. We have collected material and created a biobank of samples of muscle tissues of crab-eating macaque and humans. We isolated RNA and prepared CAGE-seq libraries and performed their sequencing. Profiles of the differential expression of genes in various types of muscles have been obtained.
  2. Under the supervision of employees of the Laboratory (Vsevolod Yu. Makeyev and Ivan V. Kulakovskiy), the ANANASTRA web service has been developed that allows to annotate sets of individual single-nucleotide variants, for instance, the most reliable results of full-genome research of associations, information on allele-specific binding of human transcription factors. The web service is integrated with external databases on genotype−molecular genotype associations, primarily GTEx, which will allow researchers to reliably determine key regulatory variants affecting the activity of genes.
  3. We have analyzed the expression profile of regulatory elements of the genome in various sections of the human heart muscle in the norm and in cardiac pathology. We determined over 3 000 new RNA transcription initiation sites. It was reliably demonstrated that mutations in the regulatory elements of the genome lead to changes in RNA transcription in cardiovascular system diseases. We found a number of examples when the alternative use of transcription initiation sites leads to the emergence of protein isoforms specific to diseases, which can be a potential target for the development of new therapeutic approaches.

Implementation of research results:

On the basis of data on the work of genes in the heart muscle accumulated by the Laboratory, a digital genetic portal has been created to analyze information on the activity of the regulatory elements of the genome in various sections of the heart. The database allows to conduct in silico survey and analysis of the activity of the regulatory elements of the genome in the interactive mode, to analyze the differential activity of genes and RNA transcription initiation sites.

Education and career development:

Employees of the Laboratory completed internships in Japan.

Diploma works have been defended in the domain of the project.


The Laboratory collaborates with Juntendo University (Japan) and Northwestern University (USA).

Among Russian organizations our partner is the Moscow Institute of Physics and Technology, we are maintaining close academic connections with the Institute of Biomedical Problems of the Russian Academy of Sciences.

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Ruslan M. Deviatiiarov, Anna Gams2, Roman Syunyaev, Ivan V. Kulakovskiy, Andrey Buyan, Georgy Meshcheryakov, Roman Syunyaev, Ramesh Singh, Palak Shah, Tatiana V. Tatarinova, Oleg Gusev*, Igor R. Efimov
An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure. Nature Cardiovascular Research (в печати)
Alexander Boytsov, Sergey Abramov, Ariuna Z Aiusheeva, Alexandra M Kasianova, Eugene Baulin, Ivan A Kuznetsov, Yurii S Aulchenko, Semyon Kolmykov, Ivan Yevshin, Fedor Kolpakov, Ilya E Vorontsov, Vsevolod J Makeev, Ivan V Kulakovskiy
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W51–W56, https://doi.org/10.1093/nar/gkac262
Ananeva, A, Gulnaz, A, Ryzhkova, T, Gaifullina, R, Shagimardanova, E.
The novel HLA-A*11:416 allele was identified during high-resolution HLA typing. HLA. 2022; 1- 2. doi:10.1111/tan.14866
Ananeva, A, Elvira, Z, Ryzhkova, T, Shagimardanova, E.
The identification of three novel HLA-A alleles: HLA-A*03:390:02, -A*26:112:02 and -A*26:221. HLA. 2022; 1- 2. doi:10.1111/tan.14864
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