TY - JOUR

T1 - Protein and genetic composition of four chromatin types in Drosophila melanogaster cell lines

AU - Boldyreva, Lidiya V.

AU - Goncharov, Fyodor P.

AU - Demakova, Olga V.

AU - Zykova, Tatyana Yu

AU - Levitsky, Victor G.

AU - Kolesnikov, Nikolay N.

AU - Pindyurin, Alexey V.

AU - Semeshin, Valeriy F.

AU - Zhimulev, Igor F.

PY - 2017/4/1

Y1 - 2017/4/1

N2 - Background: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. Results: Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5’ untranslated regions (5’UTRs) of the genes, is enriched in diverse “open” chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the “closed” chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.

AB - Background: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. Results: Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5’ untranslated regions (5’UTRs) of the genes, is enriched in diverse “open” chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the “closed” chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.

KW - Cell lines

KW - Chromatin types

KW - Drosophila

KW - Genome-wide protein binding data

KW - Interbands

KW - Polytene chromosomes

UR - http://www.scopus.com/inward/record.url?scp=85013885349&partnerID=8YFLogxK

U2 - 10.2174/1389202917666160512164913

DO - 10.2174/1389202917666160512164913

M3 - Article

C2 - 28367077

AN - SCOPUS:85013885349

VL - 18

SP - 214

EP - 226

JO - Current Genomics

JF - Current Genomics

SN - 1389-2029

IS - 2

ER -