1 Chromatin Structure and Function in Neurospora crassa
ABIGAIL J. COURTNEY
1
, AILEEN R. FERRARO
1
, ANDREW D. KLOCKO
2
, ZACHARY A. LEWIS
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
II. Euchromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
A. Promoters and Regulatory Regions . . . . . . . . 4
B. Coding Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . 8
III. Heterochromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
A. Constitutive Heterochromatin (RepeatAssociated Heterochromatin) . . . . . . . . . . . . . . 10
B. ERI1-Directed Facultative Heterochromatin 15
C. The Polycomb System and Facultative
Heterochromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
VI. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
I. Introduction
In eukaryotic cells, the relevant substrate for
most DNA-based processes is chromatin, a
complex of DNA and proteins that functions
to organize the genome and regulate DNAtemplated processes inside the nucleus. The
most basic unit of chromatin is the nucleosome
core particle, comprised of a histone octamer
wrapped ~1.5 times by ~146 base pairs (bp) of
DNA (Luger et al. 1997). Repeating nucleosome
units are separated by a short region of linker
DNA, giving rise to the well-known “beads on a
string” structure of chromatin (Olins and Olins
1974; Kornberg 1974; Oudet et al. 1975). Inside
the cell, the chromatin fiber is extremely
dynamic and heterogeneous. A number of
diverse mechanisms alter local chromatin
structure, providing an important layer of regulation for many genome functions. For example, DNA-templated processes are profoundly
impacted by (1) differential covalent modification of histone proteins and DNA, (2) binding
of nonhistone proteins to the chromatin fiber,
(3) replacement of core histones with histone
variants, (4) restructuring and remodeling of
nucleosomes on DNA by ATP-dependent chromatin remodeling factors, and (5) assembly of
higher-order chromatin structures that compact the chromatin fiber and organize the
genome within the three-dimensional space
inside the nucleus (Henriksen 2007; Clapier
and Cairns 2009; Henikoff and Smith 2015;
Schmitt et al. 2016; Allis and Jenuwein 2016;
Clapier et al. 2017).
Historically, chromatin has been simply
classified into two different types, euchromatin
and heterochromatin, which were originally
defined based on their distinct cytological
appearance (Heitz 1928; Zacharias 1995). DNA
associated with euchromatin is relatively accessible, gene-rich, and transcriptionally active,
whereas DNA associated with heterochromatin
is typically highly condensed, transcriptionally
repressed, and closely associated with the
nuclear periphery (Pueschel et al. 2016; Solovei
et al. 2016). Molecular analyses have now
described a large number of distinct chromatin
environments based on differential enrichment
of chromatin modifications and binding of
nonhistone proteins. Indeed, the idea that
eukaryotic chromosomes are partitioned into
many structurally and functionally distinct
domains is now widely appreciated, and local
chromatin structure is known to play important
1 Department of Microbiology, University of Georgia, Athens,
GA, Georgia; e-mail: abigail.courtney@uga.edu; aileen.ferraro25@uga.edu; zlewis@uga.edu
2 Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, USA; e-mail:
aklocko@uccs.edu
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
ABIGAIL J. COURTNEY
1
, AILEEN R. FERRARO
1
, ANDREW D. KLOCKO
2
, ZACHARY A. LEWIS
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
II. Euchromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
A. Promoters and Regulatory Regions . . . . . . . . 4
B. Coding Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . 8
III. Heterochromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
A. Constitutive Heterochromatin (RepeatAssociated Heterochromatin) . . . . . . . . . . . . . . 10
B. ERI1-Directed Facultative Heterochromatin 15
C. The Polycomb System and Facultative
Heterochromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
VI. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
I. Introduction
In eukaryotic cells, the relevant substrate for
most DNA-based processes is chromatin, a
complex of DNA and proteins that functions
to organize the genome and regulate DNAtemplated processes inside the nucleus. The
most basic unit of chromatin is the nucleosome
core particle, comprised of a histone octamer
wrapped ~1.5 times by ~146 base pairs (bp) of
DNA (Luger et al. 1997). Repeating nucleosome
units are separated by a short region of linker
DNA, giving rise to the well-known “beads on a
string” structure of chromatin (Olins and Olins
1974; Kornberg 1974; Oudet et al. 1975). Inside
the cell, the chromatin fiber is extremely
dynamic and heterogeneous. A number of
diverse mechanisms alter local chromatin
structure, providing an important layer of regulation for many genome functions. For example, DNA-templated processes are profoundly
impacted by (1) differential covalent modification of histone proteins and DNA, (2) binding
of nonhistone proteins to the chromatin fiber,
(3) replacement of core histones with histone
variants, (4) restructuring and remodeling of
nucleosomes on DNA by ATP-dependent chromatin remodeling factors, and (5) assembly of
higher-order chromatin structures that compact the chromatin fiber and organize the
genome within the three-dimensional space
inside the nucleus (Henriksen 2007; Clapier
and Cairns 2009; Henikoff and Smith 2015;
Schmitt et al. 2016; Allis and Jenuwein 2016;
Clapier et al. 2017).
Historically, chromatin has been simply
classified into two different types, euchromatin
and heterochromatin, which were originally
defined based on their distinct cytological
appearance (Heitz 1928; Zacharias 1995). DNA
associated with euchromatin is relatively accessible, gene-rich, and transcriptionally active,
whereas DNA associated with heterochromatin
is typically highly condensed, transcriptionally
repressed, and closely associated with the
nuclear periphery (Pueschel et al. 2016; Solovei
et al. 2016). Molecular analyses have now
described a large number of distinct chromatin
environments based on differential enrichment
of chromatin modifications and binding of
nonhistone proteins. Indeed, the idea that
eukaryotic chromosomes are partitioned into
many structurally and functionally distinct
domains is now widely appreciated, and local
chromatin structure is known to play important
1 Department of Microbiology, University of Georgia, Athens,
GA, Georgia; e-mail: abigail.courtney@uga.edu; aileen.ferraro25@uga.edu; zlewis@uga.edu
2 Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, USA; e-mail:
aklocko@uccs.edu
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020